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# Copyright 2012 by Wibowo Arindrarto. All rights reserved.
# 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.SearchIO parser for Exonerate vulgar output format."""
import re
from Bio._py3k import _as_bytes, _bytes_to_string
from Bio._py3k import zip
from ._base import _BaseExonerateParser, _BaseExonerateIndexer, _STRAND_MAP
__all__ = ['ExonerateVulgarParser', 'ExonerateVulgarIndexer']
# precompile regex
_RE_VULGAR = re.compile(r"""^vulgar:\s+
(\S+)\s+(\d+)\s+(\d+)\s+([\+-\.])\s+ # query: ID, start, end, strand
(\S+)\s+(\d+)\s+(\d+)\s+([\+-\.])\s+ # hit: ID, start, end, strand
(\d+)(\s+.*)$ # score, vulgar components
""", re.VERBOSE)
_RE_VCOMP = re.compile(r"""
\s+(\S+) # vulgar label (C/M: codon/match, G: gap, N: ner, 5/3: splice
# site, I: intron, S: split codon, F: frameshift)
\s+(\d+) # how many residues to advance in query sequence
\s+(\d+) # how many residues to advance in hit sequence
""", re.VERBOSE)
def parse_vulgar_comp(hsp, vulgar_comp):
"""Parses the vulgar components present in the hsp dictionary."""
# containers for block coordinates
qstarts, qends, hstarts, hends = \
[hsp['query_start']], [], [hsp['hit_start']], []
# containers for split codons
hsp['query_split_codons'], hsp['hit_split_codons'] = [], []
# containers for ner blocks
hsp['query_ner_ranges'], hsp['hit_ner_ranges'] = [], []
# sentinels for tracking query and hit positions
qpos, hpos = hsp['query_start'], hsp['hit_start']
# multiplier for determining sentinel movement
qmove = 1 if hsp['query_strand'] >= 0 else -1
hmove = 1 if hsp['hit_strand'] >= 0 else -1
vcomps = re.findall(_RE_VCOMP, vulgar_comp)
for idx, match in enumerate(vcomps):
label, qstep, hstep = match[0], int(match[1]), int(match[2])
# check for label, must be recognized
assert label in 'MCGF53INS', "Unexpected vulgar label: %r" % label
# match, codon, or gaps
if label in 'MCGS':
# if the previous comp is not an MCGS block, it's the
# start of a new block
if vcomps[idx - 1][0] not in 'MCGS':
qstarts.append(qpos)
hstarts.append(hpos)
# other labels
# store the values in the hsp dict as a tuple of (start, stop)
# we're not doing anything if the label is in '53IN', as these
# basically tell us what the inter-block coordinates are and
# inter-block coordinates are automatically calculated by
# and HSP property
if label == 'S':
# get start and stop from parsed values
qstart, hstart = qpos, hpos
qend = qstart + qstep * qmove
hend = hstart + hstep * hmove
# adjust the start-stop ranges
sqstart, sqend = min(qstart, qend), max(qstart, qend)
shstart, shend = min(hstart, hend), max(hstart, hend)
# split codons
# XXX: is it possible to have a frameshift that introduces
# a codon split? If so, this may need a different treatment..
hsp['query_split_codons'].append((sqstart, sqend))
hsp['hit_split_codons'].append((shstart, shend))
# move sentinels accordingly
qpos += qstep * qmove
hpos += hstep * hmove
# append to ends if the next comp is not an MCGS block or
# if it's the last comp
if idx == len(vcomps) - 1 or \
(label in 'MCGS' and vcomps[idx + 1][0] not in 'MCGS'):
qends.append(qpos)
hends.append(hpos)
# adjust coordinates
for seq_type in ('query_', 'hit_'):
strand = hsp[seq_type + 'strand']
# switch coordinates if strand is < 0
if strand < 0:
# switch the starts and ends
hsp[seq_type + 'start'], hsp[seq_type + 'end'] = \
hsp[seq_type + 'end'], hsp[seq_type + 'start']
if seq_type == 'query_':
qstarts, qends = qends, qstarts
else:
hstarts, hends = hends, hstarts
# set start and end ranges
hsp['query_ranges'] = list(zip(qstarts, qends))
hsp['hit_ranges'] = list(zip(hstarts, hends))
return hsp
class ExonerateVulgarParser(_BaseExonerateParser):
"""Parser for Exonerate vulgar strings."""
_ALN_MARK = 'vulgar'
def parse_alignment_block(self, header):
qresult = header['qresult']
hit = header['hit']
hsp = header['hsp']
self.read_until(lambda line: line.startswith('vulgar'))
vulgars = re.search(_RE_VULGAR, self.line)
# if the file has c4 alignments
# check if vulgar values match our previously parsed header values
if self.has_c4_alignment:
assert qresult['id'] == vulgars.group(1)
assert hsp['query_start'] == vulgars.group(2)
assert hsp['query_end'] == vulgars.group(3)
assert hsp['query_strand'] == vulgars.group(4)
assert hit['id'] == vulgars.group(5)
assert hsp['hit_start'] == vulgars.group(6)
assert hsp['hit_end'] == vulgars.group(7)
assert hsp['hit_strand'] == vulgars.group(8)
assert hsp['score'] == vulgars.group(9)
else:
qresult['id'] = vulgars.group(1)
hsp['query_start'] = vulgars.group(2)
hsp['query_end'] = vulgars.group(3)
hsp['query_strand'] = vulgars.group(4)
hit['id'] = vulgars.group(5)
hsp['hit_start'] = vulgars.group(6)
hsp['hit_end'] = vulgars.group(7)
hsp['hit_strand'] = vulgars.group(8)
hsp['score'] = vulgars.group(9)
# adjust strands
hsp['hit_strand'] = _STRAND_MAP[hsp['hit_strand']]
hsp['query_strand'] = _STRAND_MAP[hsp['query_strand']]
# cast coords into ints
hsp['query_start'] = int(hsp['query_start'])
hsp['query_end'] = int(hsp['query_end'])
hsp['hit_start'] = int(hsp['hit_start'])
hsp['hit_end'] = int(hsp['hit_end'])
# cast score into int
hsp['score'] = int(hsp['score'])
# store vulgar line and parse it
# rstrip to remove line endings (otherwise gives errors in Windows)
hsp['vulgar_comp'] = vulgars.group(10).rstrip()
hsp = parse_vulgar_comp(hsp, hsp['vulgar_comp'])
return {'qresult': qresult, 'hit': hit, 'hsp': hsp}
class ExonerateVulgarIndexer(_BaseExonerateIndexer):
"""Indexer class for exonerate vulgar lines."""
_parser = ExonerateVulgarParser
_query_mark = _as_bytes('vulgar')
def get_qresult_id(self, pos):
"""Returns the query ID of the nearest vulgar line."""
handle = self._handle
handle.seek(pos)
# get line, check if it's a vulgar line, and get query ID
line = handle.readline()
assert line.startswith(self._query_mark), line
id = re.search(_RE_VULGAR, _bytes_to_string(line))
return id.group(1)
def get_raw(self, offset):
"""Returns the raw bytes string of a QueryResult object from the given offset."""
handle = self._handle
handle.seek(offset)
qresult_key = None
qresult_raw = _as_bytes('')
while True:
line = handle.readline()
if not line:
break
elif line.startswith(self._query_mark):
cur_pos = handle.tell() - len(line)
if qresult_key is None:
qresult_key = self.get_qresult_id(cur_pos)
else:
curr_key = self.get_qresult_id(cur_pos)
if curr_key != qresult_key:
break
qresult_raw += line
return qresult_raw
# if not used as a module, run the doctest
if __name__ == "__main__":
from Bio._utils import run_doctest
run_doctest()
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