def test_run(self): """secondOrFirstField""" x = 'FIRST SECOND' self.assertTrue(biofile.firstField(x)=='FIRST') self.assertTrue(biofile.secondField(x)=='SECOND') y = 'FIRST' self.assertTrue(biofile.secondOrFirstField(y)=='FIRST')
def secondField(h): f = None try: f = biofile.secondField(h) except: f = biofile.firstField(h) return f
def secondField(h): f = None try: f = biofile.secondField(h) except: f = biofile.firstField(h) return f
info_outs = util.OutStreams(sys.stdout)
outs = util.OutStreams()
params_outs = util.OutStreams([outs])
if not options.out_fname is None:
outf = open(os.path.expanduser(options.out_fname),'w')
outs.addStream(outf)
else:
outs.addStream(sys.stdout)
orf_dict = None
gene_orf_map = None
if not options.fasta_fname is None:
fname = os.path.expanduser(options.fasta_fname)
(headers, sequences) = biofile.readFASTA(fname)
orf_dict = dict(zip([biofile.firstField(h) for h in headers], sequences))
gene_orf_map = dict([(biofile.secondField(h), biofile.firstField(h)) for h in headers])
# Set the weight matrix
try:
matrix = motif.weight_matrices[options.pssm_name]
except KeyError as ke:
outs.write("# Unable to find weight matrix {}; try one of {}\n".format(options.pssm_name, ','.join(motif.weight_matrices.keys())))
window_size = len(matrix['A']) #len(matrix.values()[0])
# for associating windows with residues, center them
mid_window = int(math.floor(window_size/2.0))
# Write out parameters
params_outs.write("# Run started {}\n".format(util.timestamp()))
params_outs.write("# Command: {}\n".format(' '.join(sys.argv)))
params_outs.write("# Parameters:\n")