Mercurial > repos > peterjc > get_orfs_or_cdss
changeset 31:eaf1d40eceb4 draft default tip
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss commit d67596914a7bbe183851437eaafe8c7305877e5a-dirty
| author | peterjc |
|---|---|
| date | Fri, 22 Feb 2019 10:15:56 -0500 |
| parents | 147353248f95 |
| children | |
| files | tools/get_orfs_or_cdss/get_orfs_or_cdss.py tools/get_orfs_or_cdss/tool_dependencies.xml |
| diffstat | 2 files changed, 139 insertions(+), 49 deletions(-) [+] |
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--- a/tools/get_orfs_or_cdss/get_orfs_or_cdss.py Fri Nov 09 10:54:51 2018 -0500 +++ b/tools/get_orfs_or_cdss/get_orfs_or_cdss.py Fri Feb 22 10:15:56 2019 -0500 @@ -42,43 +42,100 @@ parser = OptionParser(usage=usage) -parser.add_option('-i', '--input', dest='input_file', - default=None, help='Input fasta file', - metavar='FILE') -parser.add_option('-f', '--format', dest='seq_format', - default='fasta', help='Sequence format (e.g. fasta, fastq, sff)') -parser.add_option('--table', dest='table', - default=1, help='NCBI Translation table', type='int') -parser.add_option('-t', '--ftype', dest='ftype', type='choice', - choices=['CDS', 'ORF'], default='ORF', - help='Find ORF or CDSs') -parser.add_option('-e', '--ends', dest='ends', type='choice', - choices=['open', 'closed'], default='closed', - help='Open or closed. Closed ensures start/stop codons are present') -parser.add_option('-m', '--mode', dest='mode', type='choice', - choices=['all', 'top', 'one'], default='all', - help='Output all ORFs/CDSs from sequence, all ORFs/CDSs ' - 'with max length, or first with maximum length') -parser.add_option('--min_len', dest='min_len', - default=10, help='Minimum ORF/CDS length', type='int') -parser.add_option('-s', '--strand', dest='strand', type='choice', - choices=['forward', 'reverse', 'both'], default='both', - help='Strand to search for features on') -parser.add_option('--on', dest='out_nuc_file', - default=None, help='Output nucleotide sequences, or - for STDOUT', - metavar='FILE') -parser.add_option('--op', dest='out_prot_file', - default=None, help='Output protein sequences, or - for STDOUT', - metavar='FILE') -parser.add_option('--ob', dest='out_bed_file', - default=None, help='Output BED file, or - for STDOUT', - metavar='FILE') -parser.add_option('--og', dest='out_gff3_file', - default=None, help='Output GFF3 file, or - for STDOUT', - metavar='FILE') -parser.add_option('-v', '--version', dest='version', - default=False, action='store_true', - help='Show version and quit') +parser.add_option( + "-i", + "--input", + dest="input_file", + default=None, + help="Input fasta file", + metavar="FILE", +) +parser.add_option( + "-f", + "--format", + dest="seq_format", + default="fasta", + help="Sequence format (e.g. fasta, fastq, sff)", +) +parser.add_option( + "--table", dest="table", default=1, help="NCBI Translation table", type="int" +) +parser.add_option( + "-t", + "--ftype", + dest="ftype", + type="choice", + choices=["CDS", "ORF"], + default="ORF", + help="Find ORF or CDSs", +) +parser.add_option( + "-e", + "--ends", + dest="ends", + type="choice", + choices=["open", "closed"], + default="closed", + help="Open or closed. Closed ensures start/stop codons are present", +) +parser.add_option( + "-m", + "--mode", + dest="mode", + type="choice", + choices=["all", "top", "one"], + default="all", + help="Output all ORFs/CDSs from sequence, all ORFs/CDSs " + "with max length, or first with maximum length", +) +parser.add_option( + "--min_len", dest="min_len", default=10, help="Minimum ORF/CDS length", type="int" +) +parser.add_option( + "-s", + "--strand", + dest="strand", + type="choice", + choices=["forward", "reverse", "both"], + default="both", + help="Strand to search for features on", +) +parser.add_option( + "--on", + dest="out_nuc_file", + default=None, + help="Output nucleotide sequences, or - for STDOUT", + metavar="FILE", +) +parser.add_option( + "--op", + dest="out_prot_file", + default=None, + help="Output protein sequences, or - for STDOUT", + metavar="FILE", +) +parser.add_option( + "--ob", + dest="out_bed_file", + default=None, + help="Output BED file, or - for STDOUT", + metavar="FILE", +) +parser.add_option( + "--og", + dest="out_gff3_file", + default=None, + help="Output GFF3 file, or - for STDOUT", + metavar="FILE", +) +parser.add_option( + "-v", + "--version", + dest="version", + default=False, + action="store_true", + help="Show version and quit", +) options, args = parser.parse_args() @@ -89,7 +146,14 @@ if not options.input_file: sys.exit("Input file is required") -if not any((options.out_nuc_file, options.out_prot_file, options.out_bed_file, options.out_gff3_file)): +if not any( + ( + options.out_nuc_file, + options.out_prot_file, + options.out_bed_file, + options.out_gff3_file, + ) +): sys.exit("At least one output file is required") try: @@ -255,17 +319,23 @@ out_gff3 = None if out_gff3: - out_gff3.write('##gff-version 3\n') + out_gff3.write("##gff-version 3\n") for record in SeqIO.parse(options.input_file, seq_format): - for i, (f_start, f_end, f_strand, n, t) in enumerate(get_peptides(str(record.seq).upper())): + for i, (f_start, f_end, f_strand, n, t) in enumerate( + get_peptides(str(record.seq).upper()) + ): out_count += 1 if f_strand == +1: loc = "%i..%i" % (f_start + 1, f_end) else: loc = "complement(%i..%i)" % (f_start + 1, f_end) - descr = "length %i aa, %i bp, from %s of %s" \ - % (len(t), len(n), loc, record.description) + descr = "length %i aa, %i bp, from %s of %s" % ( + len(t), + len(n), + loc, + record.description, + ) fid = record.id + "|%s%i" % (options.ftype, i + 1) r = SeqRecord(Seq(n), id=fid, name="", description=descr) t = SeqRecord(Seq(t), id=fid, name="", description=descr) @@ -273,12 +343,32 @@ SeqIO.write(r, out_nuc, "fasta") if out_prot: SeqIO.write(t, out_prot, "fasta") - nice_strand = '+' if f_strand == +1 else '-' + nice_strand = "+" if f_strand == +1 else "-" if out_bed: - out_bed.write('\t'.join(map(str, [record.id, f_start, f_end, fid, 0, nice_strand])) + '\n') + out_bed.write( + "\t".join(map(str, [record.id, f_start, f_end, fid, 0, nice_strand])) + + "\n" + ) if out_gff3: - out_gff3.write('\t'.join(map(str, [record.id, 'getOrfsOrCds', 'CDS', f_start + 1, f_end, '.', - nice_strand, 0, 'ID=%s%s' % (options.ftype, i + 1)])) + '\n') + out_gff3.write( + "\t".join( + map( + str, + [ + record.id, + "getOrfsOrCds", + "CDS", + f_start + 1, + f_end, + ".", + nice_strand, + 0, + "ID=%s%s" % (options.ftype, i + 1), + ], + ) + ) + + "\n" + ) in_count += 1 if out_nuc and out_nuc is not sys.stdout: out_nuc.close()
--- a/tools/get_orfs_or_cdss/tool_dependencies.xml Fri Nov 09 10:54:51 2018 -0500 +++ b/tools/get_orfs_or_cdss/tool_dependencies.xml Fri Feb 22 10:15:56 2019 -0500 @@ -1,6 +1,6 @@ -<?xml version="1.0"?> +<?xml version="1.0" ?> <tool_dependency> <package name="biopython" version="1.67"> - <repository changeset_revision="fc45a61abc2f" name="package_biopython_1_67" owner="biopython" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="fc45a61abc2f" name="package_biopython_1_67" owner="biopython" toolshed="https://testtoolshed.g2.bx.psu.edu"/> </package> -</tool_dependency> +</tool_dependency> \ No newline at end of file