annotate tools/get_orfs_or_cdss/get_orfs_or_cdss.py @ 8:09a8be9247ca draft

v0.2.0 with GFF3 output

#!/usr/bin/env python
"""Find ORFs in a nucleotide sequence file.

For more details, see the help text and argument descriptions in the
accompanying get_orfs_or_cdss.xml file which defines a Galaxy interface.

This tool is a short Python script which requires Biopython. If you use
this tool in scientific work leading to a publication, please cite the
Biopython application note:

Cock et al 2009. Biopython: freely available Python tools for computational
molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3.
http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878.

This script is copyright 2011-2013 by Peter Cock, The James Hutton Institute
(formerly SCRI), Dundee, UK. All rights reserved.

See accompanying text file for licence details (MIT licence).
"""
import sys
import re
from optparse import OptionParser

usage = """Use as follows:

$ python get_orfs_or_cdss.py -i genome.fa -f fasta --table 11 -t CDS -e open -m all -s both --on cds.nuc.fa --op cds.protein.fa --ob cds.bed --og cds.gff3
"""

try:
    from Bio.Seq import Seq, reverse_complement, translate
    from Bio.SeqRecord import SeqRecord
    from Bio import SeqIO
    from Bio.Data import CodonTable
except ImportError:
    sys.exit("Missing Biopython library")


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')

options, args = parser.parse_args()

if options.version:
    print("v0.2.0")
    sys.exit(0)

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)):
    sys.exit("At least one output file is required")

try:
    table_obj = CodonTable.ambiguous_generic_by_id[options.table]
except KeyError:
    sys.exit("Unknown codon table %i" % options.table)

if options.seq_format.lower() == "sff":
    seq_format = "sff-trim"
elif options.seq_format.lower() == "fasta":
    seq_format = "fasta"
elif options.seq_format.lower().startswith("fastq"):
    seq_format = "fastq"
else:
    sys.exit("Unsupported file type %r" % options.seq_format)

print "Genetic code table %i" % options.table
print "Minimum length %i aa" % options.min_len
# print "Taking %s ORF(s) from %s strand(s)" % (mode, strand)

starts = sorted(table_obj.start_codons)
assert "NNN" not in starts
re_starts = re.compile("|".join(starts))

stops = sorted(table_obj.stop_codons)
assert "NNN" not in stops
re_stops = re.compile("|".join(stops))


def start_chop_and_trans(s, strict=True):
    """Returns offset, trimmed nuc, protein."""
    if strict:
        assert s[-3:] in stops, s
    assert len(s) % 3 == 0
    for match in re_starts.finditer(s):
        # Must check the start is in frame
        start = match.start()
        if start % 3 == 0:
            n = s[start:]
            assert len(n) % 3 == 0, "%s is len %i" % (n, len(n))
            if strict:
                t = translate(n, options.table, cds=True)
            else:
                # Use when missing stop codon,
                t = "M" + translate(n[3:], options.table, to_stop=True)
            return start, n, t
    return None, None, None


def break_up_frame(s):
    """Returns offset, nuc, protein."""
    start = 0
    for match in re_stops.finditer(s):
        index = match.start() + 3
        if index % 3 != 0:
            continue
        n = s[start:index]
        if options.ftype == "CDS":
            offset, n, t = start_chop_and_trans(n)
        else:
            offset = 0
            t = translate(n, options.table, to_stop=True)
        if n and len(t) >= options.min_len:
            yield start + offset, n, t
        start = index
    if options.ends == "open":
        # No stop codon, Biopython's strict CDS translate will fail
        n = s[start:]
        # Ensure we have whole codons
        # TODO - Try appending N instead?
        # TODO - Do the next four lines more elegantly
        if len(n) % 3:
            n = n[:-1]
        if len(n) % 3:
            n = n[:-1]
        if options.ftype == "CDS":
            offset, n, t = start_chop_and_trans(n, strict=False)
        else:
            offset = 0
            t = translate(n, options.table, to_stop=True)
        if n and len(t) >= options.min_len:
            yield start + offset, n, t


def get_all_peptides(nuc_seq):
    """Returns start, end, strand, nucleotides, protein.

    Co-ordinates are Python style zero-based.
    """
    # TODO - Refactor to use a generator function (in start order)
    # rather than making a list and sorting?
    answer = []
    full_len = len(nuc_seq)
    if options.strand != "reverse":
        for frame in range(0, 3):
            for offset, n, t in break_up_frame(nuc_seq[frame:]):
                start = frame + offset  # zero based
                answer.append((start, start + len(n), +1, n, t))
    if options.strand != "forward":
        rc = reverse_complement(nuc_seq)
        for frame in range(0, 3):
            for offset, n, t in break_up_frame(rc[frame:]):
                start = full_len - frame - offset  # zero based
                answer.append((start - len(n), start, -1, n, t))
    answer.sort()
    return answer


def get_top_peptides(nuc_seq):
    """Returns all peptides of max length."""
    values = list(get_all_peptides(nuc_seq))
    if not values:
        raise StopIteration
    max_len = max(len(x[-1]) for x in values)
    for x in values:
        if len(x[-1]) == max_len:
            yield x


def get_one_peptide(nuc_seq):
    """Returns first (left most) peptide with max length."""
    values = list(get_top_peptides(nuc_seq))
    if not values:
        raise StopIteration
    yield values[0]

if options.mode == "all":
    get_peptides = get_all_peptides
elif options.mode == "top":
    get_peptides = get_top_peptides
elif options.mode == "one":
    get_peptides = get_one_peptide

in_count = 0
out_count = 0
if options.out_nuc_file == "-":
    out_nuc = sys.stdout
elif options.out_nuc_file:
    out_nuc = open(options.out_nuc_file, "w")
else:
    out_nuc = None

if options.out_prot_file == "-":
    out_prot = sys.stdout
elif options.out_prot_file:
    out_prot = open(options.out_prot_file, "w")
else:
    out_prot = None

if options.out_bed_file == "-":
    out_bed = sys.stdout
elif options.out_bed_file:
    out_bed = open(options.out_bed_file, "w")
else:
    out_bed = None

if options.out_gff3_file == "-":
    out_gff3 = sys.stdout
elif options.out_gff3_file:
    out_gff3 = open(options.out_gff3_file, "w")
else:
    out_gff3 = None

if out_gff3:
    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())):
        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)
        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)
        if out_nuc:
            SeqIO.write(r, out_nuc, "fasta")
        if out_prot:
            SeqIO.write(t, out_prot, "fasta")
        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')
        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')
    in_count += 1
if out_nuc and out_nuc is not sys.stdout:
    out_nuc.close()
if out_prot and out_prot is not sys.stdout:
    out_prot.close()
if out_bed and out_bed is not sys.stdout:
    out_bed.close()

print "Found %i %ss in %i sequences" % (out_count, options.ftype, in_count)