Identify all occurrences of Phages MT880870, MT880871 and MT880872 in S. epidermidis ST2 genomes from public and clinical isolates

1. prepare typing_ST2_until_QPB07622.csv under ~/DATA/Data_Luise_Sepi_STKN/presence_absence_ST2

   #grep ">" MT880870.fasta | cut -d' ' -f1 > headers.txt
   # -- under presence_absence_ST2 --
   samtools faidx MT880870.fasta
   samtools faidx MT880870.fasta "lcl|MT880870.1_cds_QPB07572.1_1" > QPB07572.fasta
   samtools faidx MT880870.fasta "lcl|MT880870.1_cds_QPB07573.1_2" > QPB07573.fasta
   samtools faidx MT880870.fasta "lcl|MT880870.1_cds_QPB07574.1_3" > QPB07574.fasta
   samtools faidx MT880870.fasta "lcl|MT880870.1_cds_QPB07575.1_4" > QPB07575.fasta
   samtools faidx MT880870.fasta "lcl|MT880870.1_cds_QPB07576.1_5" > QPB07576.fasta
   samtools faidx MT880870.fasta "lcl|MT880870.1_cds_QPB07577.1_6" > QPB07577.fasta
   samtools faidx MT880870.fasta "lcl|MT880870.1_cds_QPB07578.1_7" > QPB07578.fasta
   samtools faidx MT880870.fasta "lcl|MT880870.1_cds_QPB07579.1_8" > QPB07579.fasta
   samtools faidx MT880870.fasta "lcl|MT880870.1_cds_QPB07580.1_9" > QPB07580.fasta
   samtools faidx MT880870.fasta "lcl|MT880870.1_cds_QPB07581.1_10" > QPB07581.fasta
   samtools faidx MT880870.fasta "lcl|MT880870.1_cds_QPB07582.1_11" > QPB07582.fasta
   samtools faidx MT880870.fasta "lcl|MT880870.1_cds_QPB07583.1_12" > QPB07583.fasta
   samtools faidx MT880870.fasta "lcl|MT880870.1_cds_QPB07584.1_13" > QPB07584.fasta
   samtools faidx MT880870.fasta "lcl|MT880870.1_cds_QPB07585.1_14" > QPB07585.fasta
   samtools faidx MT880870.fasta "lcl|MT880870.1_cds_QPB07586.1_15" > QPB07586.fasta
   samtools faidx MT880870.fasta "lcl|MT880870.1_cds_QPB07587.1_16" > QPB07587.fasta
   samtools faidx MT880870.fasta "lcl|MT880870.1_cds_QPB07588.1_17" > QPB07588.fasta
   samtools faidx MT880870.fasta "lcl|MT880870.1_cds_QPB07589.1_18" > QPB07589.fasta
   samtools faidx MT880870.fasta "lcl|MT880870.1_cds_QPB07590.1_19" > QPB07590.fasta
   samtools faidx MT880870.fasta "lcl|MT880870.1_cds_QPB07591.1_20" > QPB07591.fasta
   samtools faidx MT880870.fasta "lcl|MT880870.1_cds_QPB07592.1_21" > QPB07592.fasta
   samtools faidx MT880870.fasta "lcl|MT880870.1_cds_QPB07593.1_22" > QPB07593.fasta
   samtools faidx MT880870.fasta "lcl|MT880870.1_cds_QPB07594.1_23" > QPB07594.fasta
   samtools faidx MT880870.fasta "lcl|MT880870.1_cds_QPB07595.1_24" > QPB07595.fasta
   samtools faidx MT880870.fasta "lcl|MT880870.1_cds_QPB07596.1_25" > QPB07596.fasta
   samtools faidx MT880870.fasta "lcl|MT880870.1_cds_QPB07597.1_26" > QPB07597.fasta
   samtools faidx MT880870.fasta "lcl|MT880870.1_cds_QPB07598.1_27" > QPB07598.fasta
   samtools faidx MT880870.fasta "lcl|MT880870.1_cds_QPB07599.1_28" > QPB07599.fasta
   samtools faidx MT880870.fasta "lcl|MT880870.1_cds_QPB07600.1_29" > QPB07600.fasta
   samtools faidx MT880870.fasta "lcl|MT880870.1_cds_QPB07601.1_30" > QPB07601.fasta
   samtools faidx MT880870.fasta "lcl|MT880870.1_cds_QPB07602.1_31" > QPB07602.fasta
   samtools faidx MT880870.fasta "lcl|MT880870.1_cds_QPB07603.1_32" > QPB07603.fasta
   samtools faidx MT880870.fasta "lcl|MT880870.1_cds_QPB07604.1_33" > QPB07604.fasta
   samtools faidx MT880870.fasta "lcl|MT880870.1_cds_QPB07605.1_34" > QPB07605.fasta
   samtools faidx MT880870.fasta "lcl|MT880870.1_cds_QPB07606.1_35" > QPB07606.fasta
   samtools faidx MT880870.fasta "lcl|MT880870.1_cds_QPB07607.1_36" > QPB07607.fasta
   samtools faidx MT880870.fasta "lcl|MT880870.1_cds_QPB07608.1_37" > QPB07608.fasta
   samtools faidx MT880870.fasta "lcl|MT880870.1_cds_QPB07609.1_38" > QPB07609.fasta
   samtools faidx MT880870.fasta "lcl|MT880870.1_cds_QPB07610.1_39" > QPB07610.fasta
   samtools faidx MT880870.fasta "lcl|MT880870.1_cds_QPB07611.1_40" > QPB07611.fasta
   samtools faidx MT880870.fasta "lcl|MT880870.1_cds_QPB07612.1_41" > QPB07612.fasta
   samtools faidx MT880870.fasta "lcl|MT880870.1_cds_QPB07613.1_42" > QPB07613.fasta
   samtools faidx MT880870.fasta "lcl|MT880870.1_cds_QPB07614.1_43" > QPB07614.fasta
   samtools faidx MT880870.fasta "lcl|MT880870.1_cds_QPB07615.1_44" > QPB07615.fasta
   samtools faidx MT880870.fasta "lcl|MT880870.1_cds_QPB07616.1_45" > QPB07616.fasta
   samtools faidx MT880870.fasta "lcl|MT880870.1_cds_QPB07617.1_46" > QPB07617.fasta
   samtools faidx MT880870.fasta "lcl|MT880870.1_cds_QPB07618.1_47" > QPB07618.fasta
   samtools faidx MT880870.fasta "lcl|MT880870.1_cds_QPB07619.1_48" > QPB07619.fasta
   samtools faidx MT880870.fasta "lcl|MT880870.1_cds_QPB07620.1_49" > QPB07620.fasta
   samtools faidx MT880870.fasta "lcl|MT880870.1_cds_QPB07621.1_50" > QPB07621.fasta
   samtools faidx MT880870.fasta "lcl|MT880870.1_cds_QPB07622.1_51" > QPB07622.fasta
   
   for i in {572..622}; do
       id_1=$(printf "QPB07%03d" "$((i-1))")
       id=$(printf "QPB07%03d" "$i")
       echo "mkdir ${id}"
       echo "for sample in mibi1440 mibi1454 mibi1456 mibi1459 mibi1461 mibi1478 mibi1480 mibi1485 mibi1487 mibi1496 mibi1498 mibi1502 mibi2318 mibi2319 AP029227 CP013943 CP040883 CP045648 CP052939 CP052940 CP052955 CP052959 CP052981 CP052984 CP052990 CP052994 CP053088 CP064461 CP064467 CP064473 CP064476 CP064480 CP064485 CP064499 CP064508 CP064516 CP064525 CP064554 CP064557 CP064560 CP064572 CP064574 CP064587 CP064590 CP064599 CP064603 CP064606 CP064609 CP064613 CP064616 CP064619 CP064624 CP064631 CP064637 CP064650 CP073821 CP073824 CP073827 CP073830 CP073835 CP073836 CP073840 CP073841 CP073844 CP073847 CP073850 CP073852 CP073855 CP073857 CP073859 CP073862 CP073863 CP073878 CP073900 CP073904 CP084008 CP093173 CP093179 CP093181 CP093193 CP093196 CP093198 CP093212 CP097512 CP097514 CP120425 CP133663; do"
           echo "blastn -db \${sample}.fasta -query ${id}.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > ./${id}/\${sample}.blastn"
       echo "done"
   
   #under plotTreeHeatmap_ST2
   for i in {572..622}; do
       echo "python ~/Scripts/process_directory.py /mnt/md1/DATA_md1/Data_Luise_Sepi_STKN/presence_absence_ST2/${id} /mnt/md1/DATA_md1/Data_Luise_Sepi_STKN/plotTreeHeatmap_ST2/typing_ST2_until_${id_1}.csv /mnt/md1/DATA_md1/Data_Luise_Sepi_STKN/plotTreeHeatmap_ST2/typing_ST2_until_${id}.csv"
   done
   
   #reprace all '+' with 'MT880870' in typing_ST2_until_QPB07622.csv
   cp ../presence_absence_ST2/typing_ST2_until_QPB07622.csv ./
   sed -i 's/+/MT880870/g' typing_ST2_until_QPB07622.csv
   

2. prepare typing_ST2_until_QPB07667.csv under ~/DATA/Data_Luise_Sepi_STKN/presence_absence_ST2

   # -- under presence_absence_ST2 --
   samtools faidx MT880871.fasta
   #grep ">" MT880871.fasta | cut -d' ' -f1 > headers.txt
   samtools faidx MT880871.fasta "lcl|MT880871.1_cds_QPB07623.1_1" > QPB07623.fasta
   samtools faidx MT880871.fasta "lcl|MT880871.1_cds_QPB07624.1_2" > QPB07624.fasta
   samtools faidx MT880871.fasta "lcl|MT880871.1_cds_QPB07625.1_3" > QPB07625.fasta
   samtools faidx MT880871.fasta "lcl|MT880871.1_cds_QPB07626.1_4" > QPB07626.fasta
   samtools faidx MT880871.fasta "lcl|MT880871.1_cds_QPB07627.1_5" > QPB07627.fasta
   samtools faidx MT880871.fasta "lcl|MT880871.1_cds_QPB07628.1_6" > QPB07628.fasta
   samtools faidx MT880871.fasta "lcl|MT880871.1_cds_QPB07629.1_7" > QPB07629.fasta
   samtools faidx MT880871.fasta "lcl|MT880871.1_cds_QPB07630.1_8" > QPB07630.fasta
   samtools faidx MT880871.fasta "lcl|MT880871.1_cds_QPB07631.1_9" > QPB07631.fasta
   samtools faidx MT880871.fasta "lcl|MT880871.1_cds_QPB07632.1_10" > QPB07632.fasta
   samtools faidx MT880871.fasta "lcl|MT880871.1_cds_QPB07633.1_11" > QPB07633.fasta
   samtools faidx MT880871.fasta "lcl|MT880871.1_cds_QPB07634.1_12" > QPB07634.fasta
   samtools faidx MT880871.fasta "lcl|MT880871.1_cds_QPB07635.1_13" > QPB07635.fasta
   samtools faidx MT880871.fasta "lcl|MT880871.1_cds_QPB07636.1_14" > QPB07636.fasta
   samtools faidx MT880871.fasta "lcl|MT880871.1_cds_QPB07637.1_15" > QPB07637.fasta
   samtools faidx MT880871.fasta "lcl|MT880871.1_cds_QPB07638.1_16" > QPB07638.fasta
   samtools faidx MT880871.fasta "lcl|MT880871.1_cds_QPB07639.1_17" > QPB07639.fasta
   samtools faidx MT880871.fasta "lcl|MT880871.1_cds_QPB07640.1_18" > QPB07640.fasta
   samtools faidx MT880871.fasta "lcl|MT880871.1_cds_QPB07641.1_19" > QPB07641.fasta
   samtools faidx MT880871.fasta "lcl|MT880871.1_cds_QPB07642.1_20" > QPB07642.fasta
   samtools faidx MT880871.fasta "lcl|MT880871.1_cds_QPB07643.1_21" > QPB07643.fasta
   samtools faidx MT880871.fasta "lcl|MT880871.1_cds_QPB07644.1_22" > QPB07644.fasta
   samtools faidx MT880871.fasta "lcl|MT880871.1_cds_QPB07645.1_23" > QPB07645.fasta
   samtools faidx MT880871.fasta "lcl|MT880871.1_cds_QPB07646.1_24" > QPB07646.fasta
   samtools faidx MT880871.fasta "lcl|MT880871.1_cds_QPB07647.1_25" > QPB07647.fasta
   samtools faidx MT880871.fasta "lcl|MT880871.1_cds_QPB07648.1_26" > QPB07648.fasta
   samtools faidx MT880871.fasta "lcl|MT880871.1_cds_QPB07649.1_27" > QPB07649.fasta
   samtools faidx MT880871.fasta "lcl|MT880871.1_cds_QPB07650.1_28" > QPB07650.fasta
   samtools faidx MT880871.fasta "lcl|MT880871.1_cds_QPB07651.1_29" > QPB07651.fasta
   samtools faidx MT880871.fasta "lcl|MT880871.1_cds_QPB07652.1_30" > QPB07652.fasta
   samtools faidx MT880871.fasta "lcl|MT880871.1_cds_QPB07653.1_31" > QPB07653.fasta
   samtools faidx MT880871.fasta "lcl|MT880871.1_cds_QPB07654.1_32" > QPB07654.fasta
   samtools faidx MT880871.fasta "lcl|MT880871.1_cds_QPB07655.1_33" > QPB07655.fasta
   samtools faidx MT880871.fasta "lcl|MT880871.1_cds_QPB07656.1_34" > QPB07656.fasta
   samtools faidx MT880871.fasta "lcl|MT880871.1_cds_QPB07657.1_35" > QPB07657.fasta
   samtools faidx MT880871.fasta "lcl|MT880871.1_cds_QPB07658.1_36" > QPB07658.fasta
   samtools faidx MT880871.fasta "lcl|MT880871.1_cds_QPB07659.1_37" > QPB07659.fasta
   samtools faidx MT880871.fasta "lcl|MT880871.1_cds_QPB07660.1_38" > QPB07660.fasta
   samtools faidx MT880871.fasta "lcl|MT880871.1_cds_QPB07661.1_39" > QPB07661.fasta
   samtools faidx MT880871.fasta "lcl|MT880871.1_cds_QPB07662.1_40" > QPB07662.fasta
   samtools faidx MT880871.fasta "lcl|MT880871.1_cds_QPB07663.1_41" > QPB07663.fasta
   samtools faidx MT880871.fasta "lcl|MT880871.1_cds_QPB07664.1_42" > QPB07664.fasta
   samtools faidx MT880871.fasta "lcl|MT880871.1_cds_QPB07665.1_43" > QPB07665.fasta
   samtools faidx MT880871.fasta "lcl|MT880871.1_cds_QPB07666.1_44" > QPB07666.fasta
   samtools faidx MT880871.fasta "lcl|MT880871.1_cds_QPB07667.1_45" > QPB07667.fasta
   
   for i in {623..667}; do
       id=$(printf "QPB07%03d" "$i")
       echo "mkdir ${id}"
       echo "for sample in mibi1440 mibi1454 mibi1456 mibi1459 mibi1461 mibi1478 mibi1480 mibi1485 mibi1487 mibi1496 mibi1498 mibi1502 mibi2318 mibi2319 AP029227 CP013943 CP040883 CP045648 CP052939 CP052940 CP052955 CP052959 CP052981 CP052984 CP052990 CP052994 CP053088 CP064461 CP064467 CP064473 CP064476 CP064480 CP064485 CP064499 CP064508 CP064516 CP064525 CP064554 CP064557 CP064560 CP064572 CP064574 CP064587 CP064590 CP064599 CP064603 CP064606 CP064609 CP064613 CP064616 CP064619 CP064624 CP064631 CP064637 CP064650 CP073821 CP073824 CP073827 CP073830 CP073835 CP073836 CP073840 CP073841 CP073844 CP073847 CP073850 CP073852 CP073855 CP073857 CP073859 CP073862 CP073863 CP073878 CP073900 CP073904 CP084008 CP093173 CP093179 CP093181 CP093193 CP093196 CP093198 CP093212 CP097512 CP097514 CP120425 CP133663; do"
           echo "blastn -db \${sample}.fasta -query ${id}.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > ./${id}/\${sample}.blastn"
       echo "done"
   done
   
   for i in {660..660}; do
       id=$(printf "QPB07%03d" "$i")
       echo "mkdir ${id}"
       echo "for sample in mibi1440 mibi1454 mibi1456 mibi1459 mibi1461 mibi1478 mibi1480 mibi1485 mibi1487 mibi1496 mibi1498 mibi1502 mibi2318 mibi2319 AP029227 CP013943 CP040883 CP045648 CP052939 CP052940 CP052955 CP052959 CP052981 CP052984 CP052990 CP052994 CP053088 CP064461 CP064467 CP064473 CP064476 CP064480 CP064485 CP064499 CP064508 CP064516 CP064525 CP064554 CP064557 CP064560 CP064572 CP064574 CP064587 CP064590 CP064599 CP064603 CP064606 CP064609 CP064613 CP064616 CP064619 CP064624 CP064631 CP064637 CP064650 CP073821 CP073824 CP073827 CP073830 CP073835 CP073836 CP073840 CP073841 CP073844 CP073847 CP073850 CP073852 CP073855 CP073857 CP073859 CP073862 CP073863 CP073878 CP073900 CP073904 CP084008 CP093173 CP093179 CP093181 CP093193 CP093196 CP093198 CP093212 CP097512 CP097514 CP120425 CP133663; do"
           echo "blastn -db \${sample}.fasta -query ${id}.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > ./${id}/\${sample}.blastn"
       echo "done"
   done
   
   # -- under plotTreeHeatmap_ST2 --
   for i in {623..667}; do
       id_1=$(printf "QPB07%03d" "$((i-1))")
       id=$(printf "QPB07%03d" "$i")
       echo "python ~/Scripts/process_directory.py /mnt/md1/DATA_md1/Data_Luise_Sepi_STKN/presence_absence_ST2/${id} /mnt/md1/DATA_md1/Data_Luise_Sepi_STKN/plotTreeHeatmap_ST2/typing_ST2_until_${id_1}.csv /mnt/md1/DATA_md1/Data_Luise_Sepi_STKN/plotTreeHeatmap_ST2/typing_ST2_until_${id}.csv"
   done
   
   sed -i 's/+/MT880871/g' typing_ST2_until_QPB07667.csv
   

3. prepare typing_ST2_until_QPB07667.csv under ~/DATA/Data_Luise_Sepi_STKN/presence_absence_ST2

   # -- under presence_absence_ST2 --
   samtools faidx MT880872.fasta
   #grep ">" MT880872.fasta | cut -d' ' -f1 > headers.txt
   
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07668.1_1" > QPB07668.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07669.1_2" > QPB07669.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07670.1_3" > QPB07670.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07671.1_4" > QPB07671.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07672.1_5" > QPB07672.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07673.1_6" > QPB07673.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07674.1_7" > QPB07674.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07675.1_8" > QPB07675.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07676.1_9" > QPB07676.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07677.1_10" > QPB07677.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07678.1_11" > QPB07678.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07679.1_12" > QPB07679.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07680.1_13" > QPB07680.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07681.1_14" > QPB07681.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07682.1_15" > QPB07682.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07683.1_16" > QPB07683.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07684.1_17" > QPB07684.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07685.1_18" > QPB07685.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07686.1_19" > QPB07686.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07687.1_20" > QPB07687.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07688.1_21" > QPB07688.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07689.1_22" > QPB07689.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07690.1_23" > QPB07690.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07691.1_24" > QPB07691.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07692.1_25" > QPB07692.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07693.1_26" > QPB07693.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07694.1_27" > QPB07694.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07695.1_28" > QPB07695.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07696.1_29" > QPB07696.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07697.1_30" > QPB07697.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07698.1_31" > QPB07698.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07699.1_32" > QPB07699.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07700.1_33" > QPB07700.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07701.1_34" > QPB07701.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07702.1_35" > QPB07702.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07703.1_36" > QPB07703.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07704.1_37" > QPB07704.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07705.1_38" > QPB07705.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07706.1_39" > QPB07706.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07707.1_40" > QPB07707.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07708.1_41" > QPB07708.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07709.1_42" > QPB07709.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07710.1_43" > QPB07710.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07711.1_44" > QPB07711.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07712.1_45" > QPB07712.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07713.1_46" > QPB07713.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07714.1_47" > QPB07714.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07715.1_48" > QPB07715.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07716.1_49" > QPB07716.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07717.1_50" > QPB07717.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07718.1_51" > QPB07718.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07719.1_52" > QPB07719.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07720.1_53" > QPB07720.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07721.1_54" > QPB07721.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07722.1_55" > QPB07722.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07723.1_56" > QPB07723.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07724.1_57" > QPB07724.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07725.1_58" > QPB07725.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07726.1_59" > QPB07726.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07727.1_60" > QPB07727.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07728.1_61" > QPB07728.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07729.1_62" > QPB07729.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07730.1_63" > QPB07730.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07731.1_64" > QPB07731.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07732.1_65" > QPB07732.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07733.1_66" > QPB07733.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07734.1_67" > QPB07734.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07735.1_68" > QPB07735.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07736.1_69" > QPB07736.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07737.1_70" > QPB07737.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07738.1_71" > QPB07738.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07739.1_72" > QPB07739.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07740.1_73" > QPB07740.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07741.1_74" > QPB07741.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07742.1_75" > QPB07742.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07743.1_76" > QPB07743.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07744.1_77" > QPB07744.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07745.1_78" > QPB07745.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07746.1_79" > QPB07746.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07747.1_80" > QPB07747.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07748.1_81" > QPB07748.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07749.1_82" > QPB07749.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07750.1_83" > QPB07750.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07751.1_84" > QPB07751.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07752.1_85" > QPB07752.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07753.1_86" > QPB07753.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07754.1_87" > QPB07754.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07755.1_88" > QPB07755.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07756.1_89" > QPB07756.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07757.1_90" > QPB07757.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07758.1_91" > QPB07758.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07759.1_92" > QPB07759.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07760.1_93" > QPB07760.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07761.1_94" > QPB07761.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07762.1_95" > QPB07762.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07763.1_96" > QPB07763.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07764.1_97" > QPB07764.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07765.1_98" > QPB07765.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07766.1_99" > QPB07766.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07767.1_100" > QPB07767.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07768.1_101" > QPB07768.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07769.1_102" > QPB07769.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07770.1_103" > QPB07770.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07771.1_104" > QPB07771.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07772.1_105" > QPB07772.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07773.1_106" > QPB07773.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07774.1_107" > QPB07774.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07775.1_108" > QPB07775.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07776.1_109" > QPB07776.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07777.1_110" > QPB07777.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07778.1_111" > QPB07778.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07779.1_112" > QPB07779.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07780.1_113" > QPB07780.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07781.1_114" > QPB07781.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07782.1_115" > QPB07782.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07783.1_116" > QPB07783.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07784.1_117" > QPB07784.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07785.1_118" > QPB07785.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07786.1_119" > QPB07786.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07787.1_120" > QPB07787.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07788.1_121" > QPB07788.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07789.1_122" > QPB07789.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07790.1_123" > QPB07790.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07791.1_124" > QPB07791.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07792.1_125" > QPB07792.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07793.1_126" > QPB07793.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07794.1_127" > QPB07794.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07795.1_128" > QPB07795.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07796.1_129" > QPB07796.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07797.1_130" > QPB07797.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07798.1_131" > QPB07798.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07799.1_132" > QPB07799.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07800.1_133" > QPB07800.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07801.1_134" > QPB07801.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07802.1_135" > QPB07802.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07803.1_136" > QPB07803.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07804.1_137" > QPB07804.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07805.1_138" > QPB07805.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07806.1_139" > QPB07806.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07807.1_140" > QPB07807.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07808.1_141" > QPB07808.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07809.1_142" > QPB07809.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07810.1_143" > QPB07810.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07811.1_144" > QPB07811.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07812.1_145" > QPB07812.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07813.1_146" > QPB07813.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07814.1_147" > QPB07814.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07815.1_148" > QPB07815.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07816.1_149" > QPB07816.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07817.1_150" > QPB07817.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07818.1_151" > QPB07818.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07819.1_152" > QPB07819.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07820.1_153" > QPB07820.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07821.1_154" > QPB07821.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07822.1_155" > QPB07822.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07823.1_156" > QPB07823.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07824.1_157" > QPB07824.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07825.1_158" > QPB07825.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07826.1_159" > QPB07826.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07827.1_160" > QPB07827.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07828.1_161" > QPB07828.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07829.1_162" > QPB07829.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07830.1_163" > QPB07830.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07831.1_164" > QPB07831.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07832.1_165" > QPB07832.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07833.1_166" > QPB07833.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07834.1_167" > QPB07834.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07835.1_168" > QPB07835.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07836.1_169" > QPB07836.fasta
   samtools faidx MT880872.fasta "lcl|MT880872.1_cds_QPB07837.1_170" > QPB07837.fasta
   
   for i in {668..750}; do
       id=$(printf "QPB07%03d" "$i")
       echo "mkdir ${id}"
       echo "for sample in mibi1440 mibi1454 mibi1456 mibi1459 mibi1461 mibi1478 mibi1480 mibi1485 mibi1487 mibi1496 mibi1498 mibi1502 mibi2318 mibi2319 AP029227 CP013943 CP040883 CP045648 CP052939 CP052940 CP052955 CP052959 CP052981 CP052984 CP052990 CP052994 CP053088 CP064461 CP064467 CP064473 CP064476 CP064480 CP064485 CP064499 CP064508 CP064516 CP064525 CP064554 CP064557 CP064560 CP064572 CP064574 CP064587 CP064590 CP064599 CP064603 CP064606 CP064609 CP064613 CP064616 CP064619 CP064624 CP064631 CP064637 CP064650 CP073821 CP073824 CP073827 CP073830 CP073835 CP073836 CP073840 CP073841 CP073844 CP073847 CP073850 CP073852 CP073855 CP073857 CP073859 CP073862 CP073863 CP073878 CP073900 CP073904 CP084008 CP093173 CP093179 CP093181 CP093193 CP093196 CP093198 CP093212 CP097512 CP097514 CP120425 CP133663; do"
           echo "blastn -db \${sample}.fasta -query ${id}.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > ./${id}/\${sample}.blastn"
       echo "done"
   done
   
   for i in {751..837}; do
       id=$(printf "QPB07%03d" "$i")
       echo "mkdir ${id}"
       echo "for sample in mibi1440 mibi1454 mibi1456 mibi1459 mibi1461 mibi1478 mibi1480 mibi1485 mibi1487 mibi1496 mibi1498 mibi1502 mibi2318 mibi2319 AP029227 CP013943 CP040883 CP045648 CP052939 CP052940 CP052955 CP052959 CP052981 CP052984 CP052990 CP052994 CP053088 CP064461 CP064467 CP064473 CP064476 CP064480 CP064485 CP064499 CP064508 CP064516 CP064525 CP064554 CP064557 CP064560 CP064572 CP064574 CP064587 CP064590 CP064599 CP064603 CP064606 CP064609 CP064613 CP064616 CP064619 CP064624 CP064631 CP064637 CP064650 CP073821 CP073824 CP073827 CP073830 CP073835 CP073836 CP073840 CP073841 CP073844 CP073847 CP073850 CP073852 CP073855 CP073857 CP073859 CP073862 CP073863 CP073878 CP073900 CP073904 CP084008 CP093173 CP093179 CP093181 CP093193 CP093196 CP093198 CP093212 CP097512 CP097514 CP120425 CP133663; do"
           echo "blastn -db \${sample}.fasta -query ${id}.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > ./${id}/\${sample}.blastn"
       echo "done"
   done
   
       for i in {708..708}; do
       id=$(printf "QPB07%03d" "$i")
       echo "mkdir ${id}"
       echo "for sample in mibi1440 mibi1454 mibi1456 mibi1459 mibi1461 mibi1478 mibi1480 mibi1485 mibi1487 mibi1496 mibi1498 mibi1502 mibi2318 mibi2319 AP029227 CP013943 CP040883 CP045648 CP052939 CP052940 CP052955 CP052959 CP052981 CP052984 CP052990 CP052994 CP053088 CP064461 CP064467 CP064473 CP064476 CP064480 CP064485 CP064499 CP064508 CP064516 CP064525 CP064554 CP064557 CP064560 CP064572 CP064574 CP064587 CP064590 CP064599 CP064603 CP064606 CP064609 CP064613 CP064616 CP064619 CP064624 CP064631 CP064637 CP064650 CP073821 CP073824 CP073827 CP073830 CP073835 CP073836 CP073840 CP073841 CP073844 CP073847 CP073850 CP073852 CP073855 CP073857 CP073859 CP073862 CP073863 CP073878 CP073900 CP073904 CP084008 CP093173 CP093179 CP093181 CP093193 CP093196 CP093198 CP093212 CP097512 CP097514 CP120425 CP133663; do"
           echo "blastn -db \${sample}.fasta -query ${id}.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > ./${id}/\${sample}.blastn"
       echo "done"
   done
   
   # -- under plotTreeHeatmap_ST2 --
   for i in {668..837}; do
       id_1=$(printf "QPB07%03d" "$((i-1))")
       id=$(printf "QPB07%03d" "$i")
       echo "python ~/Scripts/process_directory.py /mnt/md1/DATA_md1/Data_Luise_Sepi_STKN/presence_absence_ST2/${id} /mnt/md1/DATA_md1/Data_Luise_Sepi_STKN/plotTreeHeatmap_ST2/typing_ST2_until_${id_1}.csv /mnt/md1/DATA_md1/Data_Luise_Sepi_STKN/plotTreeHeatmap_ST2/typing_ST2_until_${id}.csv"
   done
   
   sed -i 's/+/MT880872/g' typing_ST2_until_QPB07837.csv
   

4. plot tree heatmap under /mnt/md1/DATA_md1/Data_Luise_Sepi_STKN/plotTreeHeatmap_ST2_MT880871

   library(ggtree)
   library(ggplot2)
   library(dplyr)
   setwd("/home/jhuang/DATA/Data_Luise_Sepi_STKN/plotTreeHeatmap_ST2/")
   # -- edit tree --
   #https://icytree.org/
   #0.000780
   info <- read.csv("typing_ST2_until_QPB07837.csv", sep="\t")
   info$name <- info$Isolate
   tree <- read.tree("core_gene_alignment.aln.treefile")
   cols <- c("Public database"='purple2', "Clinical isolate"='darksalmon')  #purple2  skyblue2
   heatmapData2 <- info %>% select(Isolate, QPB07572, QPB07573, QPB07574, QPB07575, QPB07576, QPB07577, QPB07578, QPB07579, QPB07580, QPB07581, QPB07582, QPB07583, QPB07584, QPB07585, QPB07586, QPB07587, QPB07588, QPB07589, QPB07590, QPB07591, QPB07592, QPB07593, QPB07594, QPB07595, QPB07596, QPB07597, QPB07598, QPB07599, QPB07600, QPB07601, QPB07602, QPB07603, QPB07604, QPB07605, QPB07606, QPB07607, QPB07608, QPB07609, QPB07610, QPB07611, QPB07612, QPB07613, QPB07614, QPB07615, QPB07616, QPB07617, QPB07618, QPB07619, QPB07620, QPB07621, QPB07622, QPB07623, QPB07624, QPB07625, QPB07626, QPB07627, QPB07628, QPB07629, QPB07630, QPB07631, QPB07632, QPB07633, QPB07634, QPB07635, QPB07636, QPB07637, QPB07638, QPB07639, QPB07640, QPB07641, QPB07642, QPB07643, QPB07644, QPB07645, QPB07646, QPB07647, QPB07648, QPB07649, QPB07650, QPB07651, QPB07652, QPB07653, QPB07654, QPB07655, QPB07656, QPB07657, QPB07658, QPB07659, QPB07660, QPB07661, QPB07662, QPB07663, QPB07664, QPB07665, QPB07666, QPB07667, QPB07668, QPB07669, QPB07670, QPB07671, QPB07672, QPB07673, QPB07674, QPB07675, QPB07676, QPB07677, QPB07678, QPB07679, QPB07680, QPB07681, QPB07682, QPB07683, QPB07684, QPB07685, QPB07686, QPB07687, QPB07688, QPB07689, QPB07690, QPB07691, QPB07692, QPB07693, QPB07694, QPB07695, QPB07696, QPB07697, QPB07698, QPB07699, QPB07700, QPB07701, QPB07702, QPB07703, QPB07704, QPB07705, QPB07706, QPB07707, QPB07708, QPB07709, QPB07710, QPB07711, QPB07712, QPB07713, QPB07714, QPB07715, QPB07716, QPB07717, QPB07718, QPB07719, QPB07720, QPB07721, QPB07722, QPB07723, QPB07724, QPB07725, QPB07726, QPB07727, QPB07728, QPB07729, QPB07730, QPB07731, QPB07732, QPB07733, QPB07734, QPB07735, QPB07736, QPB07737, QPB07738, QPB07739, QPB07740, QPB07741, QPB07742, QPB07743, QPB07744, QPB07745, QPB07746, QPB07747, QPB07748, QPB07749, QPB07750, QPB07751, QPB07752, QPB07753, QPB07754, QPB07755, QPB07756, QPB07757, QPB07758, QPB07759, QPB07760, QPB07761, QPB07762, QPB07763, QPB07764, QPB07765, QPB07766, QPB07767, QPB07768, QPB07769, QPB07770, QPB07771, QPB07772, QPB07773, QPB07774, QPB07775, QPB07776, QPB07777, QPB07778, QPB07779, QPB07780, QPB07781, QPB07782, QPB07783, QPB07784, QPB07785, QPB07786, QPB07787, QPB07788, QPB07789, QPB07790, QPB07791, QPB07792, QPB07793, QPB07794, QPB07795, QPB07796, QPB07797, QPB07798, QPB07799, QPB07800, QPB07801, QPB07802, QPB07803, QPB07804, QPB07805, QPB07806, QPB07807, QPB07808, QPB07809, QPB07810, QPB07811, QPB07812, QPB07813, QPB07814, QPB07815, QPB07816, QPB07817, QPB07818, QPB07819, QPB07820, QPB07821, QPB07822, QPB07823, QPB07824, QPB07825, QPB07826, QPB07827, QPB07828, QPB07829, QPB07830, QPB07831, QPB07832, QPB07833, QPB07834, QPB07835, QPB07836, QPB07837)  #ST,
   rn <- heatmapData2$Isolate
   heatmapData2$Isolate <- NULL
   heatmapData2 <- as.data.frame(sapply(heatmapData2, as.character))
   rownames(heatmapData2) <- rn
   heatmap.colours <- c("darkred", "darkblue", "darkgreen", "grey")
   names(heatmap.colours) <- c("MT880870","MT880871","MT880872","-")
   #mydat$Regulation <- factor(mydat$Regulation, levels=c("up","down"))
   #circular
   p <- ggtree(tree, layout='circular', branch.length='none') %<+% info + geom_tippoint(aes(color=Source)) + scale_color_manual(values=cols) + geom_tiplab2(aes(label=name), offset=1)
   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=4, 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)))
   png("ggtree_and_gheatmap.png", width=1290, height=1000)
   gheatmap(p, heatmapData2, width=0.5, colnames_position="top", colnames_angle=90, colnames_offset_y = 0.1, hjust=0.5, font.size=0, offset = 8) + scale_fill_manual(values=heatmap.colours) +  theme(legend.text = element_text(size = 16)) + theme(legend.title = element_text(size = 16)) + guides(fill=guide_legend(title=""), color = guide_legend(override.aes = list(size = 5)))
   dev.off()
   

5. Report

   Explanation for the discrepancy between the last analysis and this one: Note that many partial genes of the phages do not match because, in the previous analysis, only the longest BLASTn hits were considered and recorded in the table.

   We have a total of 14 ST2 genomes from Luise's project, and I found 73 ST2 genomes from NCBI.

   I examined the presence and absence of all 51 + 45 + 170 genes (details below) across the 87 genomes and visualized the results in a heatmap (attached as ggtree_and_gheatmap_phages.png).

   • MT880870: 51 putative genes
   • MT880871: 45 putative genes
   • MT880872: 170 putative genes

   In the heatmap:

   Genes not present in the corresponding isolate are shown in grey. Genes present are highlighted in the corresponding colors:

   • Dark red for MT880870
   • Dark blue for MT880871
   • Dark green for MT880872

   The graphic is based on the Excel file typing_ST2.xlsx. If you have any suggestions or improvements, please let me know.

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