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# Copyright 2003 by Bartek Wilczynski. 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.
"""Parsing TRANSFAC files
"""
from Bio import motifs
from Bio.Alphabet import IUPAC
class Motif(motifs.Motif, dict):
"""A Bio.motifs.transfac.Motif stores the information in one TRANSFAC
motif. This class inherits from the Bio.motifs.Motif base class, as well
as from a Python dictionary. All motif information found by the parser
is stored as attributes of the base class when possible; see the
Bio.motifs.Motif base class for a description of these attributes. All
other information associated with the motif is stored as (key, value)
pairs in the dictionary, where the key is the two-letter fields as found
in the TRANSFAC file. References are an exception: These are stored in
the .references attribute.
These fields are commonly found in TRANSFAC files::
AC: Accession number
AS: Accession numbers, secondary
BA: Statistical basis
BF: Binding factors
BS: Factor binding sites underlying the matrix
[sequence; SITE accession number; start position for matrix
sequence; length of sequence used; number of gaps inserted;
strand orientation.]
CC: Comments
CO: Copyright notice
DE: Short factor description
DR: External databases
[database name: database accession number]
DT: Date created/updated
HC: Subfamilies
HP: Superfamilies
ID: Identifier
NA: Name of the binding factor
OC: Taxonomic classification
OS: Species/Taxon
OV: Older version
PV: Preferred version
TY: Type
XX: Empty line; these are not stored in the Record.
References are stored in an .references attribute, which is a list of
dictionaries with the following keys::
RN: Reference number
RA: Reference authors
RL: Reference data
RT: Reference title
RX: PubMed ID
For more information, see the TRANSFAC documentation.
"""
multiple_value_keys = set(['BF', 'OV', 'HP', 'BS', 'HC', 'DT', 'DR'])
# These keys can occur multiple times for one motif
reference_keys = set(['RX', 'RA', 'RT', 'RL'])
# These keys occur for references
class Record(list):
"""A Bio.motifs.transfac.Record stores the information in a TRANSFAC
matrix table. The record inherits from a list containing the individual
motifs.
Attributes:
o version: The version number, corresponding to the 'VV' field
in the TRANSFAC file;
"""
def __init__(self):
self.version = None
def __str__(self):
return write(self)
def read(handle):
"""record = read(handle)"""
annotations = {}
references = []
counts = None
record = Record()
for line in handle:
line = line.strip()
key, value = line[:2], line[4:]
if key == 'VV':
record.version = value
elif key in ('P0', 'PO'): # Old TRANSFAC files use PO instead of P0
counts = {}
assert value.split()[:4] == ['A', 'C', 'G', 'T']
length = 0
for c in "ACGT":
counts[c] = []
for line in handle:
key, value = line[:2], line[4:]
try:
i = int(key)
except ValueError:
break
length += 1
assert i == length
values = value.split()
for c, v in zip("ACGT", values):
counts[c].append(float(v))
if line == 'XX':
pass
elif key == 'RN':
index, separator, accession = value.partition(";")
assert index[0] == '['
assert index[-1] == ']'
index = int(index[1:-1])
assert len(references) == index - 1
reference = {key: value}
references.append(reference)
elif key == '//':
if counts is not None:
motif = Motif(alphabet=IUPAC.unambiguous_dna, counts=counts)
motif.update(annotations)
motif.references = references
record.append(motif)
annotations = {}
references = []
elif key in Motif.reference_keys:
reference[key] = value
elif key in Motif.multiple_value_keys:
if key not in annotations:
annotations[key] = []
annotations[key].append(value)
else:
annotations[key] = value
return record
def write(motifs):
"""Write the representation of a motif in TRANSFAC format
"""
blocks = []
try:
version = motifs.version
except AttributeError:
pass
else:
if version is not None:
block = """\
VV %s
XX
//
""" % version
blocks.append(block)
multiple_value_keys = Motif.multiple_value_keys
sections = (('AC', 'AS',), # Accession
('ID',), # ID
('DT', 'CO'), # Date, copyright
('NA',), # Name
('DE',), # Short factor description
('TY',), # Type
('OS', 'OC'), # Organism
('HP', 'HC'), # Superfamilies, subfamilies
('BF',), # Binding factors
('P0',), # Frequency matrix
('BA',), # Statistical basis
('BS',), # Factor binding sites
('CC',), # Comments
('DR',), # External databases
('OV', 'PV',), # Versions
)
for motif in motifs:
lines = []
for section in sections:
blank = False
for key in section:
if key == 'P0':
# Frequency matrix
length = motif.length
if length == 0:
continue
sequence = motif.degenerate_consensus
letters = sorted(motif.alphabet.letters)
line = " ".join(["P0"] + letters)
lines.append(line)
for i in range(length):
line = " ".join(
["%02.d"] +
["%6.20g" for l in letters]) + \
" %s"
line = line % tuple(
[i + 1] +
[motif.counts[l][i] for l in letters] +
[sequence[i]]
)
lines.append(line)
blank = True
else:
try:
value = motif.get(key)
except AttributeError:
value = None
if value is not None:
if key in multiple_value_keys:
for v in value:
line = "%s %s" % (key, v)
lines.append(line)
else:
line = "%s %s" % (key, value)
lines.append(line)
blank = True
if key == 'PV':
# References
try:
references = motif.references
except AttributeError:
pass
else:
keys = ("RN", "RX", "RA", "RT", "RL")
for reference in references:
for key in keys:
value = reference.get(key)
if value is None:
continue
line = "%s %s" % (key, value)
lines.append(line)
blank = True
if blank:
line = 'XX'
lines.append(line)
# Finished this motif; glue the lines together
line = "//"
lines.append(line)
block = "\n".join(lines) + "\n"
blocks.append(block)
# Finished all motifs; glue the blocks together
text = "".join(blocks)
return text
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