/usr/share/pyshared/Bio/SeqIO/FastaIO.py is in python-biopython 1.58-1.
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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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 | # Copyright 2006-2009 by Peter Cock. 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.
#
# This module is for reading and writing FASTA format files as SeqRecord
# objects. The code is partly inspired by earlier Biopython modules,
# Bio.Fasta.* and the now deprecated Bio.SeqIO.FASTA
"""Bio.SeqIO support for the "fasta" (aka FastA or Pearson) file format.
You are expected to use this module via the Bio.SeqIO functions."""
from Bio.Alphabet import single_letter_alphabet
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio.SeqIO.Interfaces import SequentialSequenceWriter
#This is a generator function!
def FastaIterator(handle, alphabet = single_letter_alphabet, title2ids = None):
"""Generator function to iterate over Fasta records (as SeqRecord objects).
handle - input file
alphabet - optional alphabet
title2ids - A function that, when given the title of the FASTA
file (without the beginning >), will return the id, name and
description (in that order) for the record as a tuple of strings.
If this is not given, then the entire title line will be used
as the description, and the first word as the id and name.
Note that use of title2ids matches that of Bio.Fasta.SequenceParser
but the defaults are slightly different.
"""
#Skip any text before the first record (e.g. blank lines, comments)
while True:
line = handle.readline()
if line == "" : return #Premature end of file, or just empty?
if line[0] == ">":
break
while True:
if line[0]!=">":
raise ValueError("Records in Fasta files should start with '>' character")
if title2ids:
id, name, descr = title2ids(line[1:].rstrip())
else:
descr = line[1:].rstrip()
id = descr.split()[0]
name = id
lines = []
line = handle.readline()
while True:
if not line : break
if line[0] == ">": break
#Remove trailing whitespace, and any internal spaces
#(and any embedded \r which are possible in mangled files
#when not opened in universal read lines mode)
lines.append(line.rstrip().replace(" ","").replace("\r",""))
line = handle.readline()
#Return the record and then continue...
yield SeqRecord(Seq("".join(lines), alphabet),
id = id, name = name, description = descr)
if not line : return #StopIteration
assert False, "Should not reach this line"
class FastaWriter(SequentialSequenceWriter):
"""Class to write Fasta format files."""
def __init__(self, handle, wrap=60, record2title=None):
"""Create a Fasta writer.
handle - Handle to an output file, e.g. as returned
by open(filename, "w")
wrap - Optional line length used to wrap sequence lines.
Defaults to wrapping the sequence at 60 characters
Use zero (or None) for no wrapping, giving a single
long line for the sequence.
record2title - Optional function to return the text to be
used for the title line of each record. By default the
a combination of the record.id and record.description
is used. If the record.description starts with the
record.id, then just the record.description is used.
You can either use:
myWriter = FastaWriter(open(filename,"w"))
writer.write_file(myRecords)
Or, follow the sequential file writer system, for example:
myWriter = FastaWriter(open(filename,"w"))
writer.write_header() # does nothing for Fasta files
...
Multiple calls to writer.write_record() and/or writer.write_records()
...
writer.write_footer() # does nothing for Fasta files
writer.close()
"""
SequentialSequenceWriter.__init__(self, handle)
#self.handle = handle
self.wrap = None
if wrap:
if wrap < 1:
raise ValueError
self.wrap = wrap
self.record2title = record2title
def write_record(self, record):
"""Write a single Fasta record to the file."""
assert self._header_written
assert not self._footer_written
self._record_written = True
if self.record2title:
title=self.clean(self.record2title(record))
else:
id = self.clean(record.id)
description = self.clean(record.description)
#if description[:len(id)]==id:
if description and description.split(None,1)[0]==id:
#The description includes the id at the start
title = description
elif description:
title = "%s %s" % (id, description)
else:
title = id
assert "\n" not in title
assert "\r" not in title
self.handle.write(">%s\n" % title)
data = self._get_seq_string(record) #Catches sequence being None
assert "\n" not in data
assert "\r" not in data
if self.wrap:
for i in range(0, len(data), self.wrap):
self.handle.write(data[i:i+self.wrap] + "\n")
else:
self.handle.write(data + "\n")
if __name__ == "__main__":
print "Running quick self test"
import os
from Bio.Alphabet import generic_protein, generic_nucleotide
#Download the files from here:
#ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/Nanoarchaeum_equitans
fna_filename = "NC_005213.fna"
faa_filename = "NC_005213.faa"
def genbank_name_function(text):
text, descr = text.split(None,1)
id = text.split("|")[3]
name = id.split(".",1)[0]
return id, name, descr
def print_record(record):
#See also bug 2057
#http://bugzilla.open-bio.org/show_bug.cgi?id=2057
print "ID:" + record.id
print "Name:" + record.name
print "Descr:" + record.description
print record.seq
for feature in record.annotations:
print '/%s=%s' % (feature, record.annotations[feature])
if record.dbxrefs:
print "Database cross references:"
for x in record.dbxrefs : print " - %s" % x
if os.path.isfile(fna_filename):
print "--------"
print "FastaIterator (single sequence)"
iterator = FastaIterator(open(fna_filename, "r"), alphabet=generic_nucleotide, title2ids=genbank_name_function)
count=0
for record in iterator:
count=count+1
print_record(record)
assert count == 1
print str(record.__class__)
if os.path.isfile(faa_filename):
print "--------"
print "FastaIterator (multiple sequences)"
iterator = FastaIterator(open(faa_filename, "r"), alphabet=generic_protein, title2ids=genbank_name_function)
count=0
for record in iterator:
count=count+1
print_record(record)
break
assert count>0
print str(record.__class__)
from cStringIO import StringIO
print "--------"
print "FastaIterator (empty input file)"
#Just to make sure no errors happen
iterator = FastaIterator(StringIO(""))
count = 0
for record in iterator:
count = count+1
assert count==0
print "Done"
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