-
prepare the bacto environment
cd ~/DATA/Data_Luise_Sepi_STKN
cp /home/jhuang/Tools/bacto/bacto-0.1.json .
cp /home/jhuang/Tools/bacto/cluster.json .
cp /home/jhuang/Tools/bacto/Snakefile .
ln -s /home/jhuang/Tools/bacto/local .
ln -s /home/jhuang/Tools/bacto/db .
ln -s /home/jhuang/Tools/bacto/envs .
-
prepare raw_data
mkdir raw_data; cd raw_data
ln -s ../raw_data_batch2/mibi2312/Luise_1_S33_R1_001.fastq.gz mibi2312_R1.fastq.gz
ln -s ../raw_data_batch2/mibi2312/Luise_1_S33_R2_001.fastq.gz mibi2312_R2.fastq.gz
ln -s ../raw_data_batch2/mibi2379/Luise_2_S3_R1_001.fastq.gz mibi2379_R1.fastq.gz
ln -s ../raw_data_batch2/mibi2379/Luise_2_S3_R2_001.fastq.gz mibi2379_R2.fastq.gz
ln -s ../raw_data_batch2/mibi2313/Luise_3_S34_R1_001.fastq.gz mibi2313_R1.fastq.gz
ln -s ../raw_data_batch2/mibi2313/Luise_3_S34_R2_001.fastq.gz mibi2313_R2.fastq.gz
ln -s ../raw_data_batch2/mibi2380/Luise_4_S4_R1_001.fastq.gz mibi2380_R1.fastq.gz
ln -s ../raw_data_batch2/mibi2380/Luise_4_S4_R2_001.fastq.gz mibi2380_R2.fastq.gz
ln -s ../raw_data_batch2/mibi2314/Luise_5_S35_R1_001.fastq.gz mibi2314_R1.fastq.gz
ln -s ../raw_data_batch2/mibi2314/Luise_5_S35_R2_001.fastq.gz mibi2314_R2.fastq.gz
ln -s ../raw_data_batch2/mibi2315/Luise_6_S36_R1_001.fastq.gz mibi2315_R1.fastq.gz
ln -s ../raw_data_batch2/mibi2315/Luise_6_S36_R2_001.fastq.gz mibi2315_R2.fastq.gz
ln -s ../raw_data_batch2/mibi2381/Luise_7_S5_R1_001.fastq.gz mibi2381_R1.fastq.gz
ln -s ../raw_data_batch2/mibi2381/Luise_7_S5_R2_001.fastq.gz mibi2381_R2.fastq.gz
ln -s ../raw_data_batch2/mibi2316/Luise_8_S37_R1_001.fastq.gz mibi2316_R1.fastq.gz
ln -s ../raw_data_batch2/mibi2316/Luise_8_S37_R2_001.fastq.gz mibi2316_R2.fastq.gz
ln -s ../raw_data_batch2/mibi2317/Luise_9_S38_R1_001.fastq.gz mibi2317_R1.fastq.gz
ln -s ../raw_data_batch2/mibi2317/Luise_9_S38_R2_001.fastq.gz mibi2317_R2.fastq.gz
ln -s ../raw_data_batch2/mibi2318/Luise_10_S39_R1_001.fastq.gz mibi2318_R1.fastq.gz
ln -s ../raw_data_batch2/mibi2318/Luise_10_S39_R2_001.fastq.gz mibi2318_R2.fastq.gz
ln -s ../raw_data_batch2/mibi2319/Luise_11_S40_R1_001.fastq.gz mibi2319_R1.fastq.gz
ln -s ../raw_data_batch2/mibi2319/Luise_11_S40_R2_001.fastq.gz mibi2319_R2.fastq.gz
ln -s ../raw_data_batch2/mibi2320/Luise_12_S41_R1_001.fastq.gz mibi2320_R1.fastq.gz
ln -s ../raw_data_batch2/mibi2320/Luise_12_S41_R2_001.fastq.gz mibi2320_R2.fastq.gz
ln -s ../raw_data_batch2/mibi2321/Luise_13_S42_R1_001.fastq.gz mibi2321_R1.fastq.gz
ln -s ../raw_data_batch2/mibi2321/Luise_13_S42_R2_001.fastq.gz mibi2321_R2.fastq.gz
# raw_data_batch1: mibi1435 - mibi1506
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1435/S_epi_K_38_S1_R1_001.fastq.gz mibi1435_R1.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1435/S_epi_K_38_S1_R2_001.fastq.gz mibi1435_R2.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1436/S_epi_K_68_S2_R1_001.fastq.gz mibi1436_R1.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1436/S_epi_K_68_S2_R2_001.fastq.gz mibi1436_R2.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1437/S_epi_K_70_S3_R1_001.fastq.gz mibi1437_R1.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1437/S_epi_K_70_S3_R2_001.fastq.gz mibi1437_R2.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1438/S_epi_K_71_S4_R1_001.fastq.gz mibi1438_R1.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1438/S_epi_K_71_S4_R2_001.fastq.gz mibi1438_R2.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1439/S_epi_K_48_S5_R1_001.fastq.gz mibi1439_R1.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1439/S_epi_K_48_S5_R2_001.fastq.gz mibi1439_R2.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1440/S_epi_K_51_S6_R1_001.fastq.gz mibi1440_R1.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1440/S_epi_K_51_S6_R2_001.fastq.gz mibi1440_R2.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1441/S_epi_K_53_S7_R1_001.fastq.gz mibi1441_R1.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1441/S_epi_K_53_S7_R2_001.fastq.gz mibi1441_R2.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1442/S_epi_K_54_S8_R1_001.fastq.gz mibi1442_R1.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1442/S_epi_K_54_S8_R2_001.fastq.gz mibi1442_R2.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1443/S_epi_K_56_S9_R1_001.fastq.gz mibi1443_R1.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1443/S_epi_K_56_S9_R2_001.fastq.gz mibi1443_R2.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1444/S_epi_K_63_S10_R1_001.fastq.gz mibi1444_R1.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1444/S_epi_K_63_S10_R2_001.fastq.gz mibi1444_R2.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1445/S_epi_K_64_S11_R1_001.fastq.gz mibi1445_R1.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1445/S_epi_K_64_S11_R2_001.fastq.gz mibi1445_R2.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1446/S_epi_K_65_S12_R1_001.fastq.gz mibi1446_R1.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1446/S_epi_K_65_S12_R2_001.fastq.gz mibi1446_R2.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1447/S_epi_K_75_S13_R1_001.fastq.gz mibi1447_R1.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1447/S_epi_K_75_S13_R2_001.fastq.gz mibi1447_R2.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1448/S_epi_K_11_S14_R1_001.fastq.gz mibi1448_R1.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1448/S_epi_K_11_S14_R2_001.fastq.gz mibi1448_R2.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1449/S_epi_K_12_S15_R1_001.fastq.gz mibi1449_R1.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1449/S_epi_K_12_S15_R2_001.fastq.gz mibi1449_R2.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1450/S_epi_K_13_S16_R1_001.fastq.gz mibi1450_R1.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1450/S_epi_K_13_S16_R2_001.fastq.gz mibi1450_R2.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1451/S_epi_K_77_S17_R1_001.fastq.gz mibi1451_R1.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1451/S_epi_K_77_S17_R2_001.fastq.gz mibi1451_R2.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1452/S_epi_K_79_S18_R1_001.fastq.gz mibi1452_R1.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1452/S_epi_K_79_S18_R2_001.fastq.gz mibi1452_R2.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1453/S_epi_K_80_S19_R1_001.fastq.gz mibi1453_R1.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1453/S_epi_K_80_S19_R2_001.fastq.gz mibi1453_R2.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1454/S_epi_K_1_gross_S20_R1_001.fastq.gz mibi1454_R1.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1454/S_epi_K_1_gross_S20_R2_001.fastq.gz mibi1454_R2.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1455/S_epi_K_2_S21_R1_001.fastq.gz mibi1455_R1.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1455/S_epi_K_2_S21_R2_001.fastq.gz mibi1455_R2.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1456/S_epi_K_3_S22_R1_001.fastq.gz mibi1456_R1.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1456/S_epi_K_3_S22_R2_001.fastq.gz mibi1456_R2.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1457/S_epi_K_6_S23_R1_001.fastq.gz mibi1457_R1.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1457/S_epi_K_6_S23_R2_001.fastq.gz mibi1457_R2.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1458/S_epi_K_8_S24_R1_001.fastq.gz mibi1458_R1.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1458/S_epi_K_8_S24_R2_001.fastq.gz mibi1458_R2.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1459/S_epi_K_17_S25_R1_001.fastq.gz mibi1459_R1.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1459/S_epi_K_17_S25_R2_001.fastq.gz mibi1459_R2.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1460/S_epi_K_26_S26_R1_001.fastq.gz mibi1460_R1.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1460/S_epi_K_26_S26_R2_001.fastq.gz mibi1460_R2.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1461/S_epi_K_34_S27_R1_001.fastq.gz mibi1461_R1.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1461/S_epi_K_34_S27_R2_001.fastq.gz mibi1461_R2.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1462/S_epi_K_35_S28_R1_001.fastq.gz mibi1462_R1.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1462/S_epi_K_35_S28_R2_001.fastq.gz mibi1462_R2.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1463/S_epi_K_19_S29_R1_001.fastq.gz mibi1463_R1.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1463/S_epi_K_19_S29_R2_001.fastq.gz mibi1463_R2.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1464/S_epi_K_22_S30_R1_001.fastq.gz mibi1464_R1.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1464/S_epi_K_22_S30_R2_001.fastq.gz mibi1464_R2.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1465/S_epi_K_23_S31_R1_001.fastq.gz mibi1465_R1.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1465/S_epi_K_23_S31_R2_001.fastq.gz mibi1465_R2.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1466/S_epi_K_24_S32_R1_001.fastq.gz mibi1466_R1.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1466/S_epi_K_24_S32_R2_001.fastq.gz mibi1466_R2.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1467/S_epi_K_30_S33_R1_001.fastq.gz mibi1467_R1.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1467/S_epi_K_30_S33_R2_001.fastq.gz mibi1467_R2.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1468/S_epi_K_31_S34_R1_001.fastq.gz mibi1468_R1.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1468/S_epi_K_31_S34_R2_001.fastq.gz mibi1468_R2.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1469/S_epi_K_32_S35_R1_001.fastq.gz mibi1469_R1.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1469/S_epi_K_32_S35_R2_001.fastq.gz mibi1469_R2.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1470/S_epi_K_1_klein_S36_R1_001.fastq.gz mibi1470_R1.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1470/S_epi_K_1_klein_S36_R2_001.fastq.gz mibi1470_R2.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1471/S_epi_K_37_S37_R1_001.fastq.gz mibi1471_R1.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1471/S_epi_K_37_S37_R2_001.fastq.gz mibi1471_R2.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1472/S_epi_K_46_S38_R1_001.fastq.gz mibi1472_R1.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1472/S_epi_K_46_S38_R2_001.fastq.gz mibi1472_R2.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1473/S_epi_K_57_S39_R1_001.fastq.gz mibi1473_R1.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1473/S_epi_K_57_S39_R2_001.fastq.gz mibi1473_R2.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1474/S_epi_K_59_S40_R1_001.fastq.gz mibi1474_R1.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1474/S_epi_K_59_S40_R2_001.fastq.gz mibi1474_R2.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1475/S_epi_K_58_S41_R1_001.fastq.gz mibi1475_R1.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1475/S_epi_K_58_S41_R2_001.fastq.gz mibi1475_R2.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1476/S_epi_K_60_S42_R1_001.fastq.gz mibi1476_R1.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1476/S_epi_K_60_S42_R2_001.fastq.gz mibi1476_R2.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1477/S_epi_K_61_S43_R1_001.fastq.gz mibi1477_R1.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1477/S_epi_K_61_S43_R2_001.fastq.gz mibi1477_R2.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1478/S_epi_K_28_S44_R1_001.fastq.gz mibi1478_R1.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1478/S_epi_K_28_S44_R2_001.fastq.gz mibi1478_R2.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1479/S_epi_K_33_S45_R1_001.fastq.gz mibi1479_R1.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1479/S_epi_K_33_S45_R2_001.fastq.gz mibi1479_R2.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1480/S_epi_K_39_S46_R1_001.fastq.gz mibi1480_R1.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1480/S_epi_K_39_S46_R2_001.fastq.gz mibi1480_R2.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1481/S_epi_K_40_S47_R1_001.fastq.gz mibi1481_R1.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1481/S_epi_K_40_S47_R2_001.fastq.gz mibi1481_R2.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1482/S_epi_K_43_S48_R1_001.fastq.gz mibi1482_R1.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1482/S_epi_K_43_S48_R2_001.fastq.gz mibi1482_R2.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1483/S_epi_K_97_S49_R1_001.fastq.gz mibi1483_R1.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1483/S_epi_K_97_S49_R2_001.fastq.gz mibi1483_R2.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1484/S_epi_K_84_S50_R1_001.fastq.gz mibi1484_R1.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1484/S_epi_K_84_S50_R2_001.fastq.gz mibi1484_R2.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1485/S_epi_K_85_S51_R1_001.fastq.gz mibi1485_R1.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1485/S_epi_K_85_S51_R2_001.fastq.gz mibi1485_R2.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1486/S_epi_K_86_S52_R1_001.fastq.gz mibi1486_R1.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1486/S_epi_K_86_S52_R2_001.fastq.gz mibi1486_R2.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1487/S_epi_K_116_S53_R1_001.fastq.gz mibi1487_R1.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1487/S_epi_K_116_S53_R2_001.fastq.gz mibi1487_R2.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1488/S_epi_K_118_S54_R1_001.fastq.gz mibi1488_R1.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1488/S_epi_K_118_S54_R2_001.fastq.gz mibi1488_R2.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1489/S_epi_K_120_S55_R1_001.fastq.gz mibi1489_R1.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1489/S_epi_K_120_S55_R2_001.fastq.gz mibi1489_R2.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1490/S_epi_K_123_S56_R1_001.fastq.gz mibi1490_R1.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1490/S_epi_K_123_S56_R2_001.fastq.gz mibi1490_R2.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1491/S_epi_K_124_S57_R1_001.fastq.gz mibi1491_R1.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1491/S_epi_K_124_S57_R2_001.fastq.gz mibi1491_R2.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1492/S_epi_K_127_S58_R1_001.fastq.gz mibi1492_R1.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1492/S_epi_K_127_S58_R2_001.fastq.gz mibi1492_R2.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1493/S_epi_K_29_S59_R1_001.fastq.gz mibi1493_R1.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1493/S_epi_K_29_S59_R2_001.fastq.gz mibi1493_R2.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1494/S_epi_K_72_S60_R1_001.fastq.gz mibi1494_R1.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1494/S_epi_K_72_S60_R2_001.fastq.gz mibi1494_R2.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1495/S_epi_K_89_S61_R1_001.fastq.gz mibi1495_R1.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1495/S_epi_K_89_S61_R2_001.fastq.gz mibi1495_R2.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1496/S_epi_K_110_S62_R1_001.fastq.gz mibi1496_R1.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1496/S_epi_K_110_S62_R2_001.fastq.gz mibi1496_R2.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1497/S_epi_K_112_S63_R1_001.fastq.gz mibi1497_R1.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1497/S_epi_K_112_S63_R2_001.fastq.gz mibi1497_R2.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1498/S_epi_K_114_S64_R1_001.fastq.gz mibi1498_R1.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1498/S_epi_K_114_S64_R2_001.fastq.gz mibi1498_R2.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1499/S_epi_K_91_S65_R1_001.fastq.gz mibi1499_R1.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1499/S_epi_K_91_S65_R2_001.fastq.gz mibi1499_R2.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1500/S_epi_K_92_S66_R1_001.fastq.gz mibi1500_R1.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1500/S_epi_K_92_S66_R2_001.fastq.gz mibi1500_R2.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1501/S_epi_K_95_S67_R1_001.fastq.gz mibi1501_R1.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1501/S_epi_K_95_S67_R2_001.fastq.gz mibi1501_R2.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1502/S_epi_K_96_S68_R1_001.fastq.gz mibi1502_R1.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1502/S_epi_K_96_S68_R2_001.fastq.gz mibi1502_R2.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1503/S_epi_K_98_S69_R1_001.fastq.gz mibi1503_R1.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1503/S_epi_K_98_S69_R2_001.fastq.gz mibi1503_R2.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1504/S_epi_K_100_S70_R1_001.fastq.gz mibi1504_R1.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1504/S_epi_K_100_S70_R2_001.fastq.gz mibi1504_R2.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1505/S_epi_K_106_S71_R1_001.fastq.gz mibi1505_R1.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1505/S_epi_K_106_S71_R2_001.fastq.gz mibi1505_R2.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1506/S_epi_K_108_S72_R1_001.fastq.gz mibi1506_R1.fastq.gz
ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1506/S_epi_K_108_S72_R2_001.fastq.gz mibi1506_R2.fastq.gz
-
start bacto pipeline until step shovill (set true for the first 2 steps: assembly + typing_mlst)
(bengal3_ac3) jhuang@WS-2290C:~/DATA/Data_Luise_Sepi_STKN$ /home/jhuang/miniconda3/envs/snakemake_4_3_1/bin/snakemake --printshellcmds
-
concate the first assembly
find . -name "contigs.fa" -exec sh -c 'echo -n "{}: "; wc -c < "{}"; echo " contigs: $(grep -c ">" "{}")"' \;
find . -name "contigs.fa" -exec sh -c 'wc -c < "{}" | tr -d "\n" | awk "{print \"{}: \" \$0 \" contigs: \" \$(grep -c \">\" \"{}\")} " ' \; | sort -k2,2n -k4,4n
find . -name "contigs.fa" -exec sh -c 'size=$(wc -c < "{}"); contig_count=$(grep -c ">" "{}"); printf "%s: %d bytes, contigs: %d\n" "{}" "$size" "$contig_count"' \; | sort -t: -k4,4n
grep -v '^>' contigs.fa | awk '{ total += length($0) } END { print total }'
#2399339
find . -name "contigs.fa" -exec sh -c 'total_length=$(grep -v "^>" "{}" | awk "{ total += length(\$0) } END { print total }"); printf "%s: %d\n" "{}" "$total_length"' \; | sort -t: -k2,2n
./mibi2381/contigs.fa: 1077606
./mibi1472/contigs.fa: 1145583
./mibi2380/contigs.fa: 1478149
./mibi1458/contigs.fa: 2345604
./mibi1466/contigs.fa: 2349339
./mibi1451/contigs.fa: 2375432
./mibi1441/contigs.fa: 2390897
./mibi1471/contigs.fa: 2399056
./mibi1435/contigs.fa: 2399339
./mibi1473/contigs.fa: 2416173
./mibi1474/contigs.fa: 2419849
./mibi1495/contigs.fa: 2423463
./mibi1497/contigs.fa: 2427317
./mibi1476/contigs.fa: 2428189
./mibi1463/contigs.fa: 2430568
./mibi2313/contigs.fa: 2434775
./mibi2321/contigs.fa: 2435584
./mibi1494/contigs.fa: 2436708
./mibi1481/contigs.fa: 2437976
./mibi1464/contigs.fa: 2438603
./mibi1450/contigs.fa: 2439465
./mibi1483/contigs.fa: 2440401
./mibi1506/contigs.fa: 2440413
./mibi1462/contigs.fa: 2441903
./mibi1443/contigs.fa: 2445186
./mibi1448/contigs.fa: 2447751
./mibi1439/contigs.fa: 2453223
./mibi1501/contigs.fa: 2454766
./mibi1505/contigs.fa: 2455113
./mibi1436/contigs.fa: 2457498
./mibi1499/contigs.fa: 2459216
./mibi1452/contigs.fa: 2467292
./mibi1500/contigs.fa: 2467976
./mibi1455/contigs.fa: 2468334
./mibi1445/contigs.fa: 2469433
./mibi1479/contigs.fa: 2471443
./mibi1482/contigs.fa: 2473012
./mibi1469/contigs.fa: 2475757
./mibi1468/contigs.fa: 2478455
./mibi1438/contigs.fa: 2482554
./mibi2379/contigs.fa: 2483292
./mibi1493/contigs.fa: 2483445
./mibi1488/contigs.fa: 2484950
./mibi1486/contigs.fa: 2485023
./mibi1442/contigs.fa: 2488933
./mibi1437/contigs.fa: 2489787
./mibi1460/contigs.fa: 2491014
./mibi2312/contigs.fa: 2494588
./mibi1489/contigs.fa: 2495771
./mibi1504/contigs.fa: 2501045
./mibi2317/contigs.fa: 2504746
./mibi1444/contigs.fa: 2504874
./mibi1446/contigs.fa: 2508952
./mibi1465/contigs.fa: 2509542
./mibi1467/contigs.fa: 2509571
./mibi2314/contigs.fa: 2510798
./mibi2315/contigs.fa: 2511464
./mibi1457/contigs.fa: 2513005
./mibi1490/contigs.fa: 2514271
./mibi1491/contigs.fa: 2519558
./mibi1449/contigs.fa: 2520352
./mibi1503/contigs.fa: 2521179
./mibi1475/contigs.fa: 2526469
./mibi1484/contigs.fa: 2530724
./mibi1447/contigs.fa: 2538610
./mibi1453/contigs.fa: 2543893
./mibi1477/contigs.fa: 2550922
./mibi1454/contigs.fa: 2553326
./mibi1498/contigs.fa: 2556315
./mibi2316/contigs.fa: 2556628
./mibi1492/contigs.fa: 2558492
./mibi1470/contigs.fa: 2563169
./mibi2320/contigs.fa: 2571421
./mibi1461/contigs.fa: 2582715
./mibi1478/contigs.fa: 2584524
./mibi2318/contigs.fa: 2594120
./mibi1459/contigs.fa: 2595990
./mibi1440/contigs.fa: 2604213
./mibi1456/contigs.fa: 2605647
./mibi1487/contigs.fa: 2614950
./mibi1496/contigs.fa: 2616533
./mibi2319/contigs.fa: 2621258
./mibi1480/contigs.fa: 2621312
./mibi1485/contigs.fa: 2665904
./mibi1502/contigs.fa: 2668891
cd mibi1502
awk '/^>/ {if(seen_header++) print "NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN"; next} {printf "%s", $0} END {print ""}' contigs.fa > concatenated_contigs.fasta
awk '/^>/ {if(seen_header++) print ""; print $0; next} {printf "%s", $0} END {print ""}' concatenated_contigs.fasta > concatenated_contigs.fa
sed -i '1s/^/>mibi1502\n/' concatenated_contigs.fa
seqkit seq -i concatenated_contigs.fa -m 100 > ../mibi1502.fasta
bakta --db /mnt/nvme0n1p1/bakta_db mibi1502.fasta
ATCC 14990
Genes (total) :: 2,368
CDSs (total) :: 2,284
Genes (coding) :: 2,231
CDSs (with protein) :: 2,231
Genes (RNA) :: 84
rRNAs :: 7, 6, 6 (5S, 16S, 23S)
complete rRNAs :: 7, 6, 6 (5S, 16S, 23S)
tRNAs :: 61
ncRNAs :: 4
Pseudo Genes (total) :: 53
CDSs (without protein) :: 53
Pseudo Genes (ambiguous residues) :: 0 of 53
Pseudo Genes (frameshifted) :: 34 of 53
Pseudo Genes (incomplete) :: 31 of 53
Pseudo Genes (internal stop) :: 24 of 53
Detected IPSs: 2369 This likely refers to insertion sequences or insertional plasmids (depending on the specific context). In this case, 2,369 insertion sequences were detected in the analysis, which could indicate mobile genetic elements that might affect the genome's stability or function.
predict tRNAs...
found: 61
predict tmRNAs...
found: 1
predict rRNAs...
found: 12
predict ncRNAs...
found: 55
predict ncRNA regions...
found: 26
predict CRISPR arrays...
found: 0
predict & annotate CDSs...
predicted: 2529
discarded spurious: 0
revised translational exceptions: 0
detected IPSs: 2369
found PSCs: 117
found PSCCs: 26
lookup annotations...
conduct expert systems...
amrfinder: 20
protein sequences: 54
combine annotations and mark hypotheticals...
detect pseudogenes...
pseudogene candidates: 15
found pseudogenes: 7
analyze hypothetical proteins: 96
detected Pfam hits: 1
calculated proteins statistics
revise special cases...
extract sORF...
potential: 46973
discarded due to overlaps: 37990
discarded spurious: 0
detected IPSs: 9
found PSCs: 2
lookup annotations...
filter and combine annotations...
filtered sORFs: 9
detect gaps...
found: 113
detect oriCs/oriVs...
found: 1
detect oriTs...
found: 0
apply feature overlap filters...
select features and create locus tags...
selected: 2801
improve annotations...
revised gene symbols: 9
-
generate genebank in snpEff and run spandx
#mkdir ~/miniconda3/envs/spandx/share/snpeff-5.1-2/data/NZ_CP035288
#cp NZ_CP035288.gb ~/miniconda3/envs/spandx/share/snpeff-5.1-2/data/NZ_CP035288/genes.gbk
#vim ~/miniconda3/envs/spandx/share/snpeff-5.1-2/snpEff.config
#/home/jhuang/miniconda3/envs/spandx/bin/snpEff build -genbank NZ_CP035288 #-d
cp mibi1502.gbff ../db/mibi1502.gb
#Then replace contig_1 to mibi1502 in the gb-file
cp mibi1502.fasta ../db/mibi1502.fasta
mkdir ~/miniconda3/envs/spandx/share/snpeff-5.1-2/data/mibi1502
cp mibi1502.gb ~/miniconda3/envs/spandx/share/snpeff-5.1-2/data/mibi1502/genes.gbk
vim ~/miniconda3/envs/spandx/share/snpeff-5.1-2/snpEff.config
#Protein check: mibi1502 OK: 2525 Not found: 7 Errors: 0 Error percentage: 0.0%
/home/jhuang/miniconda3/envs/spandx/bin/snpEff build -genbank mibi1502 #-d
# run the first 5 steps in bacto-pipeline ("pangenome"+"variants_calling"+"phylogeny_fasttree"+"phylogeny_raxml"+"recombination")
/home/jhuang/miniconda3/envs/snakemake_4_3_1/bin/snakemake --printshellcmds
ln -s /home/jhuang/Tools/spandx/ spandx
# cp trimmed trimmed_gzipped; cd trimmed_gzipped; gzip *.fastq; cd ..
(spandx) nextflow run spandx/main.nf --fastq "trimmed_gzipped/*_P_{1,2}.fastq.gz" --ref db/mibi1502.fasta --annotation --database mibi1502 -resume
mv work work_mibi1502
mv Outputs Outputs_mibi1502
-
filter out 4 samples for downstream analyses
#The coverages of shovill/mibi1470/contigs.fa and shovill/mibi1472/contigs.fa, and shovill/mibi2381/contigs.fa are low.
#mibi1470 could not be identified as S. epidermidis based on its MLST type.
#remove: mibi1470 2.5M
#remove: ./mibi1472/contigs.fa: 1145583
#remove: ./mibi2380/contigs.fa: 1478149
#remove: ./mibi2381/contigs.fa: 1077606
#Then we have 81 samples for downstream analysis: mibi1435 -- mibi1506 (72); mibi2312 -- mibi2321 (10); mibi2379 -- mibi2381 (3)
-
SCCmec typing and drawing with clinker
#https://www.genomicepidemiology.org/
#https://cge.food.dtu.dk/services/SCCmecFinder/
mkdir contigs; cd contigs
for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
cp ../${sample}/contigs.fa ${sample}_contigs.fa
done
#Predicted SCCmec element
grep "Predicted SCCmec element" *.txt
grep "2 SCCmec" *.txt
grep "ccr class" *.txt
grep "mec class" *.txt
mibi1435_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_IVb(2B)
mibi1436_SCCmec_out.txt:Predicted SCCmec element: none
mibi1437_SCCmec_out.txt:Predicted SCCmec element: none
mibi1438_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_IV(2B)
mibi1439_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_IVa(2B)
mibi1440_SCCmec_out.txt:Predicted SCCmec element: none
mibi1441_SCCmec_out.txt:Predicted SCCmec element: none
mibi1442_SCCmec_out.txt:Predicted SCCmec element: none
mibi1443_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_IVg(2B)
mibi1444_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_IV(2B&5)
mibi1445_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_IVa(2B)
mibi1446_SCCmec_out.txt: SCCmec_type_IV(2B) and SCCmec_type_VI(4B)
mibi1447_SCCmec_out.txt: SCCmec_type_IV(2B) and SCCmec_type_VI(4B)
mibi1448_SCCmec_out.txt:Predicted SCCmec element: none
mibi1449_SCCmec_out.txt:Predicted SCCmec element: none
mibi1450_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_IV(2B)
mibi1451_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_IV(2B)
mibi1452_SCCmec_out.txt:Predicted SCCmec element: none
mibi1453_SCCmec_out.txt:Predicted SCCmec element: none
mibi1454_SCCmec_out.txt:Predicted SCCmec element: none
mibi1455_SCCmec_out.txt:Predicted SCCmec element: none
mibi1456_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_III(3A)
mibi1457_SCCmec_out.txt: SCCmec_type_IV(2B) and SCCmec_type_VI(4B)
mibi1458_SCCmec_out.txt:Predicted SCCmec element: none
mibi1459_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_III(3A)
mibi1460_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_IVa(2B)
mibi1461_SCCmec_out.txt:Predicted SCCmec element: none
mibi1462_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_IVg(2B)
mibi1463_SCCmec_out.txt:Predicted SCCmec element: none
mibi1464_SCCmec_out.txt:Predicted SCCmec element: none
mibi1465_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_IV(2B&5)
mibi1466_SCCmec_out.txt: SCCmec_type_IV(2B) and SCCmec_type_VI(4B)
mibi1467_SCCmec_out.txt:Predicted SCCmec element: none
mibi1468_SCCmec_out.txt:Predicted SCCmec element: none
mibi1469_SCCmec_out.txt:Predicted SCCmec element: none
mibi1471_SCCmec_out.txt:Predicted SCCmec element: none
mibi1473_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_IVa(2B)
mibi1474_SCCmec_out.txt:Predicted SCCmec element: none
mibi1475_SCCmec_out.txt: SCCmec_type_IV(2B) and SCCmec_type_VI(4B)
mibi1476_SCCmec_out.txt:Predicted SCCmec element: none
mibi1477_SCCmec_out.txt:Predicted SCCmec element: none
mibi1478_SCCmec_out.txt: SCCmec_type_III(3A) and SCCmec_type_VIII(4A)
mibi1479_SCCmec_out.txt: SCCmec_type_IV(2B) and SCCmec_type_VI(4B)
mibi1480_SCCmec_out.txt: SCCmec_type_III(3A) and SCCmec_type_VIII(4A)
mibi1481_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_II(2A)
mibi1482_SCCmec_out.txt:Predicted SCCmec element: none
mibi1483_SCCmec_out.txt:Predicted SCCmec element: none
mibi1484_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_IV(2B&5)
mibi1485_SCCmec_out.txt:Predicted SCCmec element: none
mibi1486_SCCmec_out.txt:Predicted SCCmec element: none
mibi1487_SCCmec_out.txt: SCCmec_type_III(3A) and SCCmec_type_VIII(4A)
mibi1488_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_IV(2B)
mibi1489_SCCmec_out.txt:Predicted SCCmec element: none
mibi1490_SCCmec_out.txt: SCCmec_type_IV(2B) and SCCmec_type_VI(4B)
mibi1491_SCCmec_out.txt: SCCmec_type_IV(2B) and SCCmec_type_VI(4B)
mibi1492_SCCmec_out.txt:Predicted SCCmec element: none
mibi1493_SCCmec_out.txt:Predicted SCCmec element: none
mibi1494_SCCmec_out.txt:Predicted SCCmec element: none
mibi1495_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_IVa(2B)
mibi1496_SCCmec_out.txt:Predicted SCCmec element: none
mibi1497_SCCmec_out.txt:Predicted SCCmec element: none
mibi1498_SCCmec_out.txt:Predicted SCCmec element: none
mibi1499_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_IVa(2B)
mibi1500_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_IVa(2B)
mibi1501_SCCmec_out.txt: SCCmec_type_IV(2B) and SCCmec_type_VI(4B)
mibi1502_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_III(3A)
mibi1503_SCCmec_out.txt:Predicted SCCmec element: none
mibi1504_SCCmec_out.txt:Predicted SCCmec element: none
mibi1505_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_IV(2B&5)
mibi1506_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_IVg(2B)
mibi2312_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_IV(2B&5)
mibi2313_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_IV(2B)
mibi2314_SCCmec_out.txt:Predicted SCCmec element: none
mibi2315_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_IVa(2B)
mibi2316_SCCmec_out.txt:Predicted SCCmec element: none
mibi2317_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_IV(2B&5)
mibi2318_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_III(3A)
mibi2319_SCCmec_out.txt: SCCmec_type_III(3A) and SCCmec_type_VIII(4A)
mibi2320_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_IV(2B&5)
mibi2321_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_IV(2B)
mibi2379_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_IV(2B&5)
mibi1441_SCCmec_out.txt:ccr class 2
mibi1446_SCCmec_out.txt:ccr class 2
mibi1446_SCCmec_out.txt:ccr class 4
mibi1447_SCCmec_out.txt:ccr class 2
mibi1447_SCCmec_out.txt:ccr class 4
mibi1452_SCCmec_out.txt:ccr class 5
mibi1455_SCCmec_out.txt:ccr class 2
mibi1457_SCCmec_out.txt:ccr class 2
mibi1457_SCCmec_out.txt:ccr class 4
mibi1464_SCCmec_out.txt:ccr class 2
mibi1466_SCCmec_out.txt:ccr class 2
mibi1466_SCCmec_out.txt:ccr class 4
mibi1467_SCCmec_out.txt:ccr class 5
mibi1475_SCCmec_out.txt:ccr class 2
mibi1475_SCCmec_out.txt:ccr class 4
mibi1477_SCCmec_out.txt:ccr class 9
mibi1478_SCCmec_out.txt:ccr class 3
mibi1478_SCCmec_out.txt:ccr class 4
mibi1479_SCCmec_out.txt:ccr class 2
mibi1479_SCCmec_out.txt:ccr class 4
mibi1480_SCCmec_out.txt:ccr class 3
mibi1480_SCCmec_out.txt:ccr class 4
mibi1482_SCCmec_out.txt:ccr class 5
mibi1483_SCCmec_out.txt:ccr class 5
mibi1486_SCCmec_out.txt:ccr class 2
mibi1487_SCCmec_out.txt:ccr class 3
mibi1487_SCCmec_out.txt:ccr class 4
mibi1489_SCCmec_out.txt:ccr class 2
mibi1490_SCCmec_out.txt:ccr class 2
mibi1490_SCCmec_out.txt:ccr class 4
mibi1491_SCCmec_out.txt:ccr class 2
mibi1491_SCCmec_out.txt:ccr class 4
mibi1492_SCCmec_out.txt:ccr class 2
mibi1494_SCCmec_out.txt:ccr class 5
mibi1501_SCCmec_out.txt:ccr class 2
mibi1501_SCCmec_out.txt:ccr class 4
mibi1504_SCCmec_out.txt:ccr class 2
mibi1504_SCCmec_out.txt:ccr class 5&5
mibi2316_SCCmec_out.txt:ccr class 2
mibi2319_SCCmec_out.txt:ccr class 3
mibi2319_SCCmec_out.txt:ccr class 4
mibi1446_SCCmec_out.txt:mec class B
mibi1447_SCCmec_out.txt:mec class B
mibi1457_SCCmec_out.txt:mec class B
mibi1463_SCCmec_out.txt:mec class B
mibi1466_SCCmec_out.txt:mec class B
mibi1475_SCCmec_out.txt:mec class B
mibi1478_SCCmec_out.txt:mec class A
mibi1479_SCCmec_out.txt:mec class B
mibi1480_SCCmec_out.txt:mec class A
mibi1483_SCCmec_out.txt:mec class A
mibi1487_SCCmec_out.txt:mec class A
mibi1490_SCCmec_out.txt:mec class B
mibi1491_SCCmec_out.txt:mec class B
mibi1501_SCCmec_out.txt:mec class B
mibi2319_SCCmec_out.txt:mec class A
-
agr typing
for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
bakta --db /mnt/nvme0n1p1/bakta_db shovill/${sample}/contigs.fa --prefix ${sample}
done
grep "agrD" mibi1436.gbff
mibi1435 MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE AgrD I
mibi1436 MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE AgrD I
mibi1437 MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE AgrD II
mibi1438 MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE AgrD I
mibi1439 MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE AgrD II
mibi1440 MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE AgrD I
mibi1441 MNLLGGLLLKLFSNFMAVIGNAAKYNPCASYLDEPQVPEELTKLDE AgrD III
mibi1442 MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE AgrD II
mibi1443 MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE AgrD I
mibi1444 MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE AgrD I
mibi1445 MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE AgrD II
mibi1446 MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE AgrD II
mibi1447 MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE AgrD II
mibi1448 MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE AgrD I
mibi1449 MNLLGGLLLKLFSNFMAVIGNAAKYNPCASYLDEPQVPEELTKLDE AgrD III
mibi1450 MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE AgrD I
mibi1451 MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE AgrD II
mibi1452 MNLLGGLLLKLFSNFMAVIGNAAKYNPCASYLDEPQVPEELTKLDE AgrD III
mibi1453 MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE AgrD I
mibi1454 MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE AgrD I
mibi1455 MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE AgrD I
mibi1456 MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE AgrD I
mibi1457 MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE AgrD II
mibi1458 MENIFNLFIK I FTTILEF V GTVAGDSVCASYFDEPEVPEELTKLYE AgrD I* (with a 2-codon difference)
mibi1459 MENIFNLFIK F FTTILEF I GTVAGDSVCASYFDEPEVPEELTKLYE AgrD I
mibi1460 MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE AgrD II
mibi1461 MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE AgrD I
mibi1462 MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE AgrD I
mibi1463 MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE AgrD I
mibi1464 MNLLGGLLLKLFSNFMAVIGNAAKYNPCASYLDEPQVPEELTKLDE AgrD III
mibi1465 MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE AgrD II
mibi1466 MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE AgrD II
mibi1467 MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE AgrD II
mibi1468 MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE AgrD I
mibi1469 MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE AgrD I
mibi1471 MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE AgrD I
mibi1473 MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE AgrD II
mibi1474 MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE AgrD I
mibi1475 MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE AgrD II
mibi1476 MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE AgrD I
mibi1477 MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE AgrD II
mibi1478 MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE AgrD I
mibi1479 MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE AgrD II
mibi1480 MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE AgrD I
mibi1481 MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE AgrD I
mibi1482 MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE AgrD I
mibi1483 MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE AgrD I
mibi1484 none
mibi1485 MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE AgrD I
mibi1486 MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE AgrD I
mibi1487 MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE AgrD I
mibi1488 MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE AgrD I
mibi1489 MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE AgrD II
mibi1490 MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE AgrD II
mibi1491 MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE AgrD II
mibi1492 MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE AgrD II
mibi1493 MNLLGGL F LK I FSNFMAVIGNA A KYNPC AS YLDEPQVPEELTKLDE AgrD III* (with a 2-codon difference)
mibi1494 MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE AgrD I
mibi1495 MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE AgrD II
mibi1496 MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE AgrD I
mibi1497 MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE AgrD I
mibi1498 MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE AgrD I
mibi1499 MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE AgrD II
mibi1500 MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE AgrD I
mibi1501 MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE AgrD I
mibi1502 MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE AgrD I
mibi1503 MNLLGGLLLKLFSNFMAVIGNAAKYNPCASYLDEPQVPEELTKLDE AgrD III
mibi1504 MNLLGGLLLKLFSNFMAVIGNAAKYNPCASYLDEPQVPEELTKLDE AgrD III
mibi1505 MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE AgrD I
mibi1506 MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE AgrD I
mibi2312 MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE AgrD II
mibi2313 MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE AgrD I
mibi2314 MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE AgrD I
mibi2315 MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE AgrD I
mibi2316 MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE AgrD II
mibi2317 MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE AgrD II
mibi2318 MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE AgrD I
mibi2319 MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE AgrD I
mibi2320 MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE AgrD II
mibi2321 MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE AgrD I
mibi2379 MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE AgrD II
#MNLLGGL L LK L FSNFMAVIGNA A KYNPC AS YLDEPQVPEELTKLDE AgrD III (2)
#MNLLGGL L LK I FSNFMAVIGNA S KYNPC SN YLDEPQVPEELTKLDE AgrD II (4)
-- AgrD I --
Query 1 MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE 46
M + L +K F+ + IG + + C Y DEP+VPEELTKL E
Sbjct 926825 MNLLGGLLLKIFSNFMAVIGNASKYNPCVMYLDEPQVPEELTKLDE 926688
-- AgrD II --
Query 1 MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE 46
MNLLGGLLLKIFSNFMAVIGNASKYNPC YLDEPQVPEELTKLDE
Sbjct 926825 MNLLGGLLLKIFSNFMAVIGNASKYNPCVMYLDEPQVPEELTKLDE 926688
-- AgrD III --
Query 1 MNLLGGLLLKLFSNFMAVIGNAAKYNPCASYLDEPQVPEELTKLDE 46
MNLLGGLLLK+FSNFMAVIGNA+KYNPC YLDEPQVPEELTKLDE
Sbjct 926825 MNLLGGLLLKIFSNFMAVIGNASKYNPCVMYLDEPQVPEELTKLDE 926688
-
Calulate the presence-absence-matrix by searching keyword gene=gene_name in gff3-files
cut -d',' -f1 plotTreeHeatmap/typing.csv > all_isolate_names.txt
grep "gene=gyrB" *.gff3 > temp
cut -d'.' -f1 temp > temp1
diff all_isolate_names.txt temp1
grep "gene=fumC" *.gff3 > temp
cut -d'.' -f1 temp > temp1
diff all_isolate_names.txt temp1
grep "gene=gltA" *.gff3 > temp
cut -d'.' -f1 temp > temp1
diff all_isolate_names.txt temp1
grep "gene=icd" *.gff3 > temp
cut -d'.' -f1 temp > temp1
diff all_isolate_names.txt temp1
grep "gene=apsS" *.gff3 > temp
cut -d'.' -f1 temp > temp1
diff all_isolate_names.txt temp1 | wc -l
#TODO, using sequence comparisons for one record!
grep "gene=sigB" *.gff3 > temp
cut -d'.' -f1 temp > temp1
diff all_isolate_names.txt temp1
#27d26
#< mibi1461
grep "gene=sarA" *.gff3 > temp
cut -d'.' -f1 temp > temp1
diff all_isolate_names.txt temp1
#17d16
#< mibi1451
#32d30
#< mibi1466
#45d42
#< mibi1481
grep "gene=agrC" *.gff3 > temp
cut -d'.' -f1 temp > temp1
diff all_isolate_names.txt temp1 | wc -l
#TODO, using sequence comparisons for one record!
grep "gene=yycG" *.gff3 > temp
cut -d'.' -f1 temp > temp1
diff all_isolate_names.txt temp1 | wc -l
#TODO, using sequence comparisons for one record!
grep "PSM-beta" *.gff3 > temp
cut -d'.' -f1 temp > temp1
diff all_isolate_names.txt temp1 | wc -l
#TODO, using sequence comparisons for one record!
grep "PSM-delta" *.gff3 > temp
cut -d'.' -f1 temp > temp1
diff all_isolate_names.txt temp1
#9d8
#< mibi1443
grep "hlb" *.gff3 > temp
cut -d'.' -f1 temp > temp1
diff all_isolate_names.txt temp1 | wc -l
#TODO, using sequence comparisons for one record!
grep "atlE" *.gff3 > temp
cut -d'.' -f1 temp > temp1
diff all_isolate_names.txt temp1 | wc -l
#TODO, using sequence comparisons for one record!
grep "gene=atl" *.gff3 > temp
cut -d'.' -f1 temp > temp1
diff all_isolate_names.txt temp1
#19d18
#< mibi1453
grep "gene=sdrG" *.gff3 > temp
cut -d'.' -f1 temp > temp1
diff all_isolate_names.txt temp1
#2d1
< mibi1436
5d3
< mibi1439
8,9d5
< mibi1442
< mibi1443
11,12d6
< mibi1445
< mibi1446
14d7
< mibi1448
18,19d10
< mibi1452
< mibi1453
30,32d20
< mibi1464
< mibi1465
< mibi1466
34,35d21
< mibi1468
< mibi1469
37d22
< mibi1473
39d23
< mibi1475
41d24
< mibi1477
43d25
< mibi1479
47d28
< mibi1483
50d30
< mibi1486
52d31
< mibi1488
55d33
< mibi1491
63,64d40
< mibi1499
< mibi1500
67d42
< mibi1503
76d50
< mibi2317
79d52
< mibi2320
81d53
< mibi2379
grep "gene=sdrH" *.gff3 > temp
cut -d'.' -f1 temp > temp1
diff all_isolate_names.txt temp1
#24d23
#< mibi1458
#57d55
#< mibi1493
grep "gene=ebh" *.gff3 > temp
cut -d'.' -f1 temp > temp1
diff all_isolate_names.txt temp1
#1d0
#< mibi1435
6d4
< mibi1440
11,13d8
< mibi1445
< mibi1446
< mibi1447
16,18d10
< mibi1450
< mibi1451
< mibi1452
20d11
< mibi1454
22,23d12
< mibi1456
< mibi1457
25,27d13
< mibi1459
< mibi1460
< mibi1461
29d14
< mibi1463
31,32d15
< mibi1465
< mibi1466
37d19
< mibi1473
39d20
< mibi1475
41,44d21
< mibi1477
< mibi1478
< mibi1479
< mibi1480
47d23
< mibi1483
49d24
< mibi1485
51,52d25
< mibi1487
< mibi1488
54,55d26
< mibi1490
< mibi1491
59,60d29
< mibi1495
< mibi1496
62,63d30
< mibi1498
< mibi1499
66d32
< mibi1502
71d36
< mibi2312
74d38
< mibi2315
76,79d39
< mibi2317
< mibi2318
< mibi2319
< mibi2320
81d40
< mibi2379
grep "gene=ebpS" *.gff3 > temp
cut -d'.' -f1 temp > temp1
diff all_isolate_names.txt temp1
grep "gene=tagB" *.gff3 > temp
cut -d'.' -f1 temp > temp1
uniq temp1 > temp2 # 3 copies for each isolate
diff all_isolate_names.txt temp2
grep "gene=capC" *.gff3 > temp
cut -d'.' -f1 temp > temp1
diff all_isolate_names.txt temp1 | wc -l
#TODO, using sequence comparisons for one record!
grep "gene=sepA" *.gff3 > temp
cut -d'.' -f1 temp > temp1
uniq temp1 > temp2
diff all_isolate_names.txt temp2
grep "gene=dltA" *.gff3 > temp
cut -d'.' -f1 temp > temp1
diff all_isolate_names.txt temp1
grep "gene=fmtC" *.gff3 > temp
cut -d'.' -f1 temp > temp1
diff all_isolate_names.txt temp1 | wc -l
#TODO, using sequence comparisons for one record!
grep "gene=lipA" *.gff3 > temp
cut -d'.' -f1 temp > temp1
diff all_isolate_names.txt temp1
grep "gene=sceD" *.gff3 > temp
cut -d'.' -f1 temp > temp1
diff all_isolate_names.txt temp1
#TODO: check the sdrG more detailed with sequence alignments, since SE0760 is not standard gene name.
grep "gene=SE0760" *.gff3 > temp
cut -d'.' -f1 temp > temp1
diff all_isolate_names.txt temp1 | wc -l
#TODO, using sequence comparisons for one record!
grep "gene=esp" *.gff3 > temp
cut -d'.' -f1 temp > temp1
diff all_isolate_names.txt temp1 | wc -l
#TODO, using sequence comparisons for one record!
grep "gene=ecpA" *.gff3 > temp
cut -d'.' -f1 temp > temp1
diff all_isolate_names.txt temp1
17d16
< mibi1451
37d35
< mibi1473
-
Calulate the presence-absence-matrix by local blastn searching
(Optional online search) https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&PAGE_TYPE=BlastSearch&BLAST_SPEC=MicrobialGenomes
#Title:Refseq prokaryote representative genomes (contains refseq assembly)
#Molecule Type:mixed DNA
#Update date:2024/10/16
#Number of sequences:1038672
#cat gyrB_revcomp.fasta fumC_revcomp.fasta gltA.fasta icd_revcomp.fasta apsS.fasta sigB_revcomp.fasta sarA_revcomp.fasta ...
cp ~/DATA/Data_Patricia_Sepi_5Samples/presence_absence_matrix_on_gene_list/apsS.fasta .
cp ~/DATA/Data_Patricia_Sepi_5Samples/presence_absence_matrix_on_gene_list/agrC.fasta .
cp ~/DATA/Data_Patricia_Sepi_5Samples/presence_absence_matrix_on_gene_list/yycG.fasta .
cp ~/DATA/Data_Patricia_Sepi_5Samples/presence_absence_matrix_on_gene_list/psm-beta.fasta .
cp ~/DATA/Data_Patricia_Sepi_5Samples/presence_absence_matrix_on_gene_list/hlb_.fasta .
cp ~/DATA/Data_Patricia_Sepi_5Samples/presence_absence_matrix_on_gene_list/atlE.fasta .
cp ~/DATA/Data_Patricia_Sepi_5Samples/presence_absence_matrix_on_gene_list/capC.fasta .
cp ~/DATA/Data_Patricia_Sepi_5Samples/presence_absence_matrix_on_gene_list/fmtC.fasta .
cp ~/DATA/Data_Patricia_Sepi_5Samples/presence_absence_matrix_on_gene_list/SE0760.fasta .
cp ~/DATA/Data_Patricia_Sepi_5Samples/presence_absence_matrix_on_gene_list/esp.fasta .
cp ~/DATA/Data_Patricia_Sepi_5Samples/presence_absence_matrix_on_gene_list/MT880870.fasta .
cp ~/DATA/Data_Patricia_Sepi_5Samples/presence_absence_matrix_on_gene_list/MT880871.fasta .
cp ~/DATA/Data_Patricia_Sepi_5Samples/presence_absence_matrix_on_gene_list/MT880872.fasta .
for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
cd ../shovill/${sample}/
makeblastdb -in contigs.fa -dbtype nucl
cd ../../presence_absence_matrix_on_gene_list
done
# -length(apsS.fasta)=1041
for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
blastn -db ../shovill/${sample}/contigs.fa -query apsS.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > apsS_on_${sample}.blastn
done
for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
python3 analyze_blastn_res.py apsS_on_${sample}.blastn
done
apsS_on_mibi1435.blastn: 1041
apsS_on_mibi1436.blastn: 1041
apsS_on_mibi1437.blastn: 1041
apsS_on_mibi1438.blastn: 1041
apsS_on_mibi1439.blastn: 1041
apsS_on_mibi1440.blastn: 1041
apsS_on_mibi1441.blastn: 1041
apsS_on_mibi1442.blastn: 1041
apsS_on_mibi1443.blastn: 1041
apsS_on_mibi1444.blastn: 1041
apsS_on_mibi1445.blastn: 1041
apsS_on_mibi1446.blastn: 1041
apsS_on_mibi1447.blastn: 1041
apsS_on_mibi1448.blastn: 1041
apsS_on_mibi1449.blastn: 1041
apsS_on_mibi1450.blastn: 1041
apsS_on_mibi1451.blastn: 1041
apsS_on_mibi1452.blastn: 1041
apsS_on_mibi1453.blastn: 1041
apsS_on_mibi1454.blastn: 1041
apsS_on_mibi1455.blastn: 1041
apsS_on_mibi1456.blastn: 1041
apsS_on_mibi1457.blastn: 1041
apsS_on_mibi1458.blastn: 1041
apsS_on_mibi1459.blastn: 1041
apsS_on_mibi1460.blastn: 1041
apsS_on_mibi1461.blastn: 1041
apsS_on_mibi1462.blastn: 1041
apsS_on_mibi1463.blastn: 1041
apsS_on_mibi1464.blastn: 1041
apsS_on_mibi1465.blastn: 1041
apsS_on_mibi1466.blastn: 1041
apsS_on_mibi1467.blastn: 1041
apsS_on_mibi1468.blastn: 1041
apsS_on_mibi1469.blastn: 1041
apsS_on_mibi1471.blastn: 1041
apsS_on_mibi1473.blastn: 1041
apsS_on_mibi1474.blastn: 1041
apsS_on_mibi1475.blastn: 1041
apsS_on_mibi1476.blastn: 1041
apsS_on_mibi1477.blastn: 1041
apsS_on_mibi1478.blastn: 1041
apsS_on_mibi1479.blastn: 1041
apsS_on_mibi1480.blastn: 1041
apsS_on_mibi1481.blastn: 1041
apsS_on_mibi1482.blastn: 1041
apsS_on_mibi1483.blastn: 1041
apsS_on_mibi1484.blastn: 1041
apsS_on_mibi1485.blastn: 1041
apsS_on_mibi1486.blastn: 1041
apsS_on_mibi1487.blastn: 1041
apsS_on_mibi1488.blastn: 1041
apsS_on_mibi1489.blastn: 1041
apsS_on_mibi1490.blastn: 1041
apsS_on_mibi1491.blastn: 1041
apsS_on_mibi1492.blastn: 1041
apsS_on_mibi1493.blastn: 1041
apsS_on_mibi1494.blastn: 1041
apsS_on_mibi1495.blastn: 1041
apsS_on_mibi1496.blastn: 1041
apsS_on_mibi1497.blastn: 1041
apsS_on_mibi1498.blastn: 1041
apsS_on_mibi1499.blastn: 1041
apsS_on_mibi1500.blastn: 1041
apsS_on_mibi1501.blastn: 1041
apsS_on_mibi1502.blastn: 1041
apsS_on_mibi1503.blastn: 1041
apsS_on_mibi1504.blastn: 1041
apsS_on_mibi1505.blastn: 1041
apsS_on_mibi1506.blastn: 1041
apsS_on_mibi2312.blastn: 1041
apsS_on_mibi2313.blastn: 1041
apsS_on_mibi2314.blastn: 1041
apsS_on_mibi2315.blastn: 1041
apsS_on_mibi2316.blastn: 1041
apsS_on_mibi2317.blastn: 1041
apsS_on_mibi2318.blastn: 1041
apsS_on_mibi2319.blastn: 1041
apsS_on_mibi2320.blastn: 1041
apsS_on_mibi2321.blastn: 1041
apsS_on_mibi2379.blastn: 1041
# -length(sigB_revcomp.fasta)=771
for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
blastn -db ../shovill/${sample}/contigs.fa -query sigB_revcomp.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > sigB_on_${sample}.blastn
done
for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
python3 analyze_blastn_res.py sigB_on_${sample}.blastn
done
sigB_on_mibi1435.blastn: 771
sigB_on_mibi1436.blastn: 771
sigB_on_mibi1437.blastn: 771
sigB_on_mibi1438.blastn: 771
sigB_on_mibi1439.blastn: 771
sigB_on_mibi1440.blastn: 771
sigB_on_mibi1441.blastn: 771
sigB_on_mibi1442.blastn: 771
sigB_on_mibi1443.blastn: 771
sigB_on_mibi1444.blastn: 771
sigB_on_mibi1445.blastn: 771
sigB_on_mibi1446.blastn: 771
sigB_on_mibi1447.blastn: 771
sigB_on_mibi1448.blastn: 771
sigB_on_mibi1449.blastn: 771
sigB_on_mibi1450.blastn: 771
sigB_on_mibi1451.blastn: 771
sigB_on_mibi1452.blastn: 771
sigB_on_mibi1453.blastn: 771
sigB_on_mibi1454.blastn: 771
sigB_on_mibi1455.blastn: 771
sigB_on_mibi1456.blastn: 771
sigB_on_mibi1457.blastn: 771
sigB_on_mibi1458.blastn: 771
sigB_on_mibi1459.blastn: 771
sigB_on_mibi1460.blastn: 771
sigB_on_mibi1461.blastn: 0 *
sigB_on_mibi1462.blastn: 771
sigB_on_mibi1463.blastn: 771
sigB_on_mibi1464.blastn: 771
sigB_on_mibi1465.blastn: 771
sigB_on_mibi1466.blastn: 771
sigB_on_mibi1467.blastn: 771
sigB_on_mibi1468.blastn: 771
sigB_on_mibi1469.blastn: 771
sigB_on_mibi1471.blastn: 771
sigB_on_mibi1473.blastn: 771
sigB_on_mibi1474.blastn: 771
sigB_on_mibi1475.blastn: 771
sigB_on_mibi1476.blastn: 771
sigB_on_mibi1477.blastn: 771
sigB_on_mibi1478.blastn: 771
sigB_on_mibi1479.blastn: 771
sigB_on_mibi1480.blastn: 771
sigB_on_mibi1481.blastn: 771
sigB_on_mibi1482.blastn: 771
sigB_on_mibi1483.blastn: 771
sigB_on_mibi1484.blastn: 771
sigB_on_mibi1485.blastn: 771
sigB_on_mibi1486.blastn: 771
sigB_on_mibi1487.blastn: 771
sigB_on_mibi1488.blastn: 771
sigB_on_mibi1489.blastn: 771
sigB_on_mibi1490.blastn: 771
sigB_on_mibi1491.blastn: 771
sigB_on_mibi1492.blastn: 771
sigB_on_mibi1493.blastn: 771
sigB_on_mibi1494.blastn: 771
sigB_on_mibi1495.blastn: 771
sigB_on_mibi1496.blastn: 771
sigB_on_mibi1497.blastn: 771
sigB_on_mibi1498.blastn: 771
sigB_on_mibi1499.blastn: 771
sigB_on_mibi1500.blastn: 771
sigB_on_mibi1501.blastn: 771
sigB_on_mibi1502.blastn: 771
sigB_on_mibi1503.blastn: 771
sigB_on_mibi1504.blastn: 771
sigB_on_mibi1505.blastn: 771
sigB_on_mibi1506.blastn: 771
sigB_on_mibi2312.blastn: 771
sigB_on_mibi2313.blastn: 771
sigB_on_mibi2314.blastn: 771
sigB_on_mibi2315.blastn: 771
sigB_on_mibi2316.blastn: 771
sigB_on_mibi2317.blastn: 771
sigB_on_mibi2318.blastn: 771
sigB_on_mibi2319.blastn: 771
sigB_on_mibi2320.blastn: 771
sigB_on_mibi2321.blastn: 771
sigB_on_mibi2379.blastn: 771
# - length(sarA_revcomp.fasta)=375
for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
blastn -db ../shovill/${sample}/contigs.fa -query sarA_revcomp.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > sarA_on_${sample}.blastn
done
for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
python3 analyze_blastn_res.py sarA_on_${sample}.blastn
done
sarA_on_mibi1435.blastn: 375
sarA_on_mibi1436.blastn: 375
sarA_on_mibi1437.blastn: 375
sarA_on_mibi1438.blastn: 375
sarA_on_mibi1439.blastn: 375
sarA_on_mibi1440.blastn: 375
sarA_on_mibi1441.blastn: 375
sarA_on_mibi1442.blastn: 375
sarA_on_mibi1443.blastn: 375
sarA_on_mibi1444.blastn: 375
sarA_on_mibi1445.blastn: 375
sarA_on_mibi1446.blastn: 375
sarA_on_mibi1447.blastn: 375
sarA_on_mibi1448.blastn: 375
sarA_on_mibi1449.blastn: 375
sarA_on_mibi1450.blastn: 375
sarA_on_mibi1451.blastn: 0 *
sarA_on_mibi1452.blastn: 375
sarA_on_mibi1453.blastn: 375
sarA_on_mibi1454.blastn: 375
sarA_on_mibi1455.blastn: 375
sarA_on_mibi1456.blastn: 375
sarA_on_mibi1457.blastn: 375
sarA_on_mibi1458.blastn: 375
sarA_on_mibi1459.blastn: 375
sarA_on_mibi1460.blastn: 375
sarA_on_mibi1461.blastn: 375
sarA_on_mibi1462.blastn: 375
sarA_on_mibi1463.blastn: 375
sarA_on_mibi1464.blastn: 375
sarA_on_mibi1465.blastn: 375
sarA_on_mibi1466.blastn: 208 *
sarA_on_mibi1467.blastn: 375
sarA_on_mibi1468.blastn: 375
sarA_on_mibi1469.blastn: 375
sarA_on_mibi1471.blastn: 375
sarA_on_mibi1473.blastn: 375
sarA_on_mibi1474.blastn: 375
sarA_on_mibi1475.blastn: 375
sarA_on_mibi1476.blastn: 375
sarA_on_mibi1477.blastn: 375
sarA_on_mibi1478.blastn: 375
sarA_on_mibi1479.blastn: 375
sarA_on_mibi1480.blastn: 375
sarA_on_mibi1481.blastn: 248 *
sarA_on_mibi1482.blastn: 375
sarA_on_mibi1483.blastn: 375
sarA_on_mibi1484.blastn: 375
sarA_on_mibi1485.blastn: 375
sarA_on_mibi1486.blastn: 375
sarA_on_mibi1487.blastn: 375
sarA_on_mibi1488.blastn: 375
sarA_on_mibi1489.blastn: 375
sarA_on_mibi1490.blastn: 375
sarA_on_mibi1491.blastn: 375
sarA_on_mibi1492.blastn: 375
sarA_on_mibi1493.blastn: 375
sarA_on_mibi1494.blastn: 375
sarA_on_mibi1495.blastn: 375
sarA_on_mibi1496.blastn: 375
sarA_on_mibi1497.blastn: 375
sarA_on_mibi1498.blastn: 375
sarA_on_mibi1499.blastn: 375
sarA_on_mibi1500.blastn: 375
sarA_on_mibi1501.blastn: 375
sarA_on_mibi1502.blastn: 375
sarA_on_mibi1503.blastn: 375
sarA_on_mibi1504.blastn: 375
sarA_on_mibi1505.blastn: 375
sarA_on_mibi1506.blastn: 357
sarA_on_mibi2312.blastn: 375
sarA_on_mibi2313.blastn: 375
sarA_on_mibi2314.blastn: 375
sarA_on_mibi2315.blastn: 375
sarA_on_mibi2316.blastn: 375
sarA_on_mibi2317.blastn: 375
sarA_on_mibi2318.blastn: 375
sarA_on_mibi2319.blastn: 375
sarA_on_mibi2320.blastn: 375
sarA_on_mibi2321.blastn: 375
sarA_on_mibi2379.blastn: 375
# -length(agrC.fasta)=1290
samtools faidx agrABCD_hld.fasta "gi|3320006|emb|Z49220.1|":1494-2783
for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
blastn -db ../shovill/${sample}/contigs.fa -query agrC.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > agrC_on_${sample}.blastn
done
for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
python3 analyze_blastn_res.py agrC_on_${sample}.blastn
done
agrC_on_mibi1435.blastn: 1002
agrC_on_mibi1436.blastn: 1290
agrC_on_mibi1437.blastn: 688
agrC_on_mibi1438.blastn: 1290
agrC_on_mibi1439.blastn: 688
agrC_on_mibi1440.blastn: 1290
agrC_on_mibi1441.blastn: 861
agrC_on_mibi1442.blastn: 688
agrC_on_mibi1443.blastn: 1290
agrC_on_mibi1444.blastn: 1290
agrC_on_mibi1445.blastn: 688
agrC_on_mibi1446.blastn: 688
agrC_on_mibi1447.blastn: 688
agrC_on_mibi1448.blastn: 1290
agrC_on_mibi1449.blastn: 861
agrC_on_mibi1450.blastn: 1290
agrC_on_mibi1451.blastn: 688
agrC_on_mibi1452.blastn: 818
agrC_on_mibi1453.blastn: 1290
agrC_on_mibi1454.blastn: 1290
agrC_on_mibi1455.blastn: 1290
agrC_on_mibi1456.blastn: 1290
agrC_on_mibi1457.blastn: 688
agrC_on_mibi1458.blastn: 1290
agrC_on_mibi1459.blastn: 1290
agrC_on_mibi1460.blastn: 688
agrC_on_mibi1461.blastn: 1290
agrC_on_mibi1462.blastn: 1290
agrC_on_mibi1463.blastn: 1290
agrC_on_mibi1464.blastn: 861
agrC_on_mibi1465.blastn: 688
agrC_on_mibi1466.blastn: 541
agrC_on_mibi1467.blastn: 688
agrC_on_mibi1468.blastn: 1290
agrC_on_mibi1469.blastn: 1290
agrC_on_mibi1471.blastn: 1165
agrC_on_mibi1473.blastn: 688
agrC_on_mibi1474.blastn: 1290
agrC_on_mibi1475.blastn: 688
agrC_on_mibi1476.blastn: 1290
agrC_on_mibi1477.blastn: 688
agrC_on_mibi1478.blastn: 442
agrC_on_mibi1479.blastn: 688
agrC_on_mibi1480.blastn: 1290
agrC_on_mibi1481.blastn: 862
agrC_on_mibi1482.blastn: 1290
agrC_on_mibi1483.blastn: 1290
agrC_on_mibi1484.blastn: 491
agrC_on_mibi1485.blastn: 1290
agrC_on_mibi1486.blastn: 1290
agrC_on_mibi1487.blastn: 1290
agrC_on_mibi1488.blastn: 1290
agrC_on_mibi1489.blastn: 688
agrC_on_mibi1490.blastn: 688
agrC_on_mibi1491.blastn: 688
agrC_on_mibi1492.blastn: 688
agrC_on_mibi1493.blastn: 818
agrC_on_mibi1494.blastn: 1290
agrC_on_mibi1495.blastn: 688
agrC_on_mibi1496.blastn: 1290
agrC_on_mibi1497.blastn: 911
agrC_on_mibi1498.blastn: 1290
agrC_on_mibi1499.blastn: 688
agrC_on_mibi1500.blastn: 1290
agrC_on_mibi1501.blastn: 1290
agrC_on_mibi1502.blastn: 1094
agrC_on_mibi1503.blastn: 818
agrC_on_mibi1504.blastn: 861
agrC_on_mibi1505.blastn: 1290
agrC_on_mibi1506.blastn: 1290
agrC_on_mibi2312.blastn: 688
agrC_on_mibi2313.blastn: 1290
agrC_on_mibi2314.blastn: 1290
agrC_on_mibi2315.blastn: 1290
agrC_on_mibi2316.blastn: 688
agrC_on_mibi2317.blastn: 688
agrC_on_mibi2318.blastn: 1290
agrC_on_mibi2319.blastn: 1290
agrC_on_mibi2320.blastn: 688
agrC_on_mibi2321.blastn: 1290
agrC_on_mibi2379.blastn: 688
partial, 1002/1290 nt present
+
partial, 688/1290 nt present
+
partial, 688/1290 nt present
+
partial, 861/1290 nt present
partial, 688/1290 nt present
+
+
partial, 688/1290 nt present
partial, 688/1290 nt present
partial, 688/1290 nt present
+
partial, 861/1290 nt present
+
partial, 688/1290 nt present
partial, 818/1290 nt present
+
+
+
+
partial, 688/1290 nt present
+
+
partial, 688/1290 nt present
+
+
+
partial, 861/1290 nt present
partial, 688/1290 nt present
partial, 541/1290 nt present
partial, 688/1290 nt present
+
+
partial, 1165/1290 nt present
partial, 688/1290 nt present
+
partial, 688/1290 nt present
+
partial, 688/1290 nt present
partial, 442/1290 nt present
partial, 688/1290 nt present
+
partial, 862/1290 nt present
+
+
partial, 491/1290 nt present
+
+
+
+
partial, 688/1290 nt present
partial, 688/1290 nt present
partial, 688/1290 nt present
partial, 688/1290 nt present
partial, 818/1290 nt present
+
partial, 688/1290 nt present
+
partial, 911/1290 nt present
+
partial, 688/1290 nt present
+
+
partial, 1094/1290 nt present
partial, 818/1290 nt present
partial, 861/1290 nt present
+
+
partial, 688/1290 nt present
+
+
+
partial, 688/1290 nt present
partial, 688/1290 nt present
+
+
partial, 688/1290 nt present
+
partial, 688/1290 nt present
# - length(yycG.fasta)=1827
gene complement(2589240..2591072)
/gene="yycG"
samtools faidx CP000029.fasta "gi|57636010|gb|CP000029.1|":2589240-2591072 > yycG.fasta
for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
blastn -db ../shovill/${sample}/contigs.fa -query yycG_revcomp.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > yycG_on_${sample}.blastn
done
for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
python3 analyze_blastn_res.py yycG_on_${sample}.blastn
done
#-->WARNING: Only 80% similarity, not the same gene!
yycG_on_mibi1435.blastn: 1833
yycG_on_mibi1436.blastn: 1833
yycG_on_mibi1437.blastn: 1833
yycG_on_mibi1438.blastn: 1833
yycG_on_mibi1439.blastn: 1833
yycG_on_mibi1440.blastn: 1833
yycG_on_mibi1441.blastn: 1833
yycG_on_mibi1442.blastn: 1833
yycG_on_mibi1443.blastn: 1833
yycG_on_mibi1444.blastn: 1833
yycG_on_mibi1445.blastn: 1833
yycG_on_mibi1446.blastn: 1833
yycG_on_mibi1447.blastn: 1833
yycG_on_mibi1448.blastn: 1833
yycG_on_mibi1449.blastn: 1833
yycG_on_mibi1450.blastn: 1833
yycG_on_mibi1451.blastn: 1833
yycG_on_mibi1452.blastn: 1833
yycG_on_mibi1453.blastn: 1833
yycG_on_mibi1454.blastn: 1833
yycG_on_mibi1455.blastn: 1833
yycG_on_mibi1456.blastn: 1833
yycG_on_mibi1457.blastn: 1833
yycG_on_mibi1458.blastn: 1833
yycG_on_mibi1459.blastn: 1833
yycG_on_mibi1460.blastn: 1833
yycG_on_mibi1461.blastn: 1833
yycG_on_mibi1462.blastn: 1833
yycG_on_mibi1463.blastn: 1833
yycG_on_mibi1464.blastn: 1833
yycG_on_mibi1465.blastn: 1833
yycG_on_mibi1466.blastn: 1833
yycG_on_mibi1467.blastn: 1833
yycG_on_mibi1468.blastn: 1833
yycG_on_mibi1469.blastn: 1833
yycG_on_mibi1471.blastn: 1833
yycG_on_mibi1473.blastn: 1833
yycG_on_mibi1474.blastn: 1833
yycG_on_mibi1475.blastn: 1833
yycG_on_mibi1476.blastn: 1833
yycG_on_mibi1477.blastn: 1833
yycG_on_mibi1478.blastn: 1833
yycG_on_mibi1479.blastn: 1833
yycG_on_mibi1480.blastn: 1833
yycG_on_mibi1481.blastn: 1833
yycG_on_mibi1482.blastn: 1833
yycG_on_mibi1483.blastn: 1833
yycG_on_mibi1484.blastn: 1833
yycG_on_mibi1485.blastn: 1833
yycG_on_mibi1486.blastn: 1833
yycG_on_mibi1487.blastn: 1833
yycG_on_mibi1488.blastn: 1833
yycG_on_mibi1489.blastn: 1833
yycG_on_mibi1490.blastn: 1833
yycG_on_mibi1491.blastn: 1833
yycG_on_mibi1492.blastn: 1833
yycG_on_mibi1493.blastn: 1833
yycG_on_mibi1494.blastn: 1833
yycG_on_mibi1495.blastn: 1833
yycG_on_mibi1496.blastn: 1833
yycG_on_mibi1497.blastn: 1833
yycG_on_mibi1498.blastn: 1833
yycG_on_mibi1499.blastn: 1833
yycG_on_mibi1500.blastn: 1833
yycG_on_mibi1501.blastn: 1833
yycG_on_mibi1502.blastn: 1833
yycG_on_mibi1503.blastn: 1833
yycG_on_mibi1504.blastn: 1833
yycG_on_mibi1505.blastn: 1833
yycG_on_mibi1506.blastn: 1833
yycG_on_mibi2312.blastn: 1833
yycG_on_mibi2313.blastn: 1833
yycG_on_mibi2314.blastn: 1833
yycG_on_mibi2315.blastn: 1833
yycG_on_mibi2316.blastn: 1833
yycG_on_mibi2317.blastn: 1833
yycG_on_mibi2318.blastn: 1833
yycG_on_mibi2319.blastn: 1833
yycG_on_mibi2320.blastn: 1833
yycG_on_mibi2321.blastn: 1833
yycG_on_mibi2379.blastn: 1833
#TODOs: exact the gene sequence for psm-delta and atl
#https://www.ncbi.nlm.nih.gov/nuccore (psm gene) AND "Staphylococcus aureus"[porgn:__txid1280]
#grep "PSM-delta" mibi1435.gbff
# /product="Phenol-soluble modulin PSM-delta"
#grep "atl" mibi1435.gbff
# /gene="atl"
# /gene="atl"
https://www.ncbi.nlm.nih.gov/nuccore/JQ066320.1
# -length(psm-beta1.fasta)=135
for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
blastn -db ../shovill/${sample}/contigs.fa -query psm-beta1.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > psm-beta1_on_${sample}.blastn
done
for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
python3 analyze_blastn_res.py psm-beta1_on_${sample}.blastn
done
psm-beta1_on_mibi1435.blastn: 0
psm-beta1_on_mibi1436.blastn: 0
psm-beta1_on_mibi1437.blastn: 0
psm-beta1_on_mibi1438.blastn: 0
psm-beta1_on_mibi1439.blastn: 0
psm-beta1_on_mibi1440.blastn: 0
psm-beta1_on_mibi1441.blastn: 0
psm-beta1_on_mibi1442.blastn: 0
psm-beta1_on_mibi1443.blastn: 0
psm-beta1_on_mibi1444.blastn: 0
psm-beta1_on_mibi1445.blastn: 0
psm-beta1_on_mibi1446.blastn: 0
psm-beta1_on_mibi1447.blastn: 0
psm-beta1_on_mibi1448.blastn: 0
psm-beta1_on_mibi1449.blastn: 0
psm-beta1_on_mibi1450.blastn: 0
psm-beta1_on_mibi1451.blastn: 0
psm-beta1_on_mibi1452.blastn: 0
psm-beta1_on_mibi1453.blastn: 0
psm-beta1_on_mibi1454.blastn: 0
psm-beta1_on_mibi1455.blastn: 0
psm-beta1_on_mibi1456.blastn: 0
psm-beta1_on_mibi1457.blastn: 0
psm-beta1_on_mibi1458.blastn: 0
psm-beta1_on_mibi1459.blastn: 0
psm-beta1_on_mibi1460.blastn: 0
psm-beta1_on_mibi1461.blastn: 0
psm-beta1_on_mibi1462.blastn: 0
psm-beta1_on_mibi1463.blastn: 0
psm-beta1_on_mibi1464.blastn: 0
psm-beta1_on_mibi1465.blastn: 0
psm-beta1_on_mibi1466.blastn: 0
psm-beta1_on_mibi1467.blastn: 0
psm-beta1_on_mibi1468.blastn: 0
psm-beta1_on_mibi1469.blastn: 0
psm-beta1_on_mibi1471.blastn: 0
psm-beta1_on_mibi1473.blastn: 0
psm-beta1_on_mibi1474.blastn: 0
psm-beta1_on_mibi1475.blastn: 0
psm-beta1_on_mibi1476.blastn: 0
psm-beta1_on_mibi1477.blastn: 0
psm-beta1_on_mibi1478.blastn: 0
psm-beta1_on_mibi1479.blastn: 0
psm-beta1_on_mibi1480.blastn: 0
psm-beta1_on_mibi1481.blastn: 0
psm-beta1_on_mibi1482.blastn: 0
psm-beta1_on_mibi1483.blastn: 0
psm-beta1_on_mibi1484.blastn: 0
psm-beta1_on_mibi1485.blastn: 0
psm-beta1_on_mibi1486.blastn: 0
psm-beta1_on_mibi1487.blastn: 0
psm-beta1_on_mibi1488.blastn: 0
psm-beta1_on_mibi1489.blastn: 0
psm-beta1_on_mibi1490.blastn: 0
psm-beta1_on_mibi1491.blastn: 0
psm-beta1_on_mibi1492.blastn: 0
psm-beta1_on_mibi1493.blastn: 0
psm-beta1_on_mibi1494.blastn: 0
psm-beta1_on_mibi1495.blastn: 0
psm-beta1_on_mibi1496.blastn: 0
psm-beta1_on_mibi1497.blastn: 0
psm-beta1_on_mibi1498.blastn: 0
psm-beta1_on_mibi1499.blastn: 0
psm-beta1_on_mibi1500.blastn: 0
psm-beta1_on_mibi1501.blastn: 0
psm-beta1_on_mibi1502.blastn: 0
psm-beta1_on_mibi1503.blastn: 0
psm-beta1_on_mibi1504.blastn: 0
psm-beta1_on_mibi1505.blastn: 0
psm-beta1_on_mibi1506.blastn: 0
psm-beta1_on_mibi2312.blastn: 0
psm-beta1_on_mibi2313.blastn: 0
psm-beta1_on_mibi2314.blastn: 0
psm-beta1_on_mibi2315.blastn: 0
psm-beta1_on_mibi2316.blastn: 0
psm-beta1_on_mibi2317.blastn: 0
psm-beta1_on_mibi2318.blastn: 0
psm-beta1_on_mibi2319.blastn: 0
psm-beta1_on_mibi2320.blastn: 0
psm-beta1_on_mibi2321.blastn: 0
psm-beta1_on_mibi2379.blastn: 0
# -length(hlb.fasta)=993
for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
blastn -db ../shovill/${sample}/contigs.fa -query psm-beta.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > hlb_on_${sample}.blastn
done
for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
python3 analyze_blastn_res.py hlb_on_${sample}.blastn
done
hlb_on_mibi1435.blastn: 0
hlb_on_mibi1436.blastn: 0
hlb_on_mibi1437.blastn: 0
hlb_on_mibi1438.blastn: 0
hlb_on_mibi1439.blastn: 0
hlb_on_mibi1440.blastn: 0
hlb_on_mibi1441.blastn: 0
hlb_on_mibi1442.blastn: 0
hlb_on_mibi1443.blastn: 0
hlb_on_mibi1444.blastn: 0
hlb_on_mibi1445.blastn: 0
hlb_on_mibi1446.blastn: 0
hlb_on_mibi1447.blastn: 0
hlb_on_mibi1448.blastn: 0
hlb_on_mibi1449.blastn: 0
hlb_on_mibi1450.blastn: 0
hlb_on_mibi1451.blastn: 0
hlb_on_mibi1452.blastn: 0
hlb_on_mibi1453.blastn: 0
hlb_on_mibi1454.blastn: 0
hlb_on_mibi1455.blastn: 0
hlb_on_mibi1456.blastn: 0
hlb_on_mibi1457.blastn: 0
hlb_on_mibi1458.blastn: 0
hlb_on_mibi1459.blastn: 0
hlb_on_mibi1460.blastn: 0
hlb_on_mibi1461.blastn: 0
hlb_on_mibi1462.blastn: 0
hlb_on_mibi1463.blastn: 0
hlb_on_mibi1464.blastn: 0
hlb_on_mibi1465.blastn: 0
hlb_on_mibi1466.blastn: 0
hlb_on_mibi1467.blastn: 0
hlb_on_mibi1468.blastn: 0
hlb_on_mibi1469.blastn: 0
hlb_on_mibi1471.blastn: 0
hlb_on_mibi1473.blastn: 0
hlb_on_mibi1474.blastn: 0
hlb_on_mibi1475.blastn: 0
hlb_on_mibi1476.blastn: 0
hlb_on_mibi1477.blastn: 0
hlb_on_mibi1478.blastn: 0
hlb_on_mibi1479.blastn: 0
hlb_on_mibi1480.blastn: 0
hlb_on_mibi1481.blastn: 0
hlb_on_mibi1482.blastn: 0
hlb_on_mibi1483.blastn: 0
hlb_on_mibi1484.blastn: 0
hlb_on_mibi1485.blastn: 0
hlb_on_mibi1486.blastn: 0
hlb_on_mibi1487.blastn: 0
hlb_on_mibi1488.blastn: 0
hlb_on_mibi1489.blastn: 0
hlb_on_mibi1490.blastn: 0
hlb_on_mibi1491.blastn: 0
hlb_on_mibi1492.blastn: 0
hlb_on_mibi1493.blastn: 0
hlb_on_mibi1494.blastn: 0
hlb_on_mibi1495.blastn: 0
hlb_on_mibi1496.blastn: 0
hlb_on_mibi1497.blastn: 0
hlb_on_mibi1498.blastn: 0
hlb_on_mibi1499.blastn: 0
hlb_on_mibi1500.blastn: 0
hlb_on_mibi1501.blastn: 0
hlb_on_mibi1502.blastn: 0
hlb_on_mibi1503.blastn: 0
hlb_on_mibi1504.blastn: 0
hlb_on_mibi1505.blastn: 0
hlb_on_mibi1506.blastn: 0
hlb_on_mibi2312.blastn: 0
hlb_on_mibi2313.blastn: 0
hlb_on_mibi2314.blastn: 0
hlb_on_mibi2315.blastn: 0
hlb_on_mibi2316.blastn: 0
hlb_on_mibi2317.blastn: 0
hlb_on_mibi2318.blastn: 0
hlb_on_mibi2319.blastn: 0
hlb_on_mibi2320.blastn: 0
hlb_on_mibi2321.blastn: 0
hlb_on_mibi2379.blastn: 0
## -length(altE_revcomp.fasta)=4008
#gene complement(627656..631663)
# /gene="atlE"
#samtools faidx CP000029.fasta gi|57636010|gb|CP000029.1|
samtools faidx CP000029.fasta "gi|57636010|gb|CP000029.1|":627656-631663 > atlE.fasta
revcomp atlE.fasta > atlE_revcomp.fasta
for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
blastn -db ../shovill/${sample}/contigs.fa -query atlE_revcomp.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > atlE_on_${sample}.blastn
done
for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
python3 analyze_blastn_res.py atlE_on_${sample}.blastn
done
atlE_on_mibi1435.blastn: 4008
atlE_on_mibi1436.blastn: 4008
atlE_on_mibi1437.blastn: 4465
atlE_on_mibi1438.blastn: 4008
atlE_on_mibi1439.blastn: 4008
atlE_on_mibi1440.blastn: 4008
atlE_on_mibi1441.blastn: 4450
atlE_on_mibi1442.blastn: 4450
atlE_on_mibi1443.blastn: 4008
atlE_on_mibi1444.blastn: 4008
atlE_on_mibi1445.blastn: 4008
atlE_on_mibi1446.blastn: 4008
atlE_on_mibi1447.blastn: 4008
atlE_on_mibi1448.blastn: 4008
atlE_on_mibi1449.blastn: 4008
atlE_on_mibi1450.blastn: 4008
atlE_on_mibi1451.blastn: 4008
atlE_on_mibi1452.blastn: 4450
atlE_on_mibi1453.blastn: 4008
atlE_on_mibi1454.blastn: 4008
atlE_on_mibi1455.blastn: 4008
atlE_on_mibi1456.blastn: 4008
atlE_on_mibi1457.blastn: 4008
atlE_on_mibi1458.blastn: 4450
atlE_on_mibi1459.blastn: 4008
atlE_on_mibi1460.blastn: 4008
atlE_on_mibi1461.blastn: 4008
atlE_on_mibi1462.blastn: 4008
atlE_on_mibi1463.blastn: 4450
atlE_on_mibi1464.blastn: 4450
atlE_on_mibi1465.blastn: 4008
atlE_on_mibi1466.blastn: 4008
atlE_on_mibi1467.blastn: 4450
atlE_on_mibi1468.blastn: 4465
atlE_on_mibi1469.blastn: 4465
atlE_on_mibi1471.blastn: 4008
atlE_on_mibi1473.blastn: 4008
atlE_on_mibi1474.blastn: 4008
atlE_on_mibi1475.blastn: 4008
atlE_on_mibi1476.blastn: 4008
atlE_on_mibi1477.blastn: 4008
atlE_on_mibi1478.blastn: 4008
atlE_on_mibi1479.blastn: 4008
atlE_on_mibi1480.blastn: 4008
atlE_on_mibi1481.blastn: 4008
atlE_on_mibi1482.blastn: 4008
atlE_on_mibi1483.blastn: 4450
atlE_on_mibi1484.blastn: 4008
atlE_on_mibi1485.blastn: 4008
atlE_on_mibi1486.blastn: 4450
atlE_on_mibi1487.blastn: 4008
atlE_on_mibi1488.blastn: 4008
atlE_on_mibi1489.blastn: 4450
atlE_on_mibi1490.blastn: 4008
atlE_on_mibi1491.blastn: 4008
atlE_on_mibi1492.blastn: 4008
atlE_on_mibi1493.blastn: 4450
atlE_on_mibi1494.blastn: 4008
atlE_on_mibi1495.blastn: 4008
atlE_on_mibi1496.blastn: 4008
atlE_on_mibi1497.blastn: 4008
atlE_on_mibi1498.blastn: 4008
atlE_on_mibi1499.blastn: 4008
atlE_on_mibi1500.blastn: 4008
atlE_on_mibi1501.blastn: 4008
atlE_on_mibi1502.blastn: 4008
atlE_on_mibi1503.blastn: 4008
atlE_on_mibi1504.blastn: 4450
atlE_on_mibi1505.blastn: 4008
atlE_on_mibi1506.blastn: 4008
atlE_on_mibi2312.blastn: 4008
atlE_on_mibi2313.blastn: 4008
atlE_on_mibi2314.blastn: 4008
atlE_on_mibi2315.blastn: 4008
atlE_on_mibi2316.blastn: 4008
atlE_on_mibi2317.blastn: 4008
atlE_on_mibi2318.blastn: 4008
atlE_on_mibi2319.blastn: 4008
atlE_on_mibi2320.blastn: 4008
atlE_on_mibi2321.blastn: 4008
atlE_on_mibi2379.blastn: 4008
# -length(sdrG)=2796
for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
blastn -db ../shovill/${sample}/contigs.fa -query sdrG.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > sdrG_on_${sample}.blastn
done
for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
python3 analyze_blastn_res.py sdrG_on_${sample}.blastn
done
sdrG_on_mibi1435.blastn: 2973
sdrG_on_mibi1436.blastn: 2967
sdrG_on_mibi1437.blastn: 2821
sdrG_on_mibi1438.blastn: 2796
sdrG_on_mibi1439.blastn: 3155
sdrG_on_mibi1440.blastn: 2967
sdrG_on_mibi1441.blastn: 2797
sdrG_on_mibi1442.blastn: 2801
sdrG_on_mibi1443.blastn: 2966
sdrG_on_mibi1444.blastn: 2796
sdrG_on_mibi1445.blastn: 3158
sdrG_on_mibi1446.blastn: 3155
sdrG_on_mibi1447.blastn: 2966
sdrG_on_mibi1448.blastn: 2797
sdrG_on_mibi1449.blastn: 2712
sdrG_on_mibi1450.blastn: 2794
sdrG_on_mibi1451.blastn: 2946
sdrG_on_mibi1452.blastn: 3166
sdrG_on_mibi1453.blastn: 2970
sdrG_on_mibi1454.blastn: 2976
sdrG_on_mibi1455.blastn: 2797
sdrG_on_mibi1456.blastn: 2967
sdrG_on_mibi1457.blastn: 2963
sdrG_on_mibi1458.blastn: 2794
sdrG_on_mibi1459.blastn: 3153
sdrG_on_mibi1460.blastn: 2566
sdrG_on_mibi1461.blastn: 2500
sdrG_on_mibi1462.blastn: 2966
sdrG_on_mibi1463.blastn: 2971
sdrG_on_mibi1464.blastn: 2530
sdrG_on_mibi1465.blastn: 2981
sdrG_on_mibi1466.blastn: 1547 *
sdrG_on_mibi1467.blastn: 2794
sdrG_on_mibi1468.blastn: 2967
sdrG_on_mibi1469.blastn: 2967
sdrG_on_mibi1471.blastn: 2796
sdrG_on_mibi1473.blastn: 2976
sdrG_on_mibi1474.blastn: 2797
sdrG_on_mibi1475.blastn: 2981
sdrG_on_mibi1476.blastn: 2794
sdrG_on_mibi1477.blastn: 2967
sdrG_on_mibi1478.blastn: 1511 *
sdrG_on_mibi1479.blastn: 2966
sdrG_on_mibi1480.blastn: 2976
sdrG_on_mibi1481.blastn: 2797
sdrG_on_mibi1482.blastn: 2797
sdrG_on_mibi1483.blastn: 2797
sdrG_on_mibi1484.blastn: 2976
sdrG_on_mibi1485.blastn: 3001
sdrG_on_mibi1486.blastn: 2797
sdrG_on_mibi1487.blastn: 2976
sdrG_on_mibi1488.blastn: 2963
sdrG_on_mibi1489.blastn: 2797
sdrG_on_mibi1490.blastn: 2981
sdrG_on_mibi1491.blastn: 3155
sdrG_on_mibi1492.blastn: 2982
sdrG_on_mibi1493.blastn: 2904
sdrG_on_mibi1494.blastn: 2980
sdrG_on_mibi1495.blastn: 2976
sdrG_on_mibi1496.blastn: 2994
sdrG_on_mibi1497.blastn: 2797
sdrG_on_mibi1498.blastn: 2967
sdrG_on_mibi1499.blastn: 2976
sdrG_on_mibi1500.blastn: 2797
sdrG_on_mibi1501.blastn: 2797
sdrG_on_mibi1502.blastn: 2976
sdrG_on_mibi1503.blastn: 2976
sdrG_on_mibi1504.blastn: 2634
sdrG_on_mibi1505.blastn: 2970
sdrG_on_mibi1506.blastn: 2985
sdrG_on_mibi2312.blastn: 2866
sdrG_on_mibi2313.blastn: 2794
sdrG_on_mibi2314.blastn: 3171
sdrG_on_mibi2315.blastn: 2797
sdrG_on_mibi2316.blastn: 3158
sdrG_on_mibi2317.blastn: 2975
sdrG_on_mibi2318.blastn: 2976
sdrG_on_mibi2319.blastn: 2613
sdrG_on_mibi2320.blastn: 2972
sdrG_on_mibi2321.blastn: 2794
sdrG_on_mibi2379.blastn: 2975
##length(sdrH)=1446
for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
blastn -db ../shovill/${sample}/contigs.fa -query sdrH_revcomp.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > sdrH_on_${sample}.blastn
done
for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
python3 analyze_blastn_res.py sdrH_on_${sample}.blastn
done
sdrH_on_mibi1435.blastn: 1647
sdrH_on_mibi1436.blastn: 1683
sdrH_on_mibi1437.blastn: 1482
sdrH_on_mibi1438.blastn: 1608
sdrH_on_mibi1439.blastn: 1739
sdrH_on_mibi1440.blastn: 1644
sdrH_on_mibi1441.blastn: 1446
sdrH_on_mibi1442.blastn: 1482
sdrH_on_mibi1443.blastn: 1683
sdrH_on_mibi1444.blastn: 1683
sdrH_on_mibi1445.blastn: 1482
sdrH_on_mibi1446.blastn: 1482
sdrH_on_mibi1447.blastn: 1482
sdrH_on_mibi1448.blastn: 1446
sdrH_on_mibi1449.blastn: 1450
sdrH_on_mibi1450.blastn: 1446
sdrH_on_mibi1451.blastn: 1487
sdrH_on_mibi1452.blastn: 1446
sdrH_on_mibi1453.blastn: 1464
sdrH_on_mibi1454.blastn: 1647
sdrH_on_mibi1455.blastn: 1644
sdrH_on_mibi1456.blastn: 1647
sdrH_on_mibi1457.blastn: 1572
sdrH_on_mibi1458.blastn: 1632
sdrH_on_mibi1459.blastn: 1647
sdrH_on_mibi1460.blastn: 1482
sdrH_on_mibi1461.blastn: 1647
sdrH_on_mibi1462.blastn: 1683
sdrH_on_mibi1463.blastn: 1647
sdrH_on_mibi1464.blastn: 1739
sdrH_on_mibi1465.blastn: 1464
sdrH_on_mibi1466.blastn: 1305
sdrH_on_mibi1467.blastn: 1482
sdrH_on_mibi1468.blastn: 1559
sdrH_on_mibi1469.blastn: 1556
sdrH_on_mibi1471.blastn: 1572
sdrH_on_mibi1473.blastn: 1482
sdrH_on_mibi1474.blastn: 1446
sdrH_on_mibi1475.blastn: 1482
sdrH_on_mibi1476.blastn: 1458
sdrH_on_mibi1477.blastn: 1647
sdrH_on_mibi1478.blastn: 710 *
sdrH_on_mibi1479.blastn: 1482
sdrH_on_mibi1480.blastn: 1647
sdrH_on_mibi1481.blastn: 1412
sdrH_on_mibi1482.blastn: 1647
sdrH_on_mibi1483.blastn: 1647
sdrH_on_mibi1484.blastn: 1448
sdrH_on_mibi1485.blastn: 1647
sdrH_on_mibi1486.blastn: 1827
sdrH_on_mibi1487.blastn: 1647
sdrH_on_mibi1488.blastn: 1683
sdrH_on_mibi1489.blastn: 1739
sdrH_on_mibi1490.blastn: 1482
sdrH_on_mibi1491.blastn: 1482
sdrH_on_mibi1492.blastn: 1482
sdrH_on_mibi1493.blastn: 1440
sdrH_on_mibi1494.blastn: 1458
sdrH_on_mibi1495.blastn: 1482
sdrH_on_mibi1496.blastn: 1644
sdrH_on_mibi1497.blastn: 1736
sdrH_on_mibi1498.blastn: 1647
sdrH_on_mibi1499.blastn: 1482
sdrH_on_mibi1500.blastn: 1683
sdrH_on_mibi1501.blastn: 1647
sdrH_on_mibi1502.blastn: 1647
sdrH_on_mibi1503.blastn: 1745
sdrH_on_mibi1504.blastn: 1683
sdrH_on_mibi1505.blastn: 1736
sdrH_on_mibi1506.blastn: 1683
sdrH_on_mibi2312.blastn: 1556
sdrH_on_mibi2313.blastn: 1464
sdrH_on_mibi2314.blastn: 1464
sdrH_on_mibi2315.blastn: 1683
sdrH_on_mibi2316.blastn: 1482
sdrH_on_mibi2317.blastn: 1464
sdrH_on_mibi2318.blastn: 1647
sdrH_on_mibi2319.blastn: 1644
sdrH_on_mibi2320.blastn: 1464
sdrH_on_mibi2321.blastn: 1464
sdrH_on_mibi2379.blastn: 1647
# -length(ebh_revcomp.fasta)=30450
for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
blastn -db ../shovill/${sample}/contigs.fa -query ebh_revcomp.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > ebh_on_${sample}.blastn
done
for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
python3 analyze_blastn_res.py ebh_on_${sample}.blastn
done
ebh_on_mibi1435.blastn: 30450
ebh_on_mibi1436.blastn: 30450
ebh_on_mibi1437.blastn: 29490
ebh_on_mibi1438.blastn: 25428
ebh_on_mibi1439.blastn: 30452
ebh_on_mibi1440.blastn: 11933
ebh_on_mibi1441.blastn: 30450
ebh_on_mibi1442.blastn: 30463
ebh_on_mibi1443.blastn: 30450
ebh_on_mibi1444.blastn: 30450
ebh_on_mibi1445.blastn: 30450
ebh_on_mibi1446.blastn: 30450
ebh_on_mibi1447.blastn: 30450
ebh_on_mibi1448.blastn: 30450
ebh_on_mibi1449.blastn: 30450
ebh_on_mibi1450.blastn: 30450
ebh_on_mibi1451.blastn: 30450
ebh_on_mibi1452.blastn: 21401
ebh_on_mibi1453.blastn: 30450
ebh_on_mibi1454.blastn: 11933
ebh_on_mibi1455.blastn: 30450
ebh_on_mibi1456.blastn: 11933
ebh_on_mibi1457.blastn: 30450
ebh_on_mibi1458.blastn: 29955
ebh_on_mibi1459.blastn: 11933
ebh_on_mibi1460.blastn: 30450
ebh_on_mibi1461.blastn: 11933
ebh_on_mibi1462.blastn: 30450
ebh_on_mibi1463.blastn: 20602
ebh_on_mibi1464.blastn: 30450
ebh_on_mibi1465.blastn: 30450
ebh_on_mibi1466.blastn: 14964
ebh_on_mibi1467.blastn: 30463
ebh_on_mibi1468.blastn: 30450
ebh_on_mibi1469.blastn: 30450
ebh_on_mibi1471.blastn: 25428
ebh_on_mibi1473.blastn: 30450
ebh_on_mibi1474.blastn: 30450
ebh_on_mibi1475.blastn: 30450
ebh_on_mibi1476.blastn: 30450
ebh_on_mibi1477.blastn: 30384
ebh_on_mibi1478.blastn: 11933
ebh_on_mibi1479.blastn: 30450
ebh_on_mibi1480.blastn: 11933
ebh_on_mibi1481.blastn: 25694
ebh_on_mibi1482.blastn: 30450
ebh_on_mibi1483.blastn: 30450
ebh_on_mibi1484.blastn: 30450
ebh_on_mibi1485.blastn: 11933
ebh_on_mibi1486.blastn: 30450
ebh_on_mibi1487.blastn: 11933
ebh_on_mibi1488.blastn: 30450
ebh_on_mibi1489.blastn: 30450
ebh_on_mibi1490.blastn: 30450
ebh_on_mibi1491.blastn: 30450
ebh_on_mibi1492.blastn: 30450
ebh_on_mibi1493.blastn: 30465
ebh_on_mibi1494.blastn: 30450
ebh_on_mibi1495.blastn: 30450
ebh_on_mibi1496.blastn: 11933
ebh_on_mibi1497.blastn: 30450
ebh_on_mibi1498.blastn: 11933
ebh_on_mibi1499.blastn: 30450
ebh_on_mibi1500.blastn: 30450
ebh_on_mibi1501.blastn: 30450
ebh_on_mibi1502.blastn: 11933
ebh_on_mibi1503.blastn: 30450
ebh_on_mibi1504.blastn: 30450
ebh_on_mibi1505.blastn: 30450
ebh_on_mibi1506.blastn: 30450
ebh_on_mibi2312.blastn: 30450
ebh_on_mibi2313.blastn: 30450
ebh_on_mibi2314.blastn: 30450
ebh_on_mibi2315.blastn: 30461
ebh_on_mibi2316.blastn: 30450
ebh_on_mibi2317.blastn: 30450
ebh_on_mibi2318.blastn: 11933
ebh_on_mibi2319.blastn: 11933
ebh_on_mibi2320.blastn: 30110
ebh_on_mibi2321.blastn: 30450
ebh_on_mibi2379.blastn: 30450
#For gene: ebpS, tagB, capC, sepA, dltA, fmtC
# -length(SE0760)=1383
for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
blastn -db ../shovill/${sample}/contigs.fa -query ebpS_revcomp.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > ebpS_on_${sample}.blastn
done
for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
python3 analyze_blastn_res.py ebpS_on_${sample}.blastn
done
ebpS_on_mibi1435.blastn: 1383
ebpS_on_mibi1436.blastn: 1383
ebpS_on_mibi1437.blastn: 1383
ebpS_on_mibi1438.blastn: 1383
ebpS_on_mibi1439.blastn: 1383
ebpS_on_mibi1440.blastn: 1383
ebpS_on_mibi1441.blastn: 1383
ebpS_on_mibi1442.blastn: 1408
ebpS_on_mibi1443.blastn: 1383
ebpS_on_mibi1444.blastn: 1383
ebpS_on_mibi1445.blastn: 1383
ebpS_on_mibi1446.blastn: 1383
ebpS_on_mibi1447.blastn: 1383
ebpS_on_mibi1448.blastn: 1383
ebpS_on_mibi1449.blastn: 1383
ebpS_on_mibi1450.blastn: 1383
ebpS_on_mibi1451.blastn: 1383
ebpS_on_mibi1452.blastn: 1408
ebpS_on_mibi1453.blastn: 1383
ebpS_on_mibi1454.blastn: 1383
ebpS_on_mibi1455.blastn: 1383
ebpS_on_mibi1456.blastn: 1383
ebpS_on_mibi1457.blastn: 1383
ebpS_on_mibi1458.blastn: 1408
ebpS_on_mibi1459.blastn: 1383
ebpS_on_mibi1460.blastn: 1383
ebpS_on_mibi1461.blastn: 1383
ebpS_on_mibi1462.blastn: 1383
ebpS_on_mibi1463.blastn: 1383
ebpS_on_mibi1464.blastn: 1392
ebpS_on_mibi1465.blastn: 1383
ebpS_on_mibi1466.blastn: 1383
ebpS_on_mibi1467.blastn: 1420
ebpS_on_mibi1468.blastn: 1383
ebpS_on_mibi1469.blastn: 1383
ebpS_on_mibi1471.blastn: 1383
ebpS_on_mibi1473.blastn: 1383
ebpS_on_mibi1474.blastn: 1383
ebpS_on_mibi1475.blastn: 1383
ebpS_on_mibi1476.blastn: 1383
ebpS_on_mibi1477.blastn: 1275
ebpS_on_mibi1478.blastn: 1383
ebpS_on_mibi1479.blastn: 1383
ebpS_on_mibi1480.blastn: 1383
ebpS_on_mibi1481.blastn: 1383
ebpS_on_mibi1482.blastn: 1383
ebpS_on_mibi1483.blastn: 1383
ebpS_on_mibi1484.blastn: 1383
ebpS_on_mibi1485.blastn: 1383
ebpS_on_mibi1486.blastn: 1383
ebpS_on_mibi1487.blastn: 1383
ebpS_on_mibi1488.blastn: 1383
ebpS_on_mibi1489.blastn: 1383
ebpS_on_mibi1490.blastn: 1383
ebpS_on_mibi1491.blastn: 1383
ebpS_on_mibi1492.blastn: 1383
ebpS_on_mibi1493.blastn: 1420
ebpS_on_mibi1494.blastn: 1383
ebpS_on_mibi1495.blastn: 1383
ebpS_on_mibi1496.blastn: 1383
ebpS_on_mibi1497.blastn: 1383
ebpS_on_mibi1498.blastn: 1383
ebpS_on_mibi1499.blastn: 1383
ebpS_on_mibi1500.blastn: 1383
ebpS_on_mibi1501.blastn: 1383
ebpS_on_mibi1502.blastn: 1383
ebpS_on_mibi1503.blastn: 1383
ebpS_on_mibi1504.blastn: 1408
ebpS_on_mibi1505.blastn: 1383
ebpS_on_mibi1506.blastn: 1383
ebpS_on_mibi2312.blastn: 1383
ebpS_on_mibi2313.blastn: 1383
ebpS_on_mibi2314.blastn: 1383
ebpS_on_mibi2315.blastn: 1383
ebpS_on_mibi2316.blastn: 1383
ebpS_on_mibi2317.blastn: 1383
ebpS_on_mibi2318.blastn: 1383
ebpS_on_mibi2319.blastn: 1383
ebpS_on_mibi2320.blastn: 1383
ebpS_on_mibi2321.blastn: 1383
ebpS_on_mibi2379.blastn: 1383
# -length(tagB)=1680
#mibi1435.gff3:contig_2 Prodigal CDS 146190 147869 . - 0 ID=MMJCKL_03035;Name=CDP-glycerol glycerophosphotransferase%2C TagB/SpsB family;locus_tag=MMJCKL_03035;product=CDP-glycerol glycerophosphotransferase%2C TagB/SpsB family;Dbxref=COG:COG1887,COG:MI,RefSeq:WP_001831509.1,SO:0001217,UniParc:UPI00004BA7A8,UniRef:UniRef100_A0A4Q9W688,UniRef:UniRef50_A0A0H2VI21,UniRef:UniRef90_A0A0H2VI21;gene=tagB
samtools faidx mibi1435.fna contig_2:146190-147869 > tagB_mibi1435.fasta
revcomp tagB_mibi1435.fasta > tagB_mibi1435_revcomp.fasta
for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
blastn -db ../shovill/${sample}/contigs.fa -query tagB_mibi1435_revcomp.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > tagB_on_${sample}.blastn
done
for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
python3 analyze_blastn_res.py tagB_on_${sample}.blastn
done
tagB_on_mibi1435.blastn: 1680
tagB_on_mibi1436.blastn: 1680
tagB_on_mibi1437.blastn: 1680
tagB_on_mibi1438.blastn: 1680
tagB_on_mibi1439.blastn: 1680
tagB_on_mibi1440.blastn: 1680
tagB_on_mibi1441.blastn: 1680
tagB_on_mibi1442.blastn: 1680
tagB_on_mibi1443.blastn: 1680
tagB_on_mibi1444.blastn: 1680
tagB_on_mibi1445.blastn: 1680
tagB_on_mibi1446.blastn: 1680
tagB_on_mibi1447.blastn: 1680
tagB_on_mibi1448.blastn: 1680
tagB_on_mibi1449.blastn: 1680
tagB_on_mibi1450.blastn: 1680
tagB_on_mibi1451.blastn: 1680
tagB_on_mibi1452.blastn: 1680
tagB_on_mibi1453.blastn: 1680
tagB_on_mibi1454.blastn: 1680
tagB_on_mibi1455.blastn: 1680
tagB_on_mibi1456.blastn: 1680
tagB_on_mibi1457.blastn: 1680
tagB_on_mibi1458.blastn: 1680
tagB_on_mibi1459.blastn: 1680
tagB_on_mibi1460.blastn: 1680
tagB_on_mibi1461.blastn: 1680
tagB_on_mibi1462.blastn: 1680
tagB_on_mibi1463.blastn: 1680
tagB_on_mibi1464.blastn: 1680
tagB_on_mibi1465.blastn: 1680
tagB_on_mibi1466.blastn: 1680
tagB_on_mibi1467.blastn: 1680
tagB_on_mibi1468.blastn: 1680
tagB_on_mibi1469.blastn: 1680
tagB_on_mibi1471.blastn: 1680
tagB_on_mibi1473.blastn: 1680
tagB_on_mibi1474.blastn: 1680
tagB_on_mibi1475.blastn: 1680
tagB_on_mibi1476.blastn: 1680
tagB_on_mibi1477.blastn: 1680
tagB_on_mibi1478.blastn: 1680
tagB_on_mibi1479.blastn: 1680
tagB_on_mibi1480.blastn: 1680
tagB_on_mibi1481.blastn: 1680
tagB_on_mibi1482.blastn: 1680
tagB_on_mibi1483.blastn: 1680
tagB_on_mibi1484.blastn: 1680
tagB_on_mibi1485.blastn: 1680
tagB_on_mibi1486.blastn: 1680
tagB_on_mibi1487.blastn: 1680
tagB_on_mibi1488.blastn: 1680
tagB_on_mibi1489.blastn: 1680
tagB_on_mibi1490.blastn: 1680
tagB_on_mibi1491.blastn: 1680
tagB_on_mibi1492.blastn: 1680
tagB_on_mibi1493.blastn: 1680
tagB_on_mibi1494.blastn: 1680
tagB_on_mibi1495.blastn: 1680
tagB_on_mibi1496.blastn: 1680
tagB_on_mibi1497.blastn: 1680
tagB_on_mibi1498.blastn: 1680
tagB_on_mibi1499.blastn: 1680
tagB_on_mibi1500.blastn: 1680
tagB_on_mibi1501.blastn: 1680
tagB_on_mibi1502.blastn: 1680
tagB_on_mibi1503.blastn: 1680
tagB_on_mibi1504.blastn: 1680
tagB_on_mibi1505.blastn: 1680
tagB_on_mibi1506.blastn: 1680
tagB_on_mibi2312.blastn: 1680
tagB_on_mibi2313.blastn: 1680
tagB_on_mibi2314.blastn: 1680
tagB_on_mibi2315.blastn: 1680
tagB_on_mibi2316.blastn: 1680
tagB_on_mibi2317.blastn: 1680
tagB_on_mibi2318.blastn: 1680
tagB_on_mibi2319.blastn: 1680
tagB_on_mibi2320.blastn: 1680
tagB_on_mibi2321.blastn: 1680
tagB_on_mibi2379.blastn: 1680
# -length(capC)=450
for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
blastn -db ../shovill/${sample}/contigs.fa -query capC.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > capC_on_${sample}.blastn
done
for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
python3 analyze_blastn_res.py capC_on_${sample}.blastn
done
capC_on_mibi1435.blastn: 0
capC_on_mibi1436.blastn: 0
capC_on_mibi1437.blastn: 0
capC_on_mibi1438.blastn: 0
capC_on_mibi1439.blastn: 0
capC_on_mibi1440.blastn: 0
capC_on_mibi1441.blastn: 0
capC_on_mibi1442.blastn: 0
capC_on_mibi1443.blastn: 0
capC_on_mibi1444.blastn: 0
capC_on_mibi1445.blastn: 0
capC_on_mibi1446.blastn: 0
capC_on_mibi1447.blastn: 0
capC_on_mibi1448.blastn: 0
capC_on_mibi1449.blastn: 0
capC_on_mibi1450.blastn: 0
capC_on_mibi1451.blastn: 0
capC_on_mibi1452.blastn: 0
capC_on_mibi1453.blastn: 0
capC_on_mibi1454.blastn: 0
capC_on_mibi1455.blastn: 0
capC_on_mibi1456.blastn: 0
capC_on_mibi1457.blastn: 0
capC_on_mibi1458.blastn: 0
capC_on_mibi1459.blastn: 0
capC_on_mibi1460.blastn: 0
capC_on_mibi1461.blastn: 0
capC_on_mibi1462.blastn: 0
capC_on_mibi1463.blastn: 0
capC_on_mibi1464.blastn: 0
capC_on_mibi1465.blastn: 0
capC_on_mibi1466.blastn: 0
capC_on_mibi1467.blastn: 0
capC_on_mibi1468.blastn: 0
capC_on_mibi1469.blastn: 0
capC_on_mibi1471.blastn: 0
capC_on_mibi1473.blastn: 0
capC_on_mibi1474.blastn: 0
capC_on_mibi1475.blastn: 0
capC_on_mibi1476.blastn: 0
capC_on_mibi1477.blastn: 0
capC_on_mibi1478.blastn: 0
capC_on_mibi1479.blastn: 0
capC_on_mibi1480.blastn: 0
capC_on_mibi1481.blastn: 0
capC_on_mibi1482.blastn: 0
capC_on_mibi1483.blastn: 0
capC_on_mibi1484.blastn: 0
capC_on_mibi1485.blastn: 0
capC_on_mibi1486.blastn: 0
capC_on_mibi1487.blastn: 0
capC_on_mibi1488.blastn: 0
capC_on_mibi1489.blastn: 0
capC_on_mibi1490.blastn: 0
capC_on_mibi1491.blastn: 0
capC_on_mibi1492.blastn: 0
capC_on_mibi1493.blastn: 0
capC_on_mibi1494.blastn: 0
capC_on_mibi1495.blastn: 0
capC_on_mibi1496.blastn: 0
capC_on_mibi1497.blastn: 0
capC_on_mibi1498.blastn: 0
capC_on_mibi1499.blastn: 0
capC_on_mibi1500.blastn: 0
capC_on_mibi1501.blastn: 0
capC_on_mibi1502.blastn: 0
capC_on_mibi1503.blastn: 0
capC_on_mibi1504.blastn: 0
capC_on_mibi1505.blastn: 0
capC_on_mibi1506.blastn: 0
capC_on_mibi2312.blastn: 0
capC_on_mibi2313.blastn: 0
capC_on_mibi2314.blastn: 0
capC_on_mibi2315.blastn: 0
capC_on_mibi2316.blastn: 0
capC_on_mibi2317.blastn: 0
capC_on_mibi2318.blastn: 0
capC_on_mibi2319.blastn: 0
capC_on_mibi2320.blastn: 0
capC_on_mibi2321.blastn: 0
capC_on_mibi2379.blastn: 0
# -length(sepA_mibi1435.fasta)=1524
#contig_7 Prodigal CDS 52151 53674 . + 0 ID=MMJCKL_06215;Name=Extracellular elastase;locus_tag=MMJCKL_06215;product=Extracellular elastase;Dbxref=COG:COG3227,COG:O,EC:3.4.24.-,GO:0004222,GO:0005576,GO:0006508,GO:0046872,KEGG:K01401,RefSeq:WP_002486087.1,SO:0001217,UniParc:UPI00024E17FE,UniRef:UniRef100_UPI00066C9785,UniRef:UniRef50_P0C0Q3,UniRef:UniRef90_P0C0Q3;gene=sepA
samtools faidx mibi1435.fna contig_7:52151-53674 > sepA_mibi1435.fasta
for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
blastn -db ../shovill/${sample}/contigs.fa -query sepA_mibi1435.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > sepA_on_${sample}.blastn
done
for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
python3 analyze_blastn_res.py sepA_on_${sample}.blastn
done
sepA_on_mibi1435.blastn: 1524
sepA_on_mibi1436.blastn: 1524
sepA_on_mibi1437.blastn: 1523
sepA_on_mibi1438.blastn: 1524
sepA_on_mibi1439.blastn: 1523
sepA_on_mibi1440.blastn: 1523
sepA_on_mibi1441.blastn: 1523
sepA_on_mibi1442.blastn: 1523
sepA_on_mibi1443.blastn: 1523
sepA_on_mibi1444.blastn: 1523
sepA_on_mibi1445.blastn: 1523
sepA_on_mibi1446.blastn: 1523
sepA_on_mibi1447.blastn: 1523
sepA_on_mibi1448.blastn: 1524
sepA_on_mibi1449.blastn: 1523
sepA_on_mibi1450.blastn: 1523
sepA_on_mibi1451.blastn: 1523
sepA_on_mibi1452.blastn: 1523
sepA_on_mibi1453.blastn: 1523
sepA_on_mibi1454.blastn: 1523
sepA_on_mibi1455.blastn: 1524
sepA_on_mibi1456.blastn: 1523
sepA_on_mibi1457.blastn: 1523
sepA_on_mibi1458.blastn: 1523
sepA_on_mibi1459.blastn: 1523
sepA_on_mibi1460.blastn: 1523
sepA_on_mibi1461.blastn: 1523
sepA_on_mibi1462.blastn: 1523
sepA_on_mibi1463.blastn: 1523
sepA_on_mibi1464.blastn: 1523
sepA_on_mibi1465.blastn: 1523
sepA_on_mibi1466.blastn: 1523
sepA_on_mibi1467.blastn: 1524
sepA_on_mibi1468.blastn: 1523
sepA_on_mibi1469.blastn: 1523
sepA_on_mibi1471.blastn: 1524
sepA_on_mibi1473.blastn: 1523
sepA_on_mibi1474.blastn: 1524
sepA_on_mibi1475.blastn: 1523
sepA_on_mibi1476.blastn: 1523
sepA_on_mibi1477.blastn: 1524
sepA_on_mibi1478.blastn: 1523
sepA_on_mibi1479.blastn: 1523
sepA_on_mibi1480.blastn: 1523
sepA_on_mibi1481.blastn: 1524
sepA_on_mibi1482.blastn: 1524
sepA_on_mibi1483.blastn: 1523
sepA_on_mibi1484.blastn: 1523
sepA_on_mibi1485.blastn: 1523
sepA_on_mibi1486.blastn: 1523
sepA_on_mibi1487.blastn: 1523
sepA_on_mibi1488.blastn: 1523
sepA_on_mibi1489.blastn: 1523
sepA_on_mibi1490.blastn: 1523
sepA_on_mibi1491.blastn: 1523
sepA_on_mibi1492.blastn: 1523
sepA_on_mibi1493.blastn: 1523
sepA_on_mibi1494.blastn: 1523
sepA_on_mibi1495.blastn: 1523
sepA_on_mibi1496.blastn: 1523
sepA_on_mibi1497.blastn: 1523
sepA_on_mibi1498.blastn: 1523
sepA_on_mibi1499.blastn: 1523
sepA_on_mibi1500.blastn: 1523
sepA_on_mibi1501.blastn: 1523
sepA_on_mibi1502.blastn: 1523
sepA_on_mibi1503.blastn: 1523
sepA_on_mibi1504.blastn: 1523
sepA_on_mibi1505.blastn: 1523
sepA_on_mibi1506.blastn: 1523
sepA_on_mibi2312.blastn: 1523
sepA_on_mibi2313.blastn: 1523
sepA_on_mibi2314.blastn: 1523
sepA_on_mibi2315.blastn: 1523
sepA_on_mibi2316.blastn: 1523
sepA_on_mibi2317.blastn: 1523
sepA_on_mibi2318.blastn: 1523
sepA_on_mibi2319.blastn: 1523
sepA_on_mibi2320.blastn: 1523
sepA_on_mibi2321.blastn: 1523
sepA_on_mibi2379.blastn: 1523
# -length(dltA.fasta)=1458
for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
blastn -db ../shovill/${sample}/contigs.fa -query dltA.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > dltA_on_${sample}.blastn
done
for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
python3 analyze_blastn_res.py dltA_on_${sample}.blastn
done
dltA_on_mibi1435.blastn: 1458
dltA_on_mibi1436.blastn: 1458
dltA_on_mibi1437.blastn: 1458
dltA_on_mibi1438.blastn: 1458
dltA_on_mibi1439.blastn: 1458
dltA_on_mibi1440.blastn: 1458
dltA_on_mibi1441.blastn: 1458
dltA_on_mibi1442.blastn: 1458
dltA_on_mibi1443.blastn: 1458
dltA_on_mibi1444.blastn: 1458
dltA_on_mibi1445.blastn: 1458
dltA_on_mibi1446.blastn: 1458
dltA_on_mibi1447.blastn: 1458
dltA_on_mibi1448.blastn: 1464
dltA_on_mibi1449.blastn: 1458
dltA_on_mibi1450.blastn: 1458
dltA_on_mibi1451.blastn: 1458
dltA_on_mibi1452.blastn: 1458
dltA_on_mibi1453.blastn: 1458
dltA_on_mibi1454.blastn: 1458
dltA_on_mibi1455.blastn: 1458
dltA_on_mibi1456.blastn: 1458
dltA_on_mibi1457.blastn: 1458
dltA_on_mibi1458.blastn: 1458
dltA_on_mibi1459.blastn: 1458
dltA_on_mibi1460.blastn: 1458
dltA_on_mibi1461.blastn: 1458
dltA_on_mibi1462.blastn: 1458
dltA_on_mibi1463.blastn: 1458
dltA_on_mibi1464.blastn: 1458
dltA_on_mibi1465.blastn: 1458
dltA_on_mibi1466.blastn: 1458
dltA_on_mibi1467.blastn: 1458
dltA_on_mibi1468.blastn: 1458
dltA_on_mibi1469.blastn: 1458
dltA_on_mibi1471.blastn: 1458
dltA_on_mibi1473.blastn: 1458
dltA_on_mibi1474.blastn: 1458
dltA_on_mibi1475.blastn: 1458
dltA_on_mibi1476.blastn: 1458
dltA_on_mibi1477.blastn: 1458
dltA_on_mibi1478.blastn: 1458
dltA_on_mibi1479.blastn: 1458
dltA_on_mibi1480.blastn: 1458
dltA_on_mibi1481.blastn: 1458
dltA_on_mibi1482.blastn: 1458
dltA_on_mibi1483.blastn: 1458
dltA_on_mibi1484.blastn: 1458
dltA_on_mibi1485.blastn: 1458
dltA_on_mibi1486.blastn: 1458
dltA_on_mibi1487.blastn: 1458
dltA_on_mibi1488.blastn: 1458
dltA_on_mibi1489.blastn: 1458
dltA_on_mibi1490.blastn: 1458
dltA_on_mibi1491.blastn: 1458
dltA_on_mibi1492.blastn: 1458
dltA_on_mibi1493.blastn: 1458
dltA_on_mibi1494.blastn: 1458
dltA_on_mibi1495.blastn: 1458
dltA_on_mibi1496.blastn: 1458
dltA_on_mibi1497.blastn: 1458
dltA_on_mibi1498.blastn: 1458
dltA_on_mibi1499.blastn: 1458
dltA_on_mibi1500.blastn: 1458
dltA_on_mibi1501.blastn: 1458
dltA_on_mibi1502.blastn: 1458
dltA_on_mibi1503.blastn: 1458
dltA_on_mibi1504.blastn: 1458
dltA_on_mibi1505.blastn: 1458
dltA_on_mibi1506.blastn: 1458
dltA_on_mibi2312.blastn: 1458
dltA_on_mibi2313.blastn: 1458
dltA_on_mibi2314.blastn: 1458
dltA_on_mibi2315.blastn: 1458
dltA_on_mibi2316.blastn: 1458
dltA_on_mibi2317.blastn: 1458
dltA_on_mibi2318.blastn: 1458
dltA_on_mibi2319.blastn: 1458
dltA_on_mibi2320.blastn: 1458
dltA_on_mibi2321.blastn: 1458
dltA_on_mibi2379.blastn: 1458
# -length(fmtC.fasta)=2523
for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
blastn -db ../shovill/${sample}/contigs.fa -query fmtC.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > fmtC_on_${sample}.blastn
done
for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
python3 analyze_blastn_res.py fmtC_on_${sample}.blastn
done
fmtC_on_mibi1435.blastn: 0
fmtC_on_mibi1436.blastn: 0
fmtC_on_mibi1437.blastn: 0
fmtC_on_mibi1438.blastn: 0
fmtC_on_mibi1439.blastn: 0
fmtC_on_mibi1440.blastn: 0
fmtC_on_mibi1441.blastn: 0
fmtC_on_mibi1442.blastn: 0
fmtC_on_mibi1443.blastn: 0
fmtC_on_mibi1444.blastn: 0
fmtC_on_mibi1445.blastn: 0
fmtC_on_mibi1446.blastn: 0
fmtC_on_mibi1447.blastn: 0
fmtC_on_mibi1448.blastn: 0
fmtC_on_mibi1449.blastn: 0
fmtC_on_mibi1450.blastn: 0
fmtC_on_mibi1451.blastn: 0
fmtC_on_mibi1452.blastn: 0
fmtC_on_mibi1453.blastn: 0
fmtC_on_mibi1454.blastn: 0
fmtC_on_mibi1455.blastn: 0
fmtC_on_mibi1456.blastn: 0
fmtC_on_mibi1457.blastn: 0
fmtC_on_mibi1458.blastn: 0
fmtC_on_mibi1459.blastn: 0
fmtC_on_mibi1460.blastn: 0
fmtC_on_mibi1461.blastn: 0
fmtC_on_mibi1462.blastn: 0
fmtC_on_mibi1463.blastn: 0
fmtC_on_mibi1464.blastn: 0
fmtC_on_mibi1465.blastn: 0
fmtC_on_mibi1466.blastn: 0
fmtC_on_mibi1467.blastn: 0
fmtC_on_mibi1468.blastn: 0
fmtC_on_mibi1469.blastn: 0
fmtC_on_mibi1471.blastn: 0
fmtC_on_mibi1473.blastn: 0
fmtC_on_mibi1474.blastn: 0
fmtC_on_mibi1475.blastn: 0
fmtC_on_mibi1476.blastn: 0
fmtC_on_mibi1477.blastn: 0
fmtC_on_mibi1478.blastn: 0
fmtC_on_mibi1479.blastn: 0
fmtC_on_mibi1480.blastn: 0
fmtC_on_mibi1481.blastn: 0
fmtC_on_mibi1482.blastn: 0
fmtC_on_mibi1483.blastn: 0
fmtC_on_mibi1484.blastn: 0
fmtC_on_mibi1485.blastn: 0
fmtC_on_mibi1486.blastn: 0
fmtC_on_mibi1487.blastn: 0
fmtC_on_mibi1488.blastn: 0
fmtC_on_mibi1489.blastn: 0
fmtC_on_mibi1490.blastn: 0
fmtC_on_mibi1491.blastn: 0
fmtC_on_mibi1492.blastn: 0
fmtC_on_mibi1493.blastn: 0
fmtC_on_mibi1494.blastn: 0
fmtC_on_mibi1495.blastn: 0
fmtC_on_mibi1496.blastn: 0
fmtC_on_mibi1497.blastn: 0
fmtC_on_mibi1498.blastn: 0
fmtC_on_mibi1499.blastn: 0
fmtC_on_mibi1500.blastn: 0
fmtC_on_mibi1501.blastn: 0
fmtC_on_mibi1502.blastn: 0
fmtC_on_mibi1503.blastn: 0
fmtC_on_mibi1504.blastn: 0
fmtC_on_mibi1505.blastn: 0
fmtC_on_mibi1506.blastn: 0
fmtC_on_mibi2312.blastn: 0
fmtC_on_mibi2313.blastn: 0
fmtC_on_mibi2314.blastn: 0
fmtC_on_mibi2315.blastn: 0
fmtC_on_mibi2316.blastn: 0
fmtC_on_mibi2317.blastn: 0
fmtC_on_mibi2318.blastn: 0
fmtC_on_mibi2319.blastn: 0
fmtC_on_mibi2320.blastn: 0
fmtC_on_mibi2321.blastn: 0
fmtC_on_mibi2379.blastn: 0
#-- For genes: lipA (915), sceD (699), esp (660), ecpA (1188)
for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
blastn -db ../shovill/${sample}/contigs.fa -query lipA.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > ./lipA_on_${sample}.blastn
done
for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
python3 analyze_blastn_res.py lipA_on_${sample}.blastn
done
lipA_on_mibi1435.blastn: 915
lipA_on_mibi1436.blastn: 915
lipA_on_mibi1437.blastn: 915
lipA_on_mibi1438.blastn: 915
lipA_on_mibi1439.blastn: 915
lipA_on_mibi1440.blastn: 915
lipA_on_mibi1441.blastn: 915
lipA_on_mibi1442.blastn: 915
lipA_on_mibi1443.blastn: 915
lipA_on_mibi1444.blastn: 915
lipA_on_mibi1445.blastn: 915
lipA_on_mibi1446.blastn: 915
lipA_on_mibi1447.blastn: 915
lipA_on_mibi1448.blastn: 915
lipA_on_mibi1449.blastn: 915
lipA_on_mibi1450.blastn: 915
lipA_on_mibi1451.blastn: 915
lipA_on_mibi1452.blastn: 915
lipA_on_mibi1453.blastn: 915
lipA_on_mibi1454.blastn: 915
lipA_on_mibi1455.blastn: 915
lipA_on_mibi1456.blastn: 915
lipA_on_mibi1457.blastn: 915
lipA_on_mibi1458.blastn: 915
lipA_on_mibi1459.blastn: 915
lipA_on_mibi1460.blastn: 915
lipA_on_mibi1461.blastn: 915
lipA_on_mibi1462.blastn: 915
lipA_on_mibi1463.blastn: 915
lipA_on_mibi1464.blastn: 915
lipA_on_mibi1465.blastn: 915
lipA_on_mibi1466.blastn: 915
lipA_on_mibi1467.blastn: 915
lipA_on_mibi1468.blastn: 915
lipA_on_mibi1469.blastn: 915
lipA_on_mibi1471.blastn: 915
lipA_on_mibi1473.blastn: 915
lipA_on_mibi1474.blastn: 915
lipA_on_mibi1475.blastn: 915
lipA_on_mibi1476.blastn: 915
lipA_on_mibi1477.blastn: 915
lipA_on_mibi1478.blastn: 915
lipA_on_mibi1479.blastn: 915
lipA_on_mibi1480.blastn: 915
lipA_on_mibi1481.blastn: 915
lipA_on_mibi1482.blastn: 915
lipA_on_mibi1483.blastn: 915
lipA_on_mibi1484.blastn: 915
lipA_on_mibi1485.blastn: 915
lipA_on_mibi1486.blastn: 915
lipA_on_mibi1487.blastn: 915
lipA_on_mibi1488.blastn: 915
lipA_on_mibi1489.blastn: 915
lipA_on_mibi1490.blastn: 915
lipA_on_mibi1491.blastn: 915
lipA_on_mibi1492.blastn: 915
lipA_on_mibi1493.blastn: 915
lipA_on_mibi1494.blastn: 915
lipA_on_mibi1495.blastn: 915
lipA_on_mibi1496.blastn: 915
lipA_on_mibi1497.blastn: 915
lipA_on_mibi1498.blastn: 915
lipA_on_mibi1499.blastn: 915
lipA_on_mibi1500.blastn: 915
lipA_on_mibi1501.blastn: 915
lipA_on_mibi1502.blastn: 915
lipA_on_mibi1503.blastn: 915
lipA_on_mibi1504.blastn: 915
lipA_on_mibi1505.blastn: 915
lipA_on_mibi1506.blastn: 915
lipA_on_mibi2312.blastn: 915
lipA_on_mibi2313.blastn: 915
lipA_on_mibi2314.blastn: 915
lipA_on_mibi2315.blastn: 915
lipA_on_mibi2316.blastn: 915
lipA_on_mibi2317.blastn: 915
lipA_on_mibi2318.blastn: 915
lipA_on_mibi2319.blastn: 915
lipA_on_mibi2320.blastn: 915
lipA_on_mibi2321.blastn: 915
lipA_on_mibi2379.blastn: 915
#grep "gene=sceD" mibi1435.gff3
#contig_11 Prodigal CDS 25537 26196 . - 0 ID=MMJCKL_08095;Name=putative transglycosylase SceD;locus_tag=MMJCKL_08095;product=putative transglycosylase SceD;Dbxref=EC:3.2.-.-,GO:0005576,GO:0008152,GO:0016798,RefSeq:WP_001829904.1,SO:0001217,UniParc:UPI000003B952,UniRef:UniRef100_Q5HMC6,UniRef:UniRef50_Q5HEA4,UniRef:UniRef90_Q5HMC6;gene=sceD
samtools faidx mibi1435.fna contig_11:25537-26196 > sceD_mibi1435.fasta
revcomp sceD_mibi1435.fasta > sceD_mibi1435_revcomp.fasta
cp sceD_mibi1435_revcomp.fasta ../presence_absence_matrix_on_gene_list/
for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
blastn -db ../shovill/${sample}/contigs.fa -query sceD_mibi1435_revcomp.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > ./sceD_on_${sample}.blastn
done
for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
python3 analyze_blastn_res.py sceD_on_${sample}.blastn
done
sceD_on_mibi1435.blastn: 660
sceD_on_mibi1436.blastn: 660
sceD_on_mibi1437.blastn: 660
sceD_on_mibi1438.blastn: 660
sceD_on_mibi1439.blastn: 660
sceD_on_mibi1440.blastn: 660
sceD_on_mibi1441.blastn: 660
sceD_on_mibi1442.blastn: 660
sceD_on_mibi1443.blastn: 660
sceD_on_mibi1444.blastn: 660
sceD_on_mibi1445.blastn: 660
sceD_on_mibi1446.blastn: 660
sceD_on_mibi1447.blastn: 660
sceD_on_mibi1448.blastn: 660
sceD_on_mibi1449.blastn: 660
sceD_on_mibi1450.blastn: 660
sceD_on_mibi1451.blastn: 660
sceD_on_mibi1452.blastn: 660
sceD_on_mibi1453.blastn: 660
sceD_on_mibi1454.blastn: 660
sceD_on_mibi1455.blastn: 660
sceD_on_mibi1456.blastn: 660
sceD_on_mibi1457.blastn: 660
sceD_on_mibi1458.blastn: 660
sceD_on_mibi1459.blastn: 660
sceD_on_mibi1460.blastn: 660
sceD_on_mibi1461.blastn: 660
sceD_on_mibi1462.blastn: 660
sceD_on_mibi1463.blastn: 660
sceD_on_mibi1464.blastn: 660
sceD_on_mibi1465.blastn: 660
sceD_on_mibi1466.blastn: 660
sceD_on_mibi1467.blastn: 660
sceD_on_mibi1468.blastn: 660
sceD_on_mibi1469.blastn: 660
sceD_on_mibi1471.blastn: 660
sceD_on_mibi1473.blastn: 660
sceD_on_mibi1474.blastn: 660
sceD_on_mibi1475.blastn: 660
sceD_on_mibi1476.blastn: 660
sceD_on_mibi1477.blastn: 660
sceD_on_mibi1478.blastn: 660
sceD_on_mibi1479.blastn: 660
sceD_on_mibi1480.blastn: 660
sceD_on_mibi1481.blastn: 660
sceD_on_mibi1482.blastn: 660
sceD_on_mibi1483.blastn: 660
sceD_on_mibi1484.blastn: 660
sceD_on_mibi1485.blastn: 660
sceD_on_mibi1486.blastn: 660
sceD_on_mibi1487.blastn: 660
sceD_on_mibi1488.blastn: 660
sceD_on_mibi1489.blastn: 660
sceD_on_mibi1490.blastn: 660
sceD_on_mibi1491.blastn: 660
sceD_on_mibi1492.blastn: 660
sceD_on_mibi1493.blastn: 660
sceD_on_mibi1494.blastn: 660
sceD_on_mibi1495.blastn: 660
sceD_on_mibi1496.blastn: 660
sceD_on_mibi1497.blastn: 660
sceD_on_mibi1498.blastn: 660
sceD_on_mibi1499.blastn: 660
sceD_on_mibi1500.blastn: 660
sceD_on_mibi1501.blastn: 660
sceD_on_mibi1502.blastn: 660
sceD_on_mibi1503.blastn: 660
sceD_on_mibi1504.blastn: 660
sceD_on_mibi1505.blastn: 660
sceD_on_mibi1506.blastn: 660
sceD_on_mibi2312.blastn: 660
sceD_on_mibi2313.blastn: 660
sceD_on_mibi2314.blastn: 660
sceD_on_mibi2315.blastn: 660
sceD_on_mibi2316.blastn: 660
sceD_on_mibi2317.blastn: 660
sceD_on_mibi2318.blastn: 660
sceD_on_mibi2319.blastn: 660
sceD_on_mibi2320.blastn: 660
sceD_on_mibi2321.blastn: 660
sceD_on_mibi2379.blastn: 660
for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
blastn -db ../shovill/${sample}/contigs.fa -query esp.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > ./esp_on_${sample}.blastn
done
for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
python3 analyze_blastn_res.py esp_on_${sample}.blastn
done
esp_on_mibi1435.blastn: 0
esp_on_mibi1436.blastn: 0
esp_on_mibi1437.blastn: 0
esp_on_mibi1438.blastn: 0
esp_on_mibi1439.blastn: 0
esp_on_mibi1440.blastn: 0
esp_on_mibi1441.blastn: 0
esp_on_mibi1442.blastn: 0
esp_on_mibi1443.blastn: 0
esp_on_mibi1444.blastn: 0
esp_on_mibi1445.blastn: 0
esp_on_mibi1446.blastn: 0
esp_on_mibi1447.blastn: 0
esp_on_mibi1448.blastn: 0
esp_on_mibi1449.blastn: 0
esp_on_mibi1450.blastn: 0
esp_on_mibi1451.blastn: 0
esp_on_mibi1452.blastn: 0
esp_on_mibi1453.blastn: 0
esp_on_mibi1454.blastn: 0
esp_on_mibi1455.blastn: 0
esp_on_mibi1456.blastn: 0
esp_on_mibi1457.blastn: 0
esp_on_mibi1458.blastn: 0
esp_on_mibi1459.blastn: 0
esp_on_mibi1460.blastn: 0
esp_on_mibi1461.blastn: 0
esp_on_mibi1462.blastn: 0
esp_on_mibi1463.blastn: 0
esp_on_mibi1464.blastn: 0
esp_on_mibi1465.blastn: 0
esp_on_mibi1466.blastn: 0
esp_on_mibi1467.blastn: 0
esp_on_mibi1468.blastn: 0
esp_on_mibi1469.blastn: 0
esp_on_mibi1471.blastn: 0
esp_on_mibi1473.blastn: 0
esp_on_mibi1474.blastn: 0
esp_on_mibi1475.blastn: 0
esp_on_mibi1476.blastn: 0
esp_on_mibi1477.blastn: 0
esp_on_mibi1478.blastn: 0
esp_on_mibi1479.blastn: 0
esp_on_mibi1480.blastn: 0
esp_on_mibi1481.blastn: 0
esp_on_mibi1482.blastn: 0
esp_on_mibi1483.blastn: 0
esp_on_mibi1484.blastn: 0
esp_on_mibi1485.blastn: 0
esp_on_mibi1486.blastn: 0
esp_on_mibi1487.blastn: 0
esp_on_mibi1488.blastn: 0
esp_on_mibi1489.blastn: 0
esp_on_mibi1490.blastn: 0
esp_on_mibi1491.blastn: 0
esp_on_mibi1492.blastn: 0
esp_on_mibi1493.blastn: 0
esp_on_mibi1494.blastn: 0
esp_on_mibi1495.blastn: 0
esp_on_mibi1496.blastn: 0
esp_on_mibi1497.blastn: 0
esp_on_mibi1498.blastn: 0
esp_on_mibi1499.blastn: 0
esp_on_mibi1500.blastn: 0
esp_on_mibi1501.blastn: 0
esp_on_mibi1502.blastn: 0
esp_on_mibi1503.blastn: 0
esp_on_mibi1504.blastn: 0
esp_on_mibi1505.blastn: 0
esp_on_mibi1506.blastn: 0
esp_on_mibi2312.blastn: 0
esp_on_mibi2313.blastn: 0
esp_on_mibi2314.blastn: 0
esp_on_mibi2315.blastn: 0
esp_on_mibi2316.blastn: 0
esp_on_mibi2317.blastn: 0
esp_on_mibi2318.blastn: 0
esp_on_mibi2319.blastn: 0
esp_on_mibi2320.blastn: 0
esp_on_mibi2321.blastn: 0
esp_on_mibi2379.blastn: 0
#grep "gene=ecpA" mibi1435.gff3
#contig_9 Prodigal CDS 6382 7569 . - 0 ID=MMJCKL_07070;Name=Extracellular cysteine protease;locus_tag=MMJCKL_07070;product=Extracellular cysteine protease;Dbxref=EC:3.4.22.-,GO:0005576,GO:0006508,GO:0008234,KEGG:K08258,RefSeq:WP_002497714.1,SO:0001217,UniParc:UPI00026C1A6F,UniRef:UniRef100_UPI00026C1A6F,UniRef:UniRef50_P81297,UniRef:UniRef90_Q5HKF6;gene=ecpA
samtools faidx mibi1435.fna contig_9:6382-7569 > ecpA_mibi1435.fasta
revcomp ecpA_mibi1435.fasta > ecpA_mibi1435_revcomp.fasta
cp ecpA_mibi1435_revcomp.fasta ../presence_absence_matrix_on_gene_list/
for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
blastn -db ../shovill/${sample}/contigs.fa -query ecpA_mibi1435_revcomp.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > ./ecpA_on_${sample}.blastn
done
for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
python3 analyze_blastn_res.py ecpA_on_${sample}.blastn
done
ecpA_on_mibi1435.blastn: 1188
ecpA_on_mibi1436.blastn: 1188
ecpA_on_mibi1437.blastn: 1188
ecpA_on_mibi1438.blastn: 1188
ecpA_on_mibi1439.blastn: 1188
ecpA_on_mibi1440.blastn: 1188
ecpA_on_mibi1441.blastn: 1188
ecpA_on_mibi1442.blastn: 1188
ecpA_on_mibi1443.blastn: 1188
ecpA_on_mibi1444.blastn: 1188
ecpA_on_mibi1445.blastn: 1188
ecpA_on_mibi1446.blastn: 1188
ecpA_on_mibi1447.blastn: 1188
ecpA_on_mibi1448.blastn: 1188
ecpA_on_mibi1449.blastn: 1188
ecpA_on_mibi1450.blastn: 1188
ecpA_on_mibi1451.blastn: 1188
ecpA_on_mibi1452.blastn: 1188
ecpA_on_mibi1453.blastn: 1188
ecpA_on_mibi1454.blastn: 1188
ecpA_on_mibi1455.blastn: 1188
ecpA_on_mibi1456.blastn: 1188
ecpA_on_mibi1457.blastn: 1188
ecpA_on_mibi1458.blastn: 1188
ecpA_on_mibi1459.blastn: 1188
ecpA_on_mibi1460.blastn: 1188
ecpA_on_mibi1461.blastn: 1188
ecpA_on_mibi1462.blastn: 1188
ecpA_on_mibi1463.blastn: 1188
ecpA_on_mibi1464.blastn: 1188
ecpA_on_mibi1465.blastn: 1188
ecpA_on_mibi1466.blastn: 1188
ecpA_on_mibi1467.blastn: 1188
ecpA_on_mibi1468.blastn: 1188
ecpA_on_mibi1469.blastn: 1188
ecpA_on_mibi1471.blastn: 1188
ecpA_on_mibi1473.blastn: 1188
ecpA_on_mibi1474.blastn: 1188
ecpA_on_mibi1475.blastn: 1188
ecpA_on_mibi1476.blastn: 1188
ecpA_on_mibi1477.blastn: 1188
ecpA_on_mibi1478.blastn: 1188
ecpA_on_mibi1479.blastn: 1188
ecpA_on_mibi1480.blastn: 1188
ecpA_on_mibi1481.blastn: 1188
ecpA_on_mibi1482.blastn: 1188
ecpA_on_mibi1483.blastn: 1188
ecpA_on_mibi1484.blastn: 1188
ecpA_on_mibi1485.blastn: 1188
ecpA_on_mibi1486.blastn: 1188
ecpA_on_mibi1487.blastn: 1188
ecpA_on_mibi1488.blastn: 1188
ecpA_on_mibi1489.blastn: 1188
ecpA_on_mibi1490.blastn: 1188
ecpA_on_mibi1491.blastn: 1188
ecpA_on_mibi1492.blastn: 1188
ecpA_on_mibi1493.blastn: 1188
ecpA_on_mibi1494.blastn: 1188
ecpA_on_mibi1495.blastn: 1188
ecpA_on_mibi1496.blastn: 1188
ecpA_on_mibi1497.blastn: 1188
ecpA_on_mibi1498.blastn: 1188
ecpA_on_mibi1499.blastn: 1188
ecpA_on_mibi1500.blastn: 1188
ecpA_on_mibi1501.blastn: 1188
ecpA_on_mibi1502.blastn: 1188
ecpA_on_mibi1503.blastn: 1188
ecpA_on_mibi1504.blastn: 1188
ecpA_on_mibi1505.blastn: 1188
ecpA_on_mibi1506.blastn: 1188
ecpA_on_mibi2312.blastn: 1188
ecpA_on_mibi2313.blastn: 1188
ecpA_on_mibi2314.blastn: 1188
ecpA_on_mibi2315.blastn: 1188
ecpA_on_mibi2316.blastn: 1188
ecpA_on_mibi2317.blastn: 1188
ecpA_on_mibi2318.blastn: 1188
ecpA_on_mibi2319.blastn: 1188
ecpA_on_mibi2320.blastn: 1188
ecpA_on_mibi2321.blastn: 1188
ecpA_on_mibi2379.blastn: 1188
# -length(SE0760)=798
for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
blastn -db ../shovill/${sample}/contigs.fa -query SE0760.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > SE0760_on_${sample}.blastn
done
for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
python3 analyze_blastn_res.py SE0760_on_${sample}.blastn
done
SE0760_on_mibi1435.blastn: 798
SE0760_on_mibi1436.blastn: 798
SE0760_on_mibi1437.blastn: 798
SE0760_on_mibi1438.blastn: 798
SE0760_on_mibi1439.blastn: 798
SE0760_on_mibi1440.blastn: 798
SE0760_on_mibi1441.blastn: 798
SE0760_on_mibi1442.blastn: 798
SE0760_on_mibi1443.blastn: 798
SE0760_on_mibi1444.blastn: 798
SE0760_on_mibi1445.blastn: 798
SE0760_on_mibi1446.blastn: 798
SE0760_on_mibi1447.blastn: 798
SE0760_on_mibi1448.blastn: 798
SE0760_on_mibi1449.blastn: 798
SE0760_on_mibi1450.blastn: 798
SE0760_on_mibi1451.blastn: 798
SE0760_on_mibi1452.blastn: 798
SE0760_on_mibi1453.blastn: 798
SE0760_on_mibi1454.blastn: 798
SE0760_on_mibi1455.blastn: 798
SE0760_on_mibi1456.blastn: 798
SE0760_on_mibi1457.blastn: 798
SE0760_on_mibi1458.blastn: 798
SE0760_on_mibi1459.blastn: 798
SE0760_on_mibi1460.blastn: 798
SE0760_on_mibi1461.blastn: 798
SE0760_on_mibi1462.blastn: 798
SE0760_on_mibi1463.blastn: 798
SE0760_on_mibi1464.blastn: 798
SE0760_on_mibi1465.blastn: 798
SE0760_on_mibi1466.blastn: 798
SE0760_on_mibi1467.blastn: 799
SE0760_on_mibi1468.blastn: 798
SE0760_on_mibi1469.blastn: 798
SE0760_on_mibi1471.blastn: 798
SE0760_on_mibi1473.blastn: 798
SE0760_on_mibi1474.blastn: 798
SE0760_on_mibi1475.blastn: 798
SE0760_on_mibi1476.blastn: 798
SE0760_on_mibi1477.blastn: 798
SE0760_on_mibi1478.blastn: 798
SE0760_on_mibi1479.blastn: 798
SE0760_on_mibi1480.blastn: 798
SE0760_on_mibi1481.blastn: 798
SE0760_on_mibi1482.blastn: 798
SE0760_on_mibi1483.blastn: 798
SE0760_on_mibi1484.blastn: 798
SE0760_on_mibi1485.blastn: 798
SE0760_on_mibi1486.blastn: 798
SE0760_on_mibi1487.blastn: 798
SE0760_on_mibi1488.blastn: 798
SE0760_on_mibi1489.blastn: 798
SE0760_on_mibi1490.blastn: 798
SE0760_on_mibi1491.blastn: 798
SE0760_on_mibi1492.blastn: 798
SE0760_on_mibi1493.blastn: 798
SE0760_on_mibi1494.blastn: 798
SE0760_on_mibi1495.blastn: 798
SE0760_on_mibi1496.blastn: 798
SE0760_on_mibi1497.blastn: 798
SE0760_on_mibi1498.blastn: 798
SE0760_on_mibi1499.blastn: 798
SE0760_on_mibi1500.blastn: 798
SE0760_on_mibi1501.blastn: 798
SE0760_on_mibi1502.blastn: 798
SE0760_on_mibi1503.blastn: 798
SE0760_on_mibi1504.blastn: 798
SE0760_on_mibi1505.blastn: 798
SE0760_on_mibi1506.blastn: 798
SE0760_on_mibi2312.blastn: 798
SE0760_on_mibi2313.blastn: 798
SE0760_on_mibi2314.blastn: 798
SE0760_on_mibi2315.blastn: 798
SE0760_on_mibi2316.blastn: 798
SE0760_on_mibi2317.blastn: 798
SE0760_on_mibi2318.blastn: 798
SE0760_on_mibi2319.blastn: 798
SE0760_on_mibi2320.blastn: 798
SE0760_on_mibi2321.blastn: 798
SE0760_on_mibi2379.blastn: 798
# -lenth(MT880870)=34053
for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
blastn -db ../shovill/${sample}/contigs.fa -query MT880870.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > ./MT880870_on_${sample}.blastn
done
for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
python3 analyze_blastn_res.py MT880870_on_${sample}.blastn
done
MT880870_on_mibi1435.blastn: 2366
MT880870_on_mibi1436.blastn: 3198
MT880870_on_mibi1437.blastn: 3198
MT880870_on_mibi1438.blastn: 2366
MT880870_on_mibi1439.blastn: 3198
MT880870_on_mibi1440.blastn: 34177
MT880870_on_mibi1441.blastn: 2372
MT880870_on_mibi1442.blastn: 3470
MT880870_on_mibi1443.blastn: 2366
MT880870_on_mibi1444.blastn: 2372
MT880870_on_mibi1445.blastn: 3198
MT880870_on_mibi1446.blastn: 3198
MT880870_on_mibi1447.blastn: 3198
MT880870_on_mibi1448.blastn: 3198
MT880870_on_mibi1449.blastn: 2366
MT880870_on_mibi1450.blastn: 3198
MT880870_on_mibi1451.blastn: 1085
MT880870_on_mibi1452.blastn: 1832
MT880870_on_mibi1453.blastn: 2366
MT880870_on_mibi1454.blastn: 34177
MT880870_on_mibi1455.blastn: 3198
MT880870_on_mibi1456.blastn: 34177
MT880870_on_mibi1457.blastn: 3198
MT880870_on_mibi1458.blastn: 835
MT880870_on_mibi1459.blastn: 34177
MT880870_on_mibi1460.blastn: 3198
MT880870_on_mibi1461.blastn: 34177
MT880870_on_mibi1462.blastn: 2372
MT880870_on_mibi1463.blastn: 2372
MT880870_on_mibi1464.blastn: 2311
MT880870_on_mibi1465.blastn: 3198
MT880870_on_mibi1466.blastn: 1264
MT880870_on_mibi1467.blastn: 3470
MT880870_on_mibi1468.blastn: 2372
MT880870_on_mibi1469.blastn: 2372
MT880870_on_mibi1471.blastn: 2366
MT880870_on_mibi1473.blastn: 3198
MT880870_on_mibi1474.blastn: 3198
MT880870_on_mibi1475.blastn: 3198
MT880870_on_mibi1476.blastn: 3198
MT880870_on_mibi1477.blastn: 2372
MT880870_on_mibi1478.blastn: 5918
MT880870_on_mibi1479.blastn: 3198
MT880870_on_mibi1480.blastn: 34177
MT880870_on_mibi1481.blastn: 3198
MT880870_on_mibi1482.blastn: 3198
MT880870_on_mibi1483.blastn: 3198
MT880870_on_mibi1484.blastn: 3198
MT880870_on_mibi1485.blastn: 20038
MT880870_on_mibi1486.blastn: 3198
MT880870_on_mibi1487.blastn: 28520
MT880870_on_mibi1488.blastn: 2366
MT880870_on_mibi1489.blastn: 2366
MT880870_on_mibi1490.blastn: 3198
MT880870_on_mibi1491.blastn: 3198
MT880870_on_mibi1492.blastn: 3198
MT880870_on_mibi1493.blastn: 2233
MT880870_on_mibi1494.blastn: 3198
MT880870_on_mibi1495.blastn: 3198
MT880870_on_mibi1496.blastn: 25135
MT880870_on_mibi1497.blastn: 3198
MT880870_on_mibi1498.blastn: 28012
MT880870_on_mibi1499.blastn: 3198
MT880870_on_mibi1500.blastn: 2366
MT880870_on_mibi1501.blastn: 2366
MT880870_on_mibi1502.blastn: 34177
MT880870_on_mibi1503.blastn: 2366
MT880870_on_mibi1504.blastn: 3198
MT880870_on_mibi1505.blastn: 3198
MT880870_on_mibi1506.blastn: 2372
MT880870_on_mibi2312.blastn: 3198
MT880870_on_mibi2313.blastn: 3198
MT880870_on_mibi2314.blastn: 3198
MT880870_on_mibi2315.blastn: 2366
MT880870_on_mibi2316.blastn: 3198
MT880870_on_mibi2317.blastn: 3198
MT880870_on_mibi2318.blastn: 20006
MT880870_on_mibi2319.blastn: 17544
MT880870_on_mibi2320.blastn: 3198
MT880870_on_mibi2321.blastn: 3198
MT880870_on_mibi2379.blastn: 3198
#len=36164
for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
blastn -db ../shovill/${sample}/contigs.fa -query MT880871.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > ./MT880871_on_${sample}.blastn
done
for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
python3 analyze_blastn_res.py MT880871_on_${sample}.blastn
done
MT880871_on_mibi1435.blastn: 270
MT880871_on_mibi1436.blastn: 35580
MT880871_on_mibi1437.blastn: 518
MT880871_on_mibi1438.blastn: 518
MT880871_on_mibi1439.blastn: 518
MT880871_on_mibi1440.blastn: 36682
MT880871_on_mibi1441.blastn: 519
MT880871_on_mibi1442.blastn: 514
MT880871_on_mibi1443.blastn: 0
MT880871_on_mibi1444.blastn: 0
MT880871_on_mibi1445.blastn: 518
MT880871_on_mibi1446.blastn: 518
MT880871_on_mibi1447.blastn: 518
MT880871_on_mibi1448.blastn: 518
MT880871_on_mibi1449.blastn: 518
MT880871_on_mibi1450.blastn: 518
MT880871_on_mibi1451.blastn: 0
MT880871_on_mibi1452.blastn: 30418
MT880871_on_mibi1453.blastn: 518
MT880871_on_mibi1454.blastn: 982
MT880871_on_mibi1455.blastn: 518
MT880871_on_mibi1456.blastn: 982
MT880871_on_mibi1457.blastn: 518
MT880871_on_mibi1458.blastn: 0
MT880871_on_mibi1459.blastn: 34965
MT880871_on_mibi1460.blastn: 518
MT880871_on_mibi1461.blastn: 16296
MT880871_on_mibi1462.blastn: 0
MT880871_on_mibi1463.blastn: 518
MT880871_on_mibi1464.blastn: 947
MT880871_on_mibi1465.blastn: 518
MT880871_on_mibi1466.blastn: 0
MT880871_on_mibi1467.blastn: 514
MT880871_on_mibi1468.blastn: 518
MT880871_on_mibi1469.blastn: 518
MT880871_on_mibi1471.blastn: 518
MT880871_on_mibi1473.blastn: 518
MT880871_on_mibi1474.blastn: 518
MT880871_on_mibi1475.blastn: 518
MT880871_on_mibi1476.blastn: 518
MT880871_on_mibi1477.blastn: 518
MT880871_on_mibi1478.blastn: 18607
MT880871_on_mibi1479.blastn: 518
MT880871_on_mibi1480.blastn: 36682
MT880871_on_mibi1481.blastn: 0
MT880871_on_mibi1482.blastn: 518
MT880871_on_mibi1483.blastn: 32395
MT880871_on_mibi1484.blastn: 0
MT880871_on_mibi1485.blastn: 36164
MT880871_on_mibi1486.blastn: 31072
MT880871_on_mibi1487.blastn: 36682
MT880871_on_mibi1488.blastn: 0
MT880871_on_mibi1489.blastn: 0
MT880871_on_mibi1490.blastn: 518
MT880871_on_mibi1491.blastn: 518
MT880871_on_mibi1492.blastn: 518
MT880871_on_mibi1493.blastn: 740
MT880871_on_mibi1494.blastn: 518
MT880871_on_mibi1495.blastn: 0
MT880871_on_mibi1496.blastn: 24187
MT880871_on_mibi1497.blastn: 31069
MT880871_on_mibi1498.blastn: 36682
MT880871_on_mibi1499.blastn: 518
MT880871_on_mibi1500.blastn: 0
MT880871_on_mibi1501.blastn: 0
MT880871_on_mibi1502.blastn: 36682
MT880871_on_mibi1503.blastn: 518
MT880871_on_mibi1504.blastn: 518
MT880871_on_mibi1505.blastn: 518
MT880871_on_mibi1506.blastn: 0
MT880871_on_mibi2312.blastn: 316
MT880871_on_mibi2313.blastn: 518
MT880871_on_mibi2314.blastn: 518
MT880871_on_mibi2315.blastn: 0
MT880871_on_mibi2316.blastn: 518
MT880871_on_mibi2317.blastn: 518
MT880871_on_mibi2318.blastn: 36682
MT880871_on_mibi2319.blastn: 36164
MT880871_on_mibi2320.blastn: 518
MT880871_on_mibi2321.blastn: 518
MT880871_on_mibi2379.blastn: 518
#len=147057
for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
blastn -db ../shovill/${sample}/contigs.fa -query MT880872.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > MT880872_on_${sample}.blastn
done
for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
python3 analyze_blastn_res.py MT880872_on_${sample}.blastn
done
MT880872_on_mibi1435.blastn: 19155
MT880872_on_mibi1436.blastn: 19049
MT880872_on_mibi1437.blastn: 19049
MT880872_on_mibi1438.blastn: 19045
MT880872_on_mibi1439.blastn: 19042
MT880872_on_mibi1440.blastn: 77536 *
MT880872_on_mibi1441.blastn: 19041
MT880872_on_mibi1442.blastn: 19044
MT880872_on_mibi1443.blastn: 19049
MT880872_on_mibi1444.blastn: 19049
MT880872_on_mibi1445.blastn: 19042
MT880872_on_mibi1446.blastn: 19042
MT880872_on_mibi1447.blastn: 19042
MT880872_on_mibi1448.blastn: 19049
MT880872_on_mibi1449.blastn: 19041
MT880872_on_mibi1450.blastn: 19049
MT880872_on_mibi1451.blastn: 19043
MT880872_on_mibi1452.blastn: 19047
MT880872_on_mibi1453.blastn: 19165
MT880872_on_mibi1454.blastn: 52122 *
MT880872_on_mibi1455.blastn: 20996
MT880872_on_mibi1456.blastn: 52122 *
MT880872_on_mibi1457.blastn: 19042
MT880872_on_mibi1458.blastn: 19048
MT880872_on_mibi1459.blastn: 77366 *
MT880872_on_mibi1460.blastn: 19042
MT880872_on_mibi1461.blastn: 84536 *
MT880872_on_mibi1462.blastn: 19048
MT880872_on_mibi1463.blastn: 19042
MT880872_on_mibi1464.blastn: 19049
MT880872_on_mibi1465.blastn: 19045
MT880872_on_mibi1466.blastn: 6525
MT880872_on_mibi1467.blastn: 19044
MT880872_on_mibi1468.blastn: 19037
MT880872_on_mibi1469.blastn: 19039
MT880872_on_mibi1471.blastn: 19045
MT880872_on_mibi1473.blastn: 19043
MT880872_on_mibi1474.blastn: 19052
MT880872_on_mibi1475.blastn: 19264
MT880872_on_mibi1476.blastn: 19052
MT880872_on_mibi1477.blastn: 19041
MT880872_on_mibi1478.blastn: 26492 *
MT880872_on_mibi1479.blastn: 19042
MT880872_on_mibi1480.blastn: 45789 *
MT880872_on_mibi1481.blastn: 19036
MT880872_on_mibi1482.blastn: 19036
MT880872_on_mibi1483.blastn: 19036
MT880872_on_mibi1484.blastn: 19045
MT880872_on_mibi1485.blastn: 52124 *
MT880872_on_mibi1486.blastn: 19052
MT880872_on_mibi1487.blastn: 56847 *
MT880872_on_mibi1488.blastn: 19049
MT880872_on_mibi1489.blastn: 19053
MT880872_on_mibi1490.blastn: 19045
MT880872_on_mibi1491.blastn: 19042
MT880872_on_mibi1492.blastn: 19049
MT880872_on_mibi1493.blastn: 19046
MT880872_on_mibi1494.blastn: 19049
MT880872_on_mibi1495.blastn: 19046
MT880872_on_mibi1496.blastn: 92504 *
MT880872_on_mibi1497.blastn: 19052
MT880872_on_mibi1498.blastn: 58985 *
MT880872_on_mibi1499.blastn: 19043
MT880872_on_mibi1500.blastn: 19052
MT880872_on_mibi1501.blastn: 19049
MT880872_on_mibi1502.blastn: 46101 *
MT880872_on_mibi1503.blastn: 19044
MT880872_on_mibi1504.blastn: 19041
MT880872_on_mibi1505.blastn: 19052
MT880872_on_mibi1506.blastn: 19049
MT880872_on_mibi2312.blastn: 19045
MT880872_on_mibi2313.blastn: 19049
MT880872_on_mibi2314.blastn: 19052
MT880872_on_mibi2315.blastn: 19049
MT880872_on_mibi2316.blastn: 19052
MT880872_on_mibi2317.blastn: 19042
MT880872_on_mibi2318.blastn: 78246 *
MT880872_on_mibi2319.blastn: 77512 *
MT880872_on_mibi2320.blastn: 19045
MT880872_on_mibi2321.blastn: 19052
MT880872_on_mibi2379.blastn: 19156
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yycG has only 80% similarity, but it still belongs to the gene family.
Based on the provided BLASTN result summary, determining whether it's the same gene depends on multiple factors, including sequence similarity, alignment length, and expected value (E-value).
Let’s break down the results:
Query ID: gi|49240382|emb|BX571856.1|:25617-27443
Subject ID: contig00005
Percentage Identity: 80.338%
Alignment Length: 1836 (out of 1827 in the subject sequence)
Mismatches: 349
Gap Openings: 7
E-value: 0.0 (this indicates a highly significant alignment)
Bit Score: 1380
Key Points to Consider:
Percentage Identity (80.34%): While 80% identity is relatively high, it’s not close enough to the 90-100% typically expected for identical or highly similar genes. However, the threshold for considering sequences as "the same gene" depends on the organism, type of gene, and biological context. For some genes or species, this might still be acceptable.
Alignment Length (1836 bp): The alignment covers a large portion of both sequences (1827 in the subject sequence and 1836 in the query). This is a good indication that the sequences are largely aligned.
Mismatches and Gaps: There are 349 mismatches and 7 gap openings, which suggests there are differences between the two sequences. The number of differences is significant, and the biological impact of these differences would depend on whether they occur in coding regions or regulatory elements.
E-value (0.0): The E-value of 0.0 indicates that the alignment is highly significant and not due to chance.
Conclusion:
Based on the 80.34% identity and the number of mismatches, it is unlikely that this is exactly the same gene, but it could still be a closely related gene variant, allele, or paralog. If you are looking for an exact match, this result would not qualify. However, if you are investigating gene families or variants, this sequence could be considered closely related. Further functional or experimental validation might be necessary to determine the biological significance of these differences.
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plotTreeHeatmap
FastTree -gtr -nt variants/snippy.core_without_reference.aln > plotTreeHeatmap/snippy.core.tree
library(ggtree)
library(ggplot2)
library(dplyr)
setwd("/home/jhuang/DATA/Data_Luise_Sepi_STKN/plotTreeHeatmap/")
# -- edit tree --
info <- read.csv("typing.csv", sep="\t")
info$name <- info$Isolate
tree <- read.tree("990_backup.tree")
#cols <- c(infection='purple2', commensalism='skyblue2')
#heatmapData2 <- info %>% select(Isolate, ST, SCCmec, agr.typing)
heatmapData2 <- info %>% select(Isolate, ST)
rn <- heatmapData2$Isolate
heatmapData2$Isolate <- NULL
heatmapData2 <- as.data.frame(sapply(heatmapData2, as.character))
rownames(heatmapData2) <- rn
#https://bookdown.org/hneth/ds4psy/D-3-apx-colors-basics.html
#"blueviolet","darkgoldenrod", "tomato","mediumpurple4","indianred",
#"lightcyan3","azure3",
#"magenta",
#"tan","brown",
heatmap.colours <- c("cornflowerblue","darkgreen","seagreen3","tan","red", "navyblue", "gold", "green","orange","pink","purple","magenta","brown", "darksalmon","chocolate4","darkkhaki", "azure3", "maroon","lightgreen", "blue","cyan", "skyblue2", "blueviolet","darkgrey")
#"cornflowerblue","darkgreen","seagreen3","tan","red","green","orange","pink","brown","darkgrey", #"cornflowerblue","darkgreen","red", "darkgrey")
names(heatmap.colours) <- c("2","5","7","9","14", "17","23", "35","59","73", "81","86","87","89","130","190","290", "297","325", "454","487","558","766","-")
#"SCCmec_type_II(2A)","SCCmec_type_III(3A)","SCCmec_type_III(3A) and #SCCmec_type_VIII(4A)","SCCmec_type_IV(2B)","SCCmec_type_IV(2B&5)","SCCmec_type_IV(2B) and #SCCmec_type_VI(4B)","SCCmec_type_IVa(2B)","SCCmec_type_IVb(2B)","SCCmec_type_IVg(2B)","none", "I","II","III", "none")
#circular
#scale_color_manual(values=cols) +
#geom_tippoint(aes(color=Type)) +
p <- ggtree(tree, layout='circular', branch.length='none') %<+% info +
geom_tiplab2(aes(label=name), offset=1, size=6.0)
#, geom='text', align=TRUE, linetype=NA, hjust=1.8,check.overlap=TRUE
#difference between geom_tiplab and geom_tiplab2?
#+ theme(axis.text.x = element_text(angle = 30, vjust = 0.5)) + theme(axis.text = element_text(size = 20)) + scale_size(range = c(1, 20))
#font.size=10,
png("ggtree.png", width=1260, height=1260)
#svg("ggtree.svg", width=1260, height=1260)
p
dev.off()
png("ggtree_and_gheatmap.png", width=1290, height=1000)
#svg("ggtree_and_gheatmap.svg", width=17, height=15)
gheatmap(p, heatmapData2, width=0.1,colnames_position="top", colnames_angle=90, colnames_offset_y = 0.1, hjust=0.5, font.size=6, offset = 5) + scale_fill_manual(values=heatmap.colours) + theme(legend.text = element_text(size = 14)) + theme(legend.title = element_text(size = 14)) + guides(fill=guide_legend(title=""), color = guide_legend(override.aes = list(size = 5)))
dev.off()
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Response
I’ve reviewed the 85 genomes as discussed. Four samples were filtered out due to insufficient coverage: mibi2381, mibi2380, and mibi1472. Additionally, the sample mibi1470 was excluded as it could not be identified as S. epidermidis based on its MLST type.
This leaves us with a total of 81 samples for downstream analysis.
Attached, you’ll find:
* The graphic ggtree_and_gheatmap.png
* A table, presence_absence_matrix_on_genes, providing an overview of gene presence/absence and relevant typing information
* FASTA files for all 81 genomes
