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# Copyright 2004 by James Casbon. 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.
"""Code to deal with COMPASS output, a program for profile/profile comparison.
Compass is described in:
Sadreyev R, Grishin N. COMPASS: a tool for comparison of multiple protein
alignments with assessment of statistical significance. J Mol Biol. 2003 Feb
7;326(1):317-36.
Tested with COMPASS 1.24.
"""
import re
def read(handle):
"""Reads a COMPASS file containing one COMPASS record."""
record = None
try:
line = next(handle)
record = Record()
__read_names(record, line)
line = next(handle)
__read_threshold(record, line)
line = next(handle)
__read_lengths(record, line)
line = next(handle)
__read_profilewidth(record, line)
line = next(handle)
__read_scores(record, line)
except StopIteration:
if not record:
raise ValueError("No record found in handle")
else:
raise ValueError("Unexpected end of stream.")
for line in handle:
if not line.strip(): # skip empty lines
continue
__read_query_alignment(record, line)
try:
line = next(handle)
__read_positive_alignment(record, line)
line = next(handle)
__read_hit_alignment(record, line)
except StopIteration:
raise ValueError("Unexpected end of stream.")
return record
def parse(handle):
"""Iterates over records in a COMPASS file."""
record = None
try:
line = next(handle)
except StopIteration:
return
while True:
try:
record = Record()
__read_names(record, line)
line = next(handle)
__read_threshold(record, line)
line = next(handle)
__read_lengths(record, line)
line = next(handle)
__read_profilewidth(record, line)
line = next(handle)
__read_scores(record, line)
except StopIteration:
raise ValueError("Unexpected end of stream.")
for line in handle:
if not line.strip():
continue
if "Ali1:" in line:
yield record
break
__read_query_alignment(record, line)
try:
line = next(handle)
__read_positive_alignment(record, line)
line = next(handle)
__read_hit_alignment(record, line)
except StopIteration:
raise ValueError("Unexpected end of stream.")
else:
yield record
break
class Record(object):
"""Hold information from one compass hit.
Ali1 is the query, Ali2 the hit.
"""
def __init__(self):
self.query = ''
self.hit = ''
self.gap_threshold = 0
self.query_length = 0
self.query_filtered_length = 0
self.query_nseqs = 0
self.query_neffseqs = 0
self.hit_length = 0
self.hit_filtered_length = 0
self.hit_nseqs = 0
self.hit_neffseqs = 0
self.sw_score = 0
self.evalue = -1
self.query_start = -1
self.hit_start = -1
self.query_aln = ''
self.hit_aln = ''
self.positives = ''
def query_coverage(self):
"""Return the length of the query covered in the alignment."""
s = self.query_aln.replace("=", "")
return len(s)
def hit_coverage(self):
"""Return the length of the hit covered in the alignment."""
s = self.hit_aln.replace("=", "")
return len(s)
# Everything below is private
__regex = {"names": re.compile("Ali1:\s+(\S+)\s+Ali2:\s+(\S+)\s+"),
"threshold": re.compile("Threshold of effective gap content in columns: (\S+)"),
"lengths": re.compile("length1=(\S+)\s+filtered_length1=(\S+)\s+length2=(\S+)\s+filtered_length2=(\S+)"),
"profilewidth": re.compile("Nseqs1=(\S+)\s+Neff1=(\S+)\s+Nseqs2=(\S+)\s+Neff2=(\S+)"),
"scores": re.compile("Smith-Waterman score = (\S+)\s+Evalue = (\S+)"),
"start": re.compile("(\d+)"),
"align": re.compile("^.{15}(\S+)"),
"positive_alignment": re.compile("^.{15}(.+)"),
}
def __read_names(record, line):
# Ali1: 60456.blo.gz.aln Ali2: allscop//14984.blo.gz.aln
# ------query----- -------hit-------------
if "Ali1:" not in line:
raise ValueError("Line does not contain 'Ali1:':\n%s" % line)
m = __regex["names"].search(line)
record.query = m.group(1)
record.hit = m.group(2)
def __read_threshold(record, line):
if not line.startswith("Threshold"):
raise ValueError("Line does not start with 'Threshold':\n%s" % line)
m = __regex["threshold"].search(line)
record.gap_threshold = float(m.group(1))
def __read_lengths(record, line):
if not line.startswith("length1="):
raise ValueError("Line does not start with 'length1=':\n%s" % line)
m = __regex["lengths"].search(line)
record.query_length = int(m.group(1))
record.query_filtered_length = float(m.group(2))
record.hit_length = int(m.group(3))
record.hit_filtered_length = float(m.group(4))
def __read_profilewidth(record, line):
if "Nseqs1" not in line:
raise ValueError("Line does not contain 'Nseqs1':\n%s" % line)
m = __regex["profilewidth"].search(line)
record.query_nseqs = int(m.group(1))
record.query_neffseqs = float(m.group(2))
record.hit_nseqs = int(m.group(3))
record.hit_neffseqs = float(m.group(4))
def __read_scores(record, line):
if not line.startswith("Smith-Waterman"):
raise ValueError("Line does not start with 'Smith-Waterman':\n%s" % line)
m = __regex["scores"].search(line)
if m:
record.sw_score = int(m.group(1))
record.evalue = float(m.group(2))
else:
record.sw_score = 0
record.evalue = -1.0
def __read_query_alignment(record, line):
m = __regex["start"].search(line)
if m:
record.query_start = int(m.group(1))
m = __regex["align"].match(line)
assert m is not None, "invalid match"
record.query_aln += m.group(1)
def __read_positive_alignment(record, line):
m = __regex["positive_alignment"].match(line)
assert m is not None, "invalid match"
record.positives += m.group(1)
def __read_hit_alignment(record, line):
m = __regex["start"].search(line)
if m:
record.hit_start = int(m.group(1))
m = __regex["align"].match(line)
assert m is not None, "invalid match"
record.hit_aln += m.group(1)
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