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#!/usr/bin/env python
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
#
"""
Bio.Wise contains modules for running and processing the output of
some of the models in the Wise2 package by Ewan Birney available from:
ftp://ftp.ebi.ac.uk/pub/software/unix/wise2/
http://www.ebi.ac.uk/Wise2/
Bio.Wise.psw is for protein Smith-Waterman alignments
Bio.Wise.dnal is for Smith-Waterman DNA alignments
"""
from __future__ import print_function
import os
import sys
import tempfile
from Bio import SeqIO
def _build_align_cmdline(cmdline, pair, output_filename, kbyte=None, force_type=None, quiet=False):
"""Helper function to build a command line string (PRIVATE).
>>> os.environ["WISE_KBYTE"]="300000"
>>> if os.isatty(sys.stderr.fileno()):
... c = _build_align_cmdline(["dnal"], ("seq1.fna", "seq2.fna"),
... "/tmp/output", kbyte=100000)
... assert c == 'dnal -kbyte 100000 seq1.fna seq2.fna > /tmp/output', c
... c = _build_align_cmdline(["psw"], ("seq1.faa", "seq2.faa"),
... "/tmp/output_aa")
... assert c == 'psw -kbyte 300000 seq1.faa seq2.faa > /tmp/output_aa', c
... else:
... c = _build_align_cmdline(["dnal"], ("seq1.fna", "seq2.fna"),
... "/tmp/output", kbyte=100000)
... assert c == 'dnal -kbyte 100000 -quiet seq1.fna seq2.fna > /tmp/output', c
... c = _build_align_cmdline(["psw"], ("seq1.faa", "seq2.faa"),
... "/tmp/output_aa")
... assert c == 'psw -kbyte 300000 -quiet seq1.faa seq2.faa > /tmp/output_aa', c
"""
cmdline = cmdline[:]
# XXX: force_type ignored
if kbyte is None:
try:
cmdline.extend(("-kbyte", os.environ["WISE_KBYTE"]))
except KeyError:
pass
else:
cmdline.extend(("-kbyte", str(kbyte)))
if not os.isatty(sys.stderr.fileno()):
cmdline.append("-quiet")
cmdline.extend(pair)
cmdline.extend((">", output_filename))
if quiet:
cmdline.extend(("2>", "/dev/null"))
cmdline_str = ' '.join(cmdline)
return cmdline_str
def align(cmdline, pair, kbyte=None, force_type=None, dry_run=False, quiet=False, debug=False):
"""
Returns a filehandle
"""
if not pair or len(pair) != 2:
raise ValueError("Expected pair of filename, not %s" % repr(pair))
output_file = tempfile.NamedTemporaryFile(mode='r')
input_files = tempfile.NamedTemporaryFile(mode="w"), tempfile.NamedTemporaryFile(mode="w")
if dry_run:
print(_build_align_cmdline(cmdline,
pair,
output_file.name,
kbyte,
force_type,
quiet))
return
for filename, input_file in zip(pair, input_files):
# Pipe the file through Biopython's Fasta parser/writer
# to make sure it conforms to the Fasta standard (in particular,
# Wise2 may choke on long lines in the Fasta file)
records = SeqIO.parse(open(filename), 'fasta')
SeqIO.write(records, input_file, 'fasta')
input_file.flush()
input_file_names = [input_file.name for input_file in input_files]
cmdline_str = _build_align_cmdline(cmdline,
input_file_names,
output_file.name,
kbyte,
force_type,
quiet)
if debug:
sys.stderr.write("%s\n" % cmdline_str)
status = os.system(cmdline_str) >> 8
if status > 1:
if kbyte != 0: # possible memory problem; could be None
sys.stderr.write("INFO trying again with the linear model\n")
return align(cmdline, pair, 0, force_type, dry_run, quiet, debug)
else:
raise OSError("%s returned %s" % (" ".join(cmdline), status))
return output_file
def all_pairs(singles):
"""
Generate pairs list for all-against-all alignments
>>> all_pairs(range(4))
[(0, 1), (0, 2), (0, 3), (1, 2), (1, 3), (2, 3)]
"""
pairs = []
singles = list(singles)
while singles:
suitor = singles.pop(0) # if sorted, stay sorted
pairs.extend((suitor, single) for single in singles)
return pairs
def main():
pass
def _test(*args, **keywds):
import doctest
doctest.testmod(sys.modules[__name__], *args, **keywds)
if __name__ == "__main__":
if __debug__:
_test()
main()
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