-
prepare input reads and samplesheet
ln -s ./F23A430001245_SEPiovzP/soapnuke/clean/EX_15_min_A/EX_15_min_A_1.fq.gz . ln -s ./F23A430001245_SEPiovzP/soapnuke/clean/EX_15_min_A/EX_15_min_A_2.fq.gz . ln -s ./F23A430001245_SEPiovzP/soapnuke/clean/EX_15_min_B/EX_15_min_B_1.fq.gz . ln -s ./F23A430001245_SEPiovzP/soapnuke/clean/EX_15_min_B/EX_15_min_B_2.fq.gz . ln -s ./F23A430001245_SEPiovzP/soapnuke/clean/EX_15_min_C/EX_15_min_C_1.fq.gz . ln -s ./F23A430001245_SEPiovzP/soapnuke/clean/EX_15_min_C/EX_15_min_C_2.fq.gz . ln -s ./F23A430001245_SEPiovzP/soapnuke/clean/EX_1h_A/EX_1h_A_1.fq.gz . ln -s ./F23A430001245_SEPiovzP/soapnuke/clean/EX_1h_A/EX_1h_A_2.fq.gz . ln -s ./F23A430001245_SEPiovzP/soapnuke/clean/EX_1h_B/EX_1h_B_1.fq.gz . ln -s ./F23A430001245_SEPiovzP/soapnuke/clean/EX_1h_B/EX_1h_B_2.fq.gz . ln -s ./F23A430001245_SEPiovzP/soapnuke/clean/EX_1h_C/EX_1h_C_1.fq.gz . ln -s ./F23A430001245_SEPiovzP/soapnuke/clean/EX_1h_C/EX_1h_C_2.fq.gz . ln -s ./F23A430001245_SEPiovzP/soapnuke/clean/EX_2h_A/EX_2h_A_1.fq.gz . ln -s ./F23A430001245_SEPiovzP/soapnuke/clean/EX_2h_A/EX_2h_A_2.fq.gz . ln -s ./F23A430001245_SEPiovzP/soapnuke/clean/EX_2h_B/EX_2h_B_1.fq.gz . ln -s ./F23A430001245_SEPiovzP/soapnuke/clean/EX_2h_B/EX_2h_B_2.fq.gz . ln -s ./F23A430001245_SEPiovzP/soapnuke/clean/EX_2h_C/EX_2h_C_1.fq.gz . ln -s ./F23A430001245_SEPiovzP/soapnuke/clean/EX_2h_C/EX_2h_C_2.fq.gz . ln -s ./F23A430001245_SEPiovzP/soapnuke/clean/EX_4h_A/EX_4h_A_1.fq.gz . ln -s ./F23A430001245_SEPiovzP/soapnuke/clean/EX_4h_A/EX_4h_A_2.fq.gz . ln -s ./F23A430001245_SEPiovzP/soapnuke/clean/EX_4h_B/EX_4h_B_1.fq.gz . ln -s ./F23A430001245_SEPiovzP/soapnuke/clean/EX_4h_B/EX_4h_B_2.fq.gz . ln -s ./F23A430001245_SEPiovzP/soapnuke/clean/EX_4h_C/EX_4h_C_1.fq.gz . ln -s ./F23A430001245_SEPiovzP/soapnuke/clean/EX_4h_C/EX_4h_C_2.fq.gz . ln -s ./F23A430001245_SEPiovzP/soapnuke/clean/EX_6h_A/EX_6h_A_1.fq.gz . ln -s ./F23A430001245_SEPiovzP/soapnuke/clean/EX_6h_A/EX_6h_A_2.fq.gz . ln -s ./F23A430001245-01_SEPzqcuP/soapnuke/clean/EX_6h_B/EX_6h_B_1.fq.gz . ln -s ./F23A430001245-01_SEPzqcuP/soapnuke/clean/EX_6h_B/EX_6h_B_2.fq.gz . ln -s ./F23A430001245-01_SEPzqcuP/soapnuke/clean/EX_6h_C/EX_6h_C_1.fq.gz . ln -s ./F23A430001245-01_SEPzqcuP/soapnuke/clean/EX_6h_C/EX_6h_C_2.fq.gz . ln -s ./F23A430001245_SEPiovzP/soapnuke/clean/EX_Day_4_A/EX_Day_4_A_1.fq.gz . ln -s ./F23A430001245_SEPiovzP/soapnuke/clean/EX_Day_4_A/EX_Day_4_A_2.fq.gz . ln -s ./F23A430001245_SEPiovzP/soapnuke/clean/EX_Day_4_B/EX_Day_4_B_1.fq.gz . ln -s ./F23A430001245_SEPiovzP/soapnuke/clean/EX_Day_4_B/EX_Day_4_B_2.fq.gz . ln -s ./F23A430001245_SEPiovzP/soapnuke/clean/EX_Day_4_C/EX_Day_4_C_1.fq.gz . ln -s ./F23A430001245_SEPiovzP/soapnuke/clean/EX_Day_4_C/EX_Day_4_C_2.fq.gz . sample,fastq_1,fastq_2,strandedness EX_15_min_A,EX_15_min_A_1.fq.gz,EX_15_min_A_2.fq.gz,auto EX_15_min_B,EX_15_min_B_1.fq.gz,EX_15_min_B_2.fq.gz,auto EX_15_min_C,EX_15_min_C_1.fq.gz,EX_15_min_C_2.fq.gz,auto -
Notes and Debugs
#-- NOTE1: STAR cannot work simoutenously twice at the same time! -- #-- NOTE2 -- The GTF file might be corrupted! Stop at line : NC_019234.1 RefSeq exon 1600 1977 . + 0 ID "cds-HXG45_RS00010"; Parent "gene-HXG45_RS00010"; Note "incomplete%3B partial in the middle of a contig%3B missing N-terminus and C-terminus"; Ontology_term "GO:0015074"; end_range "1977,."; gbkey "CDS"; go_process "DNA integration|0015074||IEA"; inference "COORDINATES: similar to AA sequence:RefSeq:WP_010972061.1"; locus_tag "HXG45_RS00010"; partial "true"; product "DDE-type integrase/transposase/recombinase"; pseudo "true"; start_range ".,1600"; transl_table "11" Error Message: Cannot find gene_id! #cut -d$'\t' -f2 RP62A.gtf | sort -u cmsearch GeneMarkS-2+ Protein Homology --> ProteinHomology RefSeq tRNAscan-SE #cut -d$'\t' -f3 RP62A.gtf | sort -u gene pseudogene CDS rRNA tRNA direct_repeat exon ncRNA binding_site region riboswitch RNase_P_RNA sequence_feature SRP_RNA tmRNA #-- BUG1: mamba update picard -- #2.18.27-SNAPSHOT --> bioconda::picard=3.0.0 conda install -c conda-forge mamba mamba update picard - ca-certificates 2023.7.22 hbcca054_0 conda-forge + ca-certificates 2023.11.17 hbcca054_0 conda-forge/linux-64 Cached - nextflow 20.04.1 hecda079_1 bioconda + nextflow 23.10.0 hdfd78af_0 bioconda/noarch Cached - openjdk 11.0.1 h516909a_1016 conda-forge + openjdk 17.0.3 h58dac75_5 conda-forge/linux-64 Cached - picard 3.0.0 hdfd78af_0 bioconda + picard 3.1.1 hdfd78af_0 bioconda/noarch Cached mamba update rsem #-- BUG2: mamba update gffread -- cd /mnt/h1/jhuang/DATA/Data_Marc_RNA-seq_Sepidermidis/work/b4/703a2595f234c7866e49d9a033f943 gffread \ RP62A.gff \ --keep-exon-attrs -F -T \ -o RP62A.gtf - gffread 0.9.12 0 bioconda + gffread 0.12.7 hdcf5f25_3 bioconda/linux-64 Cached #-- NOTE: If you use nf-core/rnaseq for your analysis please cite: -- #* The pipeline # https://doi.org/10.5281/zenodo.1400710 #* The nf-core framework # https://doi.org/10.1038/s41587-020-0439-x #* Software dependencies # https://github.com/nf-core/rnaseq/blob/master/CITATIONS.md #-- BUG3: under rnaseq_2021 open R -- #using R host rather than conda R mamba remove r-base #-I"/home/jhuang/miniconda3/envs/rnaseq_2021/lib/R/include" if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("SummarizedExperiment") BiocManager::install("tximport") #Error in citation("tximeta") : there is no package called ‘tximeta’ # Execution halted #sudo apt-get update #sudo apt-get install libcurl4-openssl-dev #BiocManager::install(version = "3.16") BiocManager::install(c("AnnotationDbi", "httr", "BiocFileCache", "biomaRt", "GenomicFeatures", "ensembldb", "curl", "AnnotationHub")) BiocManager::install(c("biomaRt", "GenomicFeatures", "ensembldb", "AnnotationHub", "tximeta")) BiocManager::install(c("tximeta")) #conda update -n base -c defaults conda #conda update --all #!/usr/bin/env Rscript /mnt/h1/jhuang/DATA/Data_Marc_RNA-seq_Sepidermidis/rnaseq/bin/salmon_tximport.r \ NULL \ salmon \ salmon.merged -
prepare gtf file
# --gtf_extra_attributes [string] By default, the pipeline uses the `gene_name` field to obtain additional gene identifiers from the input GTF file when running Salmon. [default: gene_name] # --gtf_group_features [string] Define the attribute type used to group features in the GTF file when running Salmon. [default: gene_id] # --featurecounts_group_type [string] The attribute type used to group feature types in the GTF file when generating the biotype plot with featureCounts. [default: gene_biotype] # --featurecounts_feature_type [string] By default, the pipeline assigns reads based on the 'exon' attribute within the GTF file. [default: exon] #--gtf_extra_attributes gene #--gtf_group_features Parent --featurecounts_group_type gene_biotype --featurecounts_feature_type CDS (outdated since [CHANGE1,2,3]) #under hamm conda activate rnaseq ln -s /home/jhuang/Tools/nf-core-rnaseq-3.12.0/ rnaseq # ------------ gff_to_gtf.py, then modify *.gtf file as follows ------------- #Upload the scripts gff_to_gtf.py and modify_gtf.py. python3 gff_to_gtf.py RP62A.gff3 RP62A.gtf #[CHANGE1] ID in gene and Parent in CDS --> gene_id; ID in exon --> transcript_id; Name in gene --> gene_name #[CHANGE2] "Protein Homology" --> "RefSeq" #[CHANGE3] CDS --> exon #[CHANGE4?] --gtf_extra_attributes ||||gene|||| refers to ID=gene-SERP_RS00220;Name=noc;gbkey=Gene;||||gene=noc||||; "gene=" exists in both gene and exon. choose gene as gtf_extra_attributes! (see --gtf_extra_attributes gene in the next command) [1] python3 gff_to_gtf.py RP62A.gff3 RP62A.gtf [2] python3 modify_gtf.py RP62A.gtf RP62A_m.gtf [3] sed -i -e 's/gene_id "rna-/gene_id "gene-/g' RP62A_m.gtf #NOTE that "ProteinHomology exon" are from "ProteinHomology CDS" [4] MANUALLY checking why two are missing, because the gene has two CDS/exons. #(rnaseq) jhuang@hamm:/mnt/h1/jhuang/DATA/Data_Marc_RNA-seq_Sepidermidis/results/genome$ grep ">cds" results/genome/genome.transcripts.fa | sed 's/>//g' - | sort > CDS_2.txt #2415 #(rnaseq) jhuang@hamm:/mnt/h1/jhuang/DATA/Data_Marc_RNA-seq_Sepidermidis/results/genome$ grep ">rna" genome.transcripts.fa | wc -l #84 #cut -d$'\t' -f9 CDS_1.txt | cut -d';' -f1 | sed 's/ID=//g' - | sort > CDS_1_.txt #2417 #2268d2267 #< cds-WP_010959142.1 #2401d2399 #< cds-WP_161384733.1 NC_002976.3 RefSeq gene 423814 424930 . + . gene_id "gene-SERP_RS02220"; gene_name "prfB"; gbkey "Gene"; gene "prfB"; gene_biotype "protein_coding"; locus_tag "SERP_RS02220"; old_locus_tag "SE0421%2CSERP0421" NC_002976.3 ProteinHomology exon 423814 423885 . + 0 transcript_id "cds-WP_010959142.1"; gene_id "gene-SERP_RS02220"; Dbxref "GenBank:WP_010959142.1"; Name "WP_010959142.1"; Note "programmed frameshift"; Ontology_term "GO:0006415,GO:0003747"; exception "ribosomal slippage"; gbkey "CDS"; gene "prfB"; go_function "translation release factor activity|0003747||IEA"; go_process "translational termination|0006415||IEA"; inference "COORDINATES: similar to AA sequence:RefSeq:WP_010959142.1"; locus_tag "SERP_RS02220"; product "peptide chain release factor 2"; protein_id "WP_010959142.1"; transl_table "11" NC_002976.3 ProteinHomology exon 423887 424930 . + 0 transcript_id "cds-WP_010959142.1"; gene_id "gene-SERP_RS02220"; Dbxref "GenBank:WP_010959142.1"; Name "WP_010959142.1"; Note "programmed frameshift"; Ontology_term "GO:0006415,GO:0003747"; exception "ribosomal slippage"; gbkey "CDS"; gene "prfB"; go_function "translation release factor activity|0003747||IEA"; go_process "translational termination|0006415||IEA"; inference "COORDINATES: similar to AA sequence:RefSeq:WP_010959142.1"; locus_tag "SERP_RS02220"; product "peptide chain release factor 2"; protein_id "WP_010959142.1"; transl_table "11" NC_002976.3 RefSeq gene 2256196 2256869 . + . gene_id "gene-SERP_RS10980"; gene_name "SERP_RS10980"; gbkey "Gene"; gene_biotype "protein_coding"; locus_tag "SERP_RS10980"; old_locus_tag "SERP2219" NC_002976.3 ProteinHomology exon 2256196 2256385 . + 0 transcript_id "cds-WP_161384733.1"; gene_id "gene-SERP_RS10980"; Dbxref "GenBank:WP_161384733.1"; Name "WP_161384733.1"; Note "programmed frameshift"; Ontology_term "GO:0004803"; exception "ribosomal slippage"; gbkey "CDS"; go_function "transposase activity|0004803||IEA"; inference "COORDINATES: similar to AA sequence:RefSeq:WP_064305258.1"; locus_tag "SERP_RS10980"; product "IS6-like element IS257 family transposase"; protein_id "WP_161384733.1"; transl_table "11" NC_002976.3 ProteinHomology exon 2256385 2256869 . + 2 transcript_id "cds-WP_161384733.1"; gene_id "gene-SERP_RS10980"; Dbxref "GenBank:WP_161384733.1"; Name "WP_161384733.1"; Note "programmed frameshift"; Ontology_term "GO:0004803"; exception "ribosomal slippage"; gbkey "CDS"; go_function "transposase activity|0004803||IEA"; inference "COORDINATES: similar to AA sequence:RefSeq:WP_064305258.1"; locus_tag "SERP_RS10980"; product "IS6-like element IS257 family transposase"; protein_id "WP_161384733.1"; transl_table "11" --> "cds-WP_010959142.1" and "cds-WP_161384733.1" occur twice! NC_002976.3 RefSeq gene 423814 424930 . + . gene_id "gene-SERP_RS02220"; gene_name "prfB"; gbkey "Gene"; gene "prfB"; gene_biotype "protein_coding"; locus_tag "SERP_RS02220"; old_locus_tag "SE0421%2CSERP0421" NC_002976.3 ProteinHomology exon 423814 424930 . + 0 transcript_id "cds-WP_010959142.1"; gene_id "gene-SERP_RS02220"; Dbxref "GenBank:WP_010959142.1"; Name "WP_010959142.1"; Note "programmed frameshift"; Ontology_term "GO:0006415,GO:0003747"; exception "ribosomal slippage"; gbkey "CDS"; gene "prfB"; go_function "translation release factor activity|0003747||IEA"; go_process "translational termination|0006415||IEA"; inference "COORDINATES: similar to AA sequence:RefSeq:WP_010959142.1"; locus_tag "SERP_RS02220"; product "peptide chain release factor 2"; protein_id "WP_010959142.1"; transl_table "11" NC_002976.3 RefSeq gene 2256196 2256869 . + . gene_id "gene-SERP_RS10980"; gene_name "SERP_RS10980"; gbkey "Gene"; gene_biotype "protein_coding"; locus_tag "SERP_RS10980"; old_locus_tag "SERP2219" NC_002976.3 ProteinHomology exon 2256196 2256869 . + 0 transcript_id "cds-WP_161384733.1"; gene_id "gene-SERP_RS10980"; Dbxref "GenBank:WP_161384733.1"; Name "WP_161384733.1"; Note "programmed frameshift"; Ontology_term "GO:0004803"; exception "ribosomal slippage"; gbkey "CDS"; go_function "transposase activity|0004803||IEA"; inference "COORDINATES: similar to AA sequence:RefSeq:WP_064305258.1"; locus_tag "SERP_RS10980"; product "IS6-like element IS257 family transposase"; protein_id "WP_161384733.1"; transl_table "11" --> "cds-WP_010959142.1" and "cds-WP_161384733.1" occur once! ln -s /home/jhuang/Tools/nf-core-rnaseq-3.12.0/ rnaseq (rnaseq) nextflow run rnaseq/main.nf --input samplesheet.csv --outdir results --fasta RP62A.fasta --gtf RP62A_m.gtf -profile test_full -resume --max_memory 100.GB --max_time 2400.h --save_reference --aligner star_salmon --skip_rseqc --skip_dupradar --skip_preseq --skip_biotype_qc --skip_deseq2_qc --min_mapped_reads 0 --gtf_extra_attributes gene #grep ">" genome.transcripts.fa | wc -l --> 2499 (2,529= CDSs (2,445) + RNA(84)) #-- Ben project: human + bacterium + plasmid -- .gff3 python3 gff_to_gtf.py CP009367.gff3 CP009367.gtf python3 modify_gtf.py CP009367.gtf CP009367_m.gtf sed -i -e 's/gene_id "rna-/gene_id "gene-/g' CP009367_m.gtf python3 gff_to_gtf.py NC_019234.gff3 NC_019234.gtf python3 modify_gtf.py NC_019234.gtf NC_019234_m.gtf sed -i -e 's/gene_id "rna-/gene_id "gene-/g' NC_019234_m.gtf python3 genbank_to_gtf.py 1585.gb 1585.gtf python3 modify_gtf.py 1585.gtf 1585_m.gtf #python3 correct_gtf.py python3 transform_gtf.py 1585_m.gtf 1585_m_.gtf sed -i -e 's/transcript_id \"/transcript_id \"tx-/g' 1585_m_.gtf sed -i -e 's/exon_id \"/exon_id \"exon-/g' 1585_m_.gtf #BUG: why 7052 >= expected 7014 #-- MANUALLY: gene positions out of boundary -- #Transcript cds-WP_011100764.1 is out of chromosome NC_019234.1's boundary! NC_019234.1 RefSeq gene 66549 67571 . + . gene_id "gene-HXG45_RS00005"; gene_name "repA"; gbkey "Gene"; gene "repA"; gene_biotype "protein_coding"; locus_tag "HXG45_RS00005"; old_locus_tag "D743_p54" NC_019234.1 RefSeq exon 66549 67571 . + 0 transcript_id "cds-WP_011100764.1"; gene_id "gene-HXG45_RS00005"; Dbxref "GenBank:WP_011100764.1"; Name "WP_011100764.1"; gbkey "CDS"; gene "repA"; inference "COORDINATES: similar to AA sequence:RefSeq:WP_011100764.1"; locus_tag "HXG45_RS00005"; product "plasmid replication initiator RepA"; protein_id "WP_011100764.1"; transl_table "11" #--> NC_019234.1 RefSeq gene 66549 66845 . + . gene_id "gene-HXG45_RS00005_1"; gene_name "repA"; gbkey "Gene"; gene "repA"; gene_biotype "protein_coding"; locus_tag "HXG45_RS00005"; old_locus_tag "D743_p54" NC_019234.1 RefSeq exon 66549 66845 . + 0 transcript_id "cds-WP_011100764.1_1"; gene_id "gene-HXG45_RS00005_1"; Dbxref "GenBank:WP_011100764.1"; Name "WP_011100764.1"; gbkey "CDS"; gene "repA"; inference "COORDINATES: similar to AA sequence:RefSeq:WP_011100764.1"; locus_tag "HXG45_RS00005"; product "plasmid replication initiator RepA"; protein_id "WP_011100764.1"; transl_table "11" NC_019234.1 RefSeq gene 1 726 . + . gene_id "gene-HXG45_RS00005_2"; gene_name "repA"; gbkey "Gene"; gene "repA"; gene_biotype "protein_coding"; locus_tag "HXG45_RS00005"; old_locus_tag "D743_p54" NC_019234.1 RefSeq exon 1 726 . + 0 transcript_id "cds-WP_011100764.1_2"; gene_id "gene-HXG45_RS00005_2"; Dbxref "GenBank:WP_011100764.1"; Name "WP_011100764.1"; gbkey "CDS"; gene "repA"; inference "COORDINATES: similar to AA sequence:RefSeq:WP_011100764.1"; locus_tag "HXG45_RS00005"; product "plasmid replication initiator RepA"; protein_id "WP_011100764.1"; transl_table "11" (rnaseq) nextflow run rnaseq/main.nf --input samplesheet.csv --outdir results_NC_019234 --fasta NC_019234.fasta --gtf NC_019234_m.gtf -profile test_full -resume --max_memory 100.GB --max_time 2400.h --save_reference --aligner star_salmon --skip_rseqc --skip_dupradar --skip_preseq --skip_biotype_qc --skip_deseq2_qc --min_mapped_reads 0 --gtf_extra_attributes gene nextflow run rnaseq/main.nf --input samplesheet.csv --outdir results_CP009367 --fasta CP009367.fasta --gtf CP009367_m.gtf -profile test_full -resume --max_memory 100.GB --max_time 2400.h --save_reference --aligner star_salmon --skip_rseqc --skip_dupradar --skip_preseq --skip_biotype_qc --skip_deseq2_qc --min_mapped_reads 0 --gtf_extra_attributes gene nextflow run rnaseq/main.nf --input samplesheet.csv --outdir results_GRCh38 --genome GRCh38 -profile test_full -resume --max_memory 100.GB --max_time 2400.h --save_align_intermeds --save_unaligned --aligner star_salmon --pseudo_aligner salmon nextflow run rnaseq/main.nf --input samplesheet.csv --outdir results_1585 --fasta 1585.fasta --gtf 1585_m_.gtf -profile test_full -resume --max_memory 100.GB --max_time 2400.h --save_reference --aligner star_salmon --skip_rseqc --skip_dupradar --skip_preseq --skip_biotype_qc --skip_deseq2_qc --min_mapped_reads 0 #TODO: look if gene-HXG45_RS00010 exist! # -- check the intermediate results -- #vim salmon.merged.gene_counts.tsv gene_id gene_name EX_15_min_A gene-SERP_RS00195 rpmH 298 gene-SERP_RS00200 rnpA 90 gene-SERP_RS00205 mnmE 1733 #vim salmon.merged.transcript_counts.tsv tx gene_id EX_15_min_A cds-WP_000240855.1 gene-SERP_RS00195 298 cds-WP_001832522.1 gene-SERP_RS00200 90 cds-WP_001831768.1 gene-SERP_RS00205 1733 -
gff_to_gtf.py (code)
import sys def gff3_to_gtf(gff3_file, gtf_file): with open(gff3_file, 'r') as gff3, open(gtf_file, 'w') as gtf: for line in gff3: if line.startswith('#'): continue # Skip header lines parts = line.strip().split('\t') if len(parts) != 9: continue # Skip invalid lines # Extract fields from GFF3 seqname, source, feature, start, end, score, strand, frame, attributes = parts # Convert attributes to GTF format attr_pairs = [f.strip() for f in attributes.split(';') if f.strip() != ''] attr_str = '; '.join([f'{key} "{value}"' for part in attr_pairs for key, value in [part.split('=')]]) # Write to GTF file gtf_line = f'{seqname}\t{source}\t{feature}\t{start}\t{end}\t{score}\t{strand}\t{frame}\t{attr_str};\n' gtf.write(gtf_line) if __name__ == "__main__": if len(sys.argv) != 3: print("Usage: python script.py <input.gff3> <output.gtf>") sys.exit(1) gff3_file = sys.argv[1] gtf_file = sys.argv[2] gff3_to_gtf(gff3_file, gtf_file) -
genbank_to_gtf.py (code)
import argparse from Bio import SeqIO def genbank_to_gtf(genbank_file, gtf_file): with open(genbank_file, "r") as input_handle, open(gtf_file, "w") as output_handle: for record in SeqIO.parse(input_handle, "genbank"): for feature in record.features: if feature.type == "gene" or feature.type == "CDS": start = feature.location.start.position + 1 end = feature.location.end.position strand = '+' if feature.location.strand == 1 else '-' attributes = [] gene_id = None if "gene_id" in feature.qualifiers: gene_id = feature.qualifiers["gene_id"][0] elif "gene" in feature.qualifiers: gene_id = feature.qualifiers["gene"][0] elif "locus_tag" in feature.qualifiers: gene_id = feature.qualifiers["locus_tag"][0] if gene_id is not None: attributes.append(f'gene_id "{gene_id}"') transcript_id = None if "locus_tag" in feature.qualifiers: transcript_id = feature.qualifiers["locus_tag"][0] attributes.append(f'transcript_id "{transcript_id}"') attribute_str = "; ".join(attributes) + ";" gtf_line = f"{record.id}\t.\t{feature.type}\t{start}\t{end}\t.\t{strand}\t.\t{attribute_str}\n" output_handle.write(gtf_line) def main(): parser = argparse.ArgumentParser(description="Convert GenBank file to GTF format.") parser.add_argument("genbank_file", help="Input GenBank file") parser.add_argument("gtf_file", help="Output GTF file") args = parser.parse_args() genbank_to_gtf(args.genbank_file, args.gtf_file) if __name__ == "__main__": main() -
modify_gtf.py (code)
“) sys.exit(1) input_file = sys.argv[1] output_file = sys.argv[2] modify_gtf(input_file, output_file)import sys def modify_gtf(input_file, output_file): with open(input_file, 'r') as infile, open(output_file, 'w') as outfile: for line in infile: if line.startswith('#'): outfile.write(line) # Copy comment lines continue parts = line.strip().split('\t') if len(parts) != 9: continue # Skip invalid lines record_type = parts[2] attributes = parts[8] # Change "Protein Homology" to "RefSeq" if parts[1] == "Protein Homology": parts[1] = "ProteinHomology" new_attributes = [] for attr in attributes.split(';'): if attr.strip(): key_value = attr.strip().split(' ', 1) # Split only on the first space if len(key_value) == 2: key, value = key_value if (record_type == 'gene' or record_type == 'pseudogene') and key == 'ID': key = 'gene_id' elif (record_type == 'gene' or record_type == 'pseudogene') and key == 'Name': key = 'gene_name' elif (record_type == 'CDS' or record_type == 'tRNA' or record_type == 'rRNA' or record_type == 'SRP_RNA') and key == 'ID': key = 'transcript_id' elif (record_type == 'CDS' or record_type == 'tRNA' or record_type == 'rRNA' or record_type == 'SRP_RNA') and key == 'Parent': key = 'gene_id' elif (record_type == 'exon') and key == 'ID': key = 'exon_id' elif (record_type == 'exon') and key == 'Parent': key = 'transcript_id' new_attributes.append(f'gene_id {value}') new_attributes.append(f'{key} {value}') else: new_attributes.append(attr.strip()) # Change record type from CDS to exon if record_type == "CDS": parts[2] = "exon" parts[8] = '; '.join(new_attributes) outfile.write('\t'.join(parts) + '\n') if __name__ == "__main__": if len(sys.argv) != 3: print("Usage: python modify_gtf.py -
correct_gtf.py (code)
input_file = '1585_m.gtf' # Replace with your input file path output_file = '1585_m_.gtf' # Replace with your desired output file path with open(input_file, 'r') as infile, open(output_file, 'w') as outfile: for line in infile: if line.strip() and not line.startswith('#'): # Skip empty or comment lines parts = line.strip().split('\t') if parts[2] == 'gene': # Check if the feature type is 'gene' attributes = parts[8].split(';') attributes = [attr.strip() for attr in attributes if 'transcript_id' not in attr] # Remove transcript_id for gene parts[8] = '; '.join(attributes) + ';' if attributes else '.' line = '\t'.join(parts) + '\n' outfile.write(line) print(f"Processed file saved as {output_file}") -
transform_gtf.py (code)
“) sys.exit(1) input_file = sys.argv[1] output_file = sys.argv[2] main(input_file, output_file)import sys def transform_data(input_data): output_data = [] for line in input_data: fields = line.split() entry_type = fields[2] attributes = ' '.join(fields[8:]) attributes_dict = dict(item.split(' ', 1) for item in attributes.split('; ')) gene_id = attributes_dict.get('gene_id').replace('"', '') transcript_id = attributes_dict.get('transcript_id').replace('"', '') if not gene_id.startswith("SF028"): gene_name = f'gene_name "{gene_id}"' gene_id = f'gene_id "{transcript_id}"' else: gene_name = '' if entry_type == "gene": gene_line = f"{fields[0]}\t{fields[1]}\tgene\t{fields[3]}\t{fields[4]}\t{fields[5]}\t{fields[6]}\t{fields[7]}\t{gene_id}; {gene_name}".strip() output_data.append(gene_line) transcript_line = f"{fields[0]}\t{fields[1]}\ttranscript\t{fields[3]}\t{fields[4]}\t{fields[5]}\t{fields[6]}\t{fields[7]}\t{gene_id}; transcript_id \"{transcript_id}\"" output_data.append(transcript_line) elif entry_type == "exon": exon_line = f"{fields[0]}\t{fields[1]}\texon\t{fields[3]}\t{fields[4]}\t{fields[5]}\t{fields[6]}\t{fields[7]}\t{gene_id}; transcript_id \"{transcript_id}\"; exon_id \"{transcript_id}\"" output_data.append(exon_line) return output_data def main(input_file, output_file): with open(input_file, 'r') as file: input_data = file.readlines() transformed_data = transform_data(input_data) with open(output_file, 'w') as file: for line in transformed_data: file.write(line + '\n') if __name__ == "__main__": if len(sys.argv) != 3: print("Usage: python script.py
RNA-seq data analysis on S. epidermidis 1585
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