comparison pick_plasmids_containing_genes.py @ 2:2dd1a0ed7cce draft

"planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/pick_plasmids_containing_genes commit 9cb01222a76ffdf89fa8d7b69f32df7c2b1f860a-dirty"

1:ffa984b55de7

        reader = csv.DictReader(f, delimiter="\t", quotechar='"')
        for row in reader:
            screen.append(row)
    return screen

def get_fieldnames(input_file):
    with open(input_file) as f:
        reader = csv.DictReader(f, delimiter="\t", quotechar='"')
        fieldnames = reader.fieldnames
    return fieldnames

def main(args):
    # create output directory
    try:
        os.mkdir(args.outdir)
    except OSError as exc:

    # parse screening file
    screen = parse_screen_file(args.abricate_report_screening_file)
    contigs_with_genes_of_interest = []
    # parse all abricate reports and determine which ones contain genes of interest
    print("\t".join(["file", "gene_detected"]))
    for abricate_report in args.abricate_reports:
        gene_of_interest_detected = False
        with open(abricate_report, 'r') as f:
            abricate_report_reader = csv.DictReader(f, delimiter="\t", quotechar='"')
            for gene in screen:
                for abricate_report_row in abricate_report_reader:
                    if re.search(gene['regex'], abricate_report_row['GENE']):
                        gene_of_interest_detected = True
                        contigs_with_genes_of_interest.append(abricate_report_row['SEQUENCE'])
                f.seek(0)
                next(abricate_report_reader)
        print("\t".join([abricate_report, str(gene_of_interest_detected)]))

    # copy the corresponding plasmid fasta files into outdir        
    for contig in contigs_with_genes_of_interest:
        for plasmid in args.plasmids:
            copy_plasmid = False

                shutil.copy2(plasmid, args.outdir)

if __name__ == '__main__':
    parser = argparse.ArgumentParser()
    parser.add_argument("--plasmids", nargs='+', help="plasmid assemblies (fasta)")
    parser.add_argument("--abricate_reports", nargs='+', help="abricate reports (tsv)")
    parser.add_argument("--abricate_report_screening_file", help="")
    parser.add_argument("--outdir", dest="outdir", default=".", help="Output directory")
    args = parser.parse_args()
    main(args)

2:2dd1a0ed7cce

        reader = csv.DictReader(f, delimiter="\t", quotechar='"')
        for row in reader:
            screen.append(row)
    return screen

def main(args):
    # create output directory
    try:
        os.mkdir(args.outdir)
    except OSError as exc:

    # parse screening file
    screen = parse_screen_file(args.abricate_report_screening_file)
    contigs_with_genes_of_interest = []
    # parse all abricate reports and determine which ones contain genes of interest
    print("\t".join(["file", "gene_detected"]))

    with open(args.concatenated_abricate_reports, 'r') as f:
        abricate_report_reader = csv.DictReader(f, delimiter="\t", quotechar='"')
        for gene in screen:
            for abricate_report_row in abricate_report_reader:
                if abricate_report_row['#FILE'] == '#FILE':
                    continue
                if re.search(gene['regex'], abricate_report_row['GENE']):
                    contigs_with_genes_of_interest.append(abricate_report_row['SEQUENCE'])
            f.seek(0)
            next(abricate_report_reader)

    # copy the corresponding plasmid fasta files into outdir        
    for contig in contigs_with_genes_of_interest:
        for plasmid in args.plasmids:
            copy_plasmid = False

                shutil.copy2(plasmid, args.outdir)

if __name__ == '__main__':
    parser = argparse.ArgumentParser()
    parser.add_argument("--plasmids", nargs='+', help="plasmid assemblies (fasta)")
    parser.add_argument("--concatenated_abricate_reports", help="abricate reports (tsv)")
    parser.add_argument("--abricate_report_screening_file", help="")
    parser.add_argument("--outdir", dest="outdir", default=".", help="Output directory")
    args = parser.parse_args()
    main(args)