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# Copyright 2008 by Bartek Wilczynski.
# Adapted from Bio.MEME.Parser by Jason A. Hackney. 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.
from Bio.Alphabet import IUPAC
from Bio.Motif.Parsers.MEME import MEMEMotif
class Record(object):
"""The class for holding the results from a MAST run.
A MAST.Record holds data about matches between motifs and sequences.
The motifs held by the Record are objects of the class MEMEMotif.
Methods:
get_motif_by_name (motif_name): returns a MEMEMotif with the given
name.
"""
def __init__ (self):
self.sequences = []
self.version = ""
self.database = ""
self.diagrams = {}
self.alphabet = None
self.motifs = []
def get_motif_by_name (self, name):
for m in self.motifs:
if m.name == name:
return m
def read(handle):
"""read(handle)"""
record = Record()
__read_version(record, handle)
__read_database_and_motifs(record, handle)
__read_section_i(record, handle)
__read_section_ii(record, handle)
__read_section_iii(record, handle)
return record
# Everything below is private
def __read_version(record, handle):
for line in handle:
if "MAST version" in line:
break
else:
raise ValueError("Improper input file. Does not begin with a line with 'MAST version'")
record.version = line.strip().split()[2]
def __read_database_and_motifs(record, handle):
for line in handle:
if line.startswith('DATABASE AND MOTIFS'):
break
line = next(handle)
if not line.startswith('****'):
raise ValueError("Line does not start with '****':\n%s" % line)
line = next(handle)
if not 'DATABASE' in line:
raise ValueError("Line does not contain 'DATABASE':\n%s" % line)
words = line.strip().split()
record.database = words[1]
if words[2] == '(nucleotide)':
record.alphabet = IUPAC.unambiguous_dna
elif words[2] == '(peptide)':
record.alphabet = IUPAC.protein
for line in handle:
if 'MOTIF WIDTH' in line:
break
line = next(handle)
if not '----' in line:
raise ValueError("Line does not contain '----':\n%s" % line)
for line in handle:
if not line.strip():
break
words = line.strip().split()
motif = MEMEMotif()
motif.alphabet = record.alphabet
motif.name = words[0]
motif.length = int(words[1])
# motif.add_instance(words[2])
record.motifs.append(motif)
def __read_section_i(record, handle):
for line in handle:
if line.startswith('SECTION I:'):
break
for line in handle:
if line.startswith('SEQUENCE NAME'):
break
line = next(handle)
if not line.startswith('---'):
raise ValueError("Line does not start with '---':\n%s" % line)
for line in handle:
if not line.strip():
break
else:
sequence, description_evalue_length = line.split(None, 1)
record.sequences.append(sequence)
line = next(handle)
if not line.startswith('****'):
raise ValueError("Line does not start with '****':\n%s" % line)
def __read_section_ii(record, handle):
for line in handle:
if line.startswith('SECTION II:'):
break
for line in handle:
if line.startswith('SEQUENCE NAME'):
break
line = next(handle)
if not line.startswith('---'):
raise ValueError("Line does not start with '---':\n%s" % line)
for line in handle:
if not line.strip():
break
elif line.startswith(" "):
diagram = line.strip()
record.diagrams[sequence] += diagram
else:
sequence, pvalue, diagram = line.split()
record.diagrams[sequence] = diagram
line = next(handle)
if not line.startswith('****'):
raise ValueError("Line does not start with '****':\n%s" % line)
def __read_section_iii(record, handle):
for line in handle:
if line.startswith('SECTION III:'):
break
for line in handle:
if line.startswith('****'):
break
for line in handle:
if line.startswith('*****'):
break
for line in handle:
if line.strip():
break
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