/usr/share/pyshared/cogent/parse/clustal.py is in python-cogent 1.5.3-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 | #/usr/bin/env python
"""Parsers for Clustal and related formats (e.g. MUSCLE).
Implementation Notes:
Currently, does not check whether sequences are the same length and are in
order. Skips any line that starts with a blank.
ClustalParser preserves the order of the sequences from the original file.
However, it does use a dict as an intermediate, so two sequences can't have
the same label. This is probably OK since Clustal will refuse to run on a
FASTA file in which two sequences have the same label, but could potentially
cause trouble with manually edited files (all the segments of the conflicting
sequences would be interleaved, possibly in an unpredictable way).
If the lines have trailing numbers (i.e. Clustal was run with -LINENOS=ON),
silently deletes them. Does not check that the numbers actually correspond to
the number of chars in the sequence printed so far.
"""
from cogent.parse.record import RecordError, DelimitedSplitter
from string import strip
__author__ = "Rob Knight"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__credits__ = ["Rob Knight", "Sandra Smit", "Gavin Huttley",
"Peter Maxwell"]
__license__ = "GPL"
__version__ = "1.5.3"
__maintainer__ = "Rob Knight"
__email__ = "rob@spot.colorado.edu"
__status__ = "Development"
def LabelLineParser(record, splitter, strict=True):
"""Returns dict mapping list of data to labels, plus list with field order.
Field order contains labels in order encountered in file.
NOTE: doesn't care if lines are out of order in different blocks. This
should never happen anyway, but it's possible that this behavior should
be changed to tighten up validation.
"""
labels = []
result = {}
for line in record:
try:
key, val = splitter(line.rstrip())
except:
if strict:
raise RecordError, \
"Failed to extract key and value from line %s" % line
else:
continue #just skip the line if not strict
if key in result:
result[key].append(val)
else:
result[key] = [val]
labels.append(key)
return result, labels
def is_clustal_seq_line(line):
"""Returns True if line starts with a non-blank character but not 'CLUSTAL'.
Useful for filtering other lines out of the file.
"""
return line and (not line[0].isspace()) and\
(not line.startswith('CLUSTAL')) and (not line.startswith('MUSCLE'))
last_space = DelimitedSplitter(None, -1)
def delete_trailing_number(line):
"""Deletes trailing number from a line.
WARNING: does not preserve internal whitespace when a number is removed!
(converts each whitespace run to a single space). Returns the original
line if it didn't end in a number.
"""
pieces = line.split()
try:
int(pieces[-1])
return ' '.join(pieces[:-1])
except ValueError: #no trailing numbers
return line
def MinimalClustalParser(record, strict=True):
"""Returns (data, label_order) tuple.
Data is dict of label -> sequence (pieces not joined).
"""
return LabelLineParser(map(delete_trailing_number, \
filter(is_clustal_seq_line, record)), last_space, strict)
def ClustalParser(record, strict=True):
seqs, labels = MinimalClustalParser(record, strict)
for l in labels:
yield l, ''.join(seqs[l])
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