/usr/lib/python2.7/dist-packages/cogent/parse/rdb.py is in python-cogent 1.9-9.
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 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 | #!/usr/bin/env python
"""Provides a parser for Rdb format files.
Data in from the European rRNA database in distribution format.
"""
from string import strip, maketrans
from cogent.parse.record_finder import DelimitedRecordFinder
from cogent.parse.record import RecordError
from cogent.core.sequence import Sequence, RnaSequence
from cogent.core.info import Info
from cogent.core.alphabet import AlphabetError
__author__ = "Sandra Smit"
__copyright__ = "Copyright 2007-2016, The Cogent Project"
__credits__ = ["Sandra Smit", "Rob Knight"]
__license__ = "GPL"
__version__ = "1.9"
__maintainer__ = "Sandra Smit"
__email__ = "sandra.smit@colorado.edu"
__status__ = "Development"
RdbFinder = DelimitedRecordFinder('//')
_field_names = {'acc':'rRNA',\
'src':'Source',\
'str':'Strain',\
'ta1':'Taxonomy1',\
'ta2':'Taxonomy2',\
'ta3':'Taxonomy3',\
'ta4':'Taxonomy4',\
'chg':'Changes',\
'rem':'Remarks',\
'aut':'Authors',\
'ttl':'Title',\
'jou':'Journal',\
'dat':'JournalYear',\
'vol':'JournalVolume',\
'pgs':'JournalPages',\
'mty':'Gene',\
'del':'Deletions',\
'seq':'Species'}
def InfoMaker(header_lines):
"""Returns an Info object constructed from the headerLines."""
info = Info()
for line in header_lines:
all = line.strip().split(':',1)
#strip out empty lines, lines without name, lines without colon
if not all[0] or len(all) != 2:
continue
try:
name = _field_names[all[0]]
except KeyError:
name = all[0]
value = all[1].strip()
info[name] = value
return info
def is_seq_label(x):
"Check if x looks like a sequence label line."""
return x.startswith('seq:')
def MinimalRdbParser(infile,strict=True):
"""Yield successive sequences as (headerLines, sequence) tuples.
If strict is True (default) raises RecordError when 'seq' label is missing
and if the record doesn't contain any sequences.
"""
for rec in RdbFinder(infile):
index = None
for line in rec:
if is_seq_label(line):
index = rec.index(line) + 1 #index of first sequence line
# if there is no line that starts with 'seq:' throw error or skip
if not index:
if strict:
raise RecordError, "Found Rdb record without seq label "\
+ "line: %s"%rec[0]
else:
continue
headerLines = rec[:index]
sequence = ''.join(rec[index:-1]) #strip off the delimiter
if sequence.endswith('*'):
sequence = sequence[:-1] #strip off '*'
#if there are no sequences throw error or skip
if not sequence:
if strict:
raise RecordError, "Found Rdb record without sequences: %s"\
%rec[0]
else:
continue
yield headerLines, sequence
def create_acceptable_sequence(sequence):
"""Return clean sequence as string, 'o' -> '?', sec. structure deleted
sequence: string of characters
SeqConstructor: constructor function for sequence creation
Will replace 'o' by '?'.
Will strip out secondary structure annotation.
"""
t = maketrans('o','?')
# strip out secondary structure annotation {}[]()^
return sequence.translate(t, "{}[]()^") #should be accepted by RnaSequence
def RdbParser(lines, SeqConstructor=RnaSequence, LabelConstructor=InfoMaker, \
strict=True):
"""Yield sequences from the Rdb record.
lines: a stream of Rdb records.
SeqConstructor: constructor function to create the final sequence object
LabelConstructor: function that creates Info dictionary from label lines
strict: boolean, when True, an error is raised when one occurs, when False,
the record is ignored when an error occurs.
This function returns proper RnaSequence objects when possible. It strips
out the secondary structure information, and it replaces 'o' by '?'. The
original sequence is stored in the info dictionary under 'OriginalSeq'.
If the original sequence is the desired end product, use MinimalRdbParser.
"""
for header, sequence in MinimalRdbParser(lines,strict=strict):
info = LabelConstructor(header)
clean_seq = create_acceptable_sequence(sequence)
# add original raw sequence to info
info['OriginalSeq'] = sequence
if strict:
#need to do error checking while constructing info and sequence
try:
yield SeqConstructor(clean_seq, Info = info)
except AlphabetError:
raise RecordError(\
"Sequence construction failed on record with reference %s."\
%(info.Refs))
else:
#not strict: just skip any record that raises an exception
try:
yield SeqConstructor(clean_seq, Info=info)
except:
continue
if __name__ == '__main__':
from sys import argv
filename = argv[1]
for sequence in RdbParser(open(filename)):
print sequence.Info.Species
print sequence
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