def __init__(self, filename, include_width_in_name=False,
target=None, motif_file='unknown_motif', genome=None,
*args, **kwargs):
fext = splitext(filename)[1].lstrip(extsep)
if fext == 'bed':
self.is_bed = True
self.is_xls = False
elif fext == 'xls':
self.is_bed = False
self.is_xls = True
else: raise InvalidFileException
motif_name = sub('\W', '_', abspath(motif_file))
target = target + sep + motif_name
super(PeaksFilenameParser, self).__init__(filename,
target = target,
*args, **kwargs)
self.fasta_file = None
for file_extension in ['fa', 'fasta', 'FA', 'FASTA']:
fasta_file = join(self.input_dir,
extsep.join([self.protoname, file_extension]))
debug("Trying", fasta_file)
if exists(fasta_file):
self.fasta_file = fasta_file
debug("Using", fasta_file)
break
if self.fasta_file is None:
warning('Could not find the FASTA file for %s',
self.input_file)
if genome is None:
raise Usage("Could not find the FASTA file for ", self.input_file,
" and no genome was specified")
else:
t = try_to_find_genome(genome)
if t is None:
raise Usage("Could not find the FASTA file for ", self.input_file,
" and failed to use %s" % genome)
else:
fasta_file = join(self.input_dir, '%s.fa' % self.protoname)
debug('Creating FASTA file %s for %s using %s',
fasta_file, self.input_file, genome)
input_fhd = open(self.input_file, 'rU')
fasta_fhd = open(fasta_file, 'w')
twobit_reader(t, input_stream=input_fhd,
write=fasta_fhd.write)
fasta_fhd.close()
self.fasta_file = fasta_file
def try_to_find_genome(genome):
"""
takes a string that may refer to a file or genome hosted on UCSC
and tries to open the 2bit file or download it if needed
"""
if exists(genome):
try:
t = TwoBitFile(genome)
return t
except TwoBitFileError:
warning('%s is not a valid .2bit file', genome)
return None
else:
try:
save_genome(genome)
try:
t = TwoBitFile("%s.2bit" % genome)
return t
except TwoBitFileError:
error('Downloaded %s.2bit but %s.2bit is not a valid .2bit file', genome)
except URLError:
warning('Download of %s.2bit failed', genome)
return None