def combine(fasta_files, output):
"""
Simply combines a given list of FASTA files together. Aside from gzip support,
this is just file concatenation.
"""
outputFile = gzOptOpen(output, mode = 'w')
for fasta in fasta_files:
fastaFile = gzOptOpen(fasta, mode = 'r')
outputFile.write(fastaFile.read())
fastaFile.close()
outputFile.close()
return output
def parse_to_generator(fasta_file, labelConverter = (lambda x: x),
filter_string = None):
'''
Parses a FASTA file and provides a generator of (header,sequence) tuples.
Can be used efficiently even on very large FASTA files.
Example usage:
for header,sequence in parse_fasta(file_name):
print header
process(sequence)
'''
fasta = gzOptOpen(fasta_file, mode = 'r')
header = ''
sequence = []
for line in fasta:
if line[0] == '>':
if header and sequence:
if (not filter_string) or filter_string not in header:
# It would be slightly more efficient to check for
# filter_string when the header is first encountered,
# and not aggregate the sequence in that case?
yield (labelConverter(header), ''.join(sequence))
sequence = []
header = line[1:].strip()
else:
sequence.append(line.strip())
yield (labelConverter(header), ''.join(sequence))
fasta.close()
def write_fasta(fasta, save_file, write_mode='w'):
'''
Creates a fasta file given a dictionary with prot: sequence or an iterator of
(prot, sequence) pairs.
This method adds ">" at the beginning of each header if there isn't one already.
The proteins will not be written in any particular order.
'''
fasta_file = gzOptOpen(save_file, mode = write_mode)
if type(fasta) == type(dict()):
for prot, seq in fasta.items():
if prot[0] == '>':
fasta_file.write("%s\n" % prot.strip())
else:
fasta_file.write(">%s\n" % prot.strip())
fasta_file.write("%s\n\n" % seq)
else:
for prot, seq in fasta:
if prot[0] == '>':
fasta_file.write("%s\n" % prot.strip())
else:
fasta_file.write(">%s\n" % prot.strip())
fasta_file.write("%s\n\n" % seq)
fasta_file.close()
def partial_database(fasta, output = None, search = '',
use_regex = False, include_matches = True):
"""
fasta -> A target FASTA-format file
output -> The output file (input file is overwritten if this is not specified.)
search -> Either a string or a list of strings.
use_regex -> If this is set to True, strings in search will be interpreted
as regular expressions. Otherwise, a search string "matches" if it is contained
by the header.
include_matches -> If this is True (the default,) FASTA entries are included in
the output if they match a search string; if False, FASTA entries are included
if they match NONE of the search strings.
Creates a new fasta database by copying each entry from the original, according
to the rules outlined above.
"""
if not output:
output = fasta + 'partial_database.fasta'
if isinstance(search, basestring):
search = [search]
if use_regex:
search = map(re.compile, search)
fastaGen = parse_to_generator(fasta)
out = gzOptOpen(output, mode = 'w')
if use_regex:
for header, sequence in fastaGen:
if any([x.search(header) for x in search]) == include_matches:
out.write('>' + header + '\n')
out.write(sequence + '\n')
else:
for header, sequence in fastaGen:
if any([x in header for x in search]) == include_matches:
out.write('>' + header + '\n')
out.write(sequence + '\n')
out.close()
return output
def parse_to_dict(fastaFile, labelConverter = (lambda x: x),
nonredundant_labels = False,
filter_string = None):
'''
Parses a FASTA file and provides a dict object from headers to corresponding
sequences. Takes longer to initialize than the generator, but random-access
lookup of sequences can be performed much faster.
'''
fasta = gzOptOpen(fastaFile, mode = 'r')
index = {}
nextKey = None
nextSeq = ''
for line in fasta:
if line[0] == ">":
if nextSeq:
if not filter_string or filter_string not in nextKey:
assert nextKey, "Missing or invalid identification line?"
index[labelConverter(nextKey.strip())] = nextSeq.replace('\n', '')
nextSeq = ''
nextKey = line[1:]
else:
nextSeq += line
if not nonredundant_labels:
label = labelConverter(nextKey.strip())
index[label] = nextSeq.replace('\n', '')
else:
seq = nextSeq.replace('\n', '')
keys = nextKey.split('\x01')
for key in keys:
index[key] = seq
fasta.close()
return index
def __init__(self, filename, line_length = 80):
self.file = gzOptOpen(filename, mode = 'w')
self.length = line_length
def iterate_spectra_simple(xmlfile):
parser = xml.iterparse(gzOptOpen(xmlfile))
for evt, obj in parser:
if obj.tag == ns('spectrum'):
yield readSpectrumXML(obj)
obj.clear()