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# Copyright 2008-2015 by Peter Cock. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Bio.SeqIO support for the "ig" (IntelliGenetics or MASE) file format.
This module is for reading and writing IntelliGenetics format files as
SeqRecord objects. This file format appears to be the same as the MASE
multiple sequence alignment format.
You are expected to use this module via the Bio.SeqIO functions.
"""
from __future__ import print_function
from Bio.Alphabet import single_letter_alphabet
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
def IgIterator(handle, alphabet=single_letter_alphabet):
"""Iterate over IntelliGenetics records (as SeqRecord objects).
handle - input file
alphabet - optional alphabet
The optional free format file header lines (which start with two
semi-colons) are ignored.
The free format commentary lines at the start of each record (which
start with a semi-colon) are recorded as a single string with embedded
new line characters in the SeqRecord's annotations dictionary under the
key 'comment'.
Examples
--------
>>> with open("IntelliGenetics/TAT_mase_nuc.txt") as handle:
... for record in IgIterator(handle):
... print("%s length %i" % (record.id, len(record)))
...
A_U455 length 303
B_HXB2R length 306
C_UG268A length 267
D_ELI length 309
F_BZ163A length 309
O_ANT70 length 342
O_MVP5180 length 348
CPZGAB length 309
CPZANT length 309
A_ROD length 390
B_EHOA length 420
D_MM251 length 390
STM_STM length 387
VER_AGM3 length 354
GRI_AGM677 length 264
SAB_SAB1C length 219
SYK_SYK length 330
"""
# Skip any file header text before the first record (;; lines)
while True:
line = handle.readline()
if not line:
break # Premature end of file, or just empty?
if not line.startswith(";;"):
break
while line:
# Now iterate over the records
if line[0] != ";":
raise ValueError(
"Records should start with ';' and not:\n%r" % line)
# Try and agree with SeqRecord convention from the GenBank parser,
# (and followed in the SwissProt parser) which stores the comments
# as a long string with newlines under annotations key 'comment'.
# Note some examples use "; ..." and others ";..."
comment_lines = []
while line.startswith(";"):
# TODO - Extract identifier from lines like "LOCUS\tB_SF2"?
comment_lines.append(line[1:].strip())
line = handle.readline()
title = line.rstrip()
seq_lines = []
while True:
line = handle.readline()
if not line:
break
if line[0] == ";":
break
# Remove trailing whitespace, and any internal spaces
seq_lines.append(line.rstrip().replace(" ", ""))
seq_str = "".join(seq_lines)
if seq_str.endswith("1"):
# Remove the optional terminator (digit one)
seq_str = seq_str[:-1]
if "1" in seq_str:
raise ValueError(
"Potential terminator digit one found within sequence.")
# Return the record and then continue...
record = SeqRecord(Seq(seq_str, alphabet),
id=title, name=title)
record.annotations['comment'] = "\n".join(comment_lines)
yield record
# We should be at the end of the file now
assert not line
if __name__ == "__main__":
from Bio._utils import run_doctest
run_doctest(verbose=0)
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