def test_parallel_align_seqs_pynast(self):
""" parallel_align_seqs_pynast functions as expected """
params = {
'min_percent_id': 0.75,
'min_length': 15,
'template_fp': self.template_fp,
'pairwise_alignment_method': 'uclust',
'blast_db': None
}
app = ParallelAlignSeqsPyNast()
r = app(self.inseqs1_fp,
self.test_out,
params,
job_prefix='PTEST',
poll_directly=True,
suppress_submit_jobs=False)
# confirm that the total number of output sequences equals the total
# number of input sequences
num_input_seqs = count_seqs_in_filepaths([self.inseqs1_fp])[1]
num_template_seqs = count_seqs_in_filepaths([self.template_fp])[1]
num_output_seqs = \
count_seqs_in_filepaths(glob(join(self.test_out, '*fasta')))[1] \
- num_input_seqs - num_template_seqs
self.assertEqual(num_input_seqs, num_output_seqs)
def test_parallel_align_seqs_pynast(self):
""" parallel_align_seqs_pynast functions as expected """
params = {
'min_percent_id': 0.75,
'min_length': 15,
'template_fp': self.template_fp,
'pairwise_alignment_method': 'uclust',
'blast_db': None
}
app = ParallelAlignSeqsPyNast()
r = app(self.inseqs1_fp,
self.test_out,
params,
job_prefix='PTEST',
poll_directly=True,
suppress_submit_jobs=False)
# confirm that the total number of output sequences equals the total
# number of input sequences
num_input_seqs = count_seqs_in_filepaths([self.inseqs1_fp])[1]
num_template_seqs = count_seqs_in_filepaths([self.template_fp])[1]
num_output_seqs = \
count_seqs_in_filepaths(glob(join(self.test_out, '*fasta')))[1] \
- num_input_seqs - num_template_seqs
self.assertEqual(num_input_seqs, num_output_seqs)
def main():
option_parser, opts, args =\
parse_command_line_parameters(**script_info)
suppress_errors = opts.suppress_errors
input_fps = []
for e in opts.input_fps.split(','):
input_fps.extend(glob(e))
input_fps = set(input_fps)
if len(input_fps) == 0:
option_parser.error(\
"No filepaths match pattern(s) passed via -i: %s" % ''.join(opts.input_fps))
output_fp = opts.output_fp
count_data, total, inaccessible_filepaths = count_seqs_in_filepaths(
input_fps)
r = format_output(count_data, total, inaccessible_filepaths,
suppress_errors)
if opts.output_fp:
f = open(output_fp, 'w')
f.write(r)
f.close()
else:
print r
def main():
option_parser, opts, args =\
parse_command_line_parameters(**script_info)
suppress_errors = opts.suppress_errors
input_fps = opts.input_fps
output_fp = opts.output_fp
count_data, total, inaccessible_filepaths = count_seqs_in_filepaths(input_fps)
r = format_output(count_data, total, inaccessible_filepaths, suppress_errors)
if opts.output_fp:
f = open(output_fp,'w')
f.write(r)
f.close()
else:
print r
def main():
option_parser, opts, args =\
parse_command_line_parameters(**script_info)
suppress_errors = opts.suppress_errors
input_fps = []
for e in opts.input_fps.split(','):
input_fps.extend(glob(e))
input_fps = set(input_fps)
if len(input_fps) == 0:
option_parser.error(\
"No filepaths match pattern(s) passed via -i: %s" % ''.join(opts.input_fps))
output_fp = opts.output_fp
count_data, total, inaccessible_filepaths = count_seqs_in_filepaths(input_fps)
r = format_output(count_data, total, inaccessible_filepaths, suppress_errors)
if opts.output_fp:
f = open(output_fp,'w')
f.write(r)
f.close()
else:
print r