def main():
option_parser, opts, args =\
parse_command_line_parameters(**script_info)
fasta_fp = opts.fasta_fp
mapping_fp = opts.mapping_fp
output_dir = opts.output_dir
truncate_option = opts.truncate_option
primer_mismatches = int(opts.primer_mismatches)
create_dir(output_dir)
if truncate_option not in ['truncate_only', 'truncate_remove']:
raise ValueError('-z option must be either truncate_only or ' +
'truncate_remove')
try:
fasta_f = open(fasta_fp, "U")
fasta_f.close()
except IOError:
raise IOError("Unable to open fasta file, please check path/" +
"permissions.")
try:
mapping_f = open(fasta_fp, "U")
mapping_f.close()
except IOError:
raise IOError("Unable to open mapping file, please check path/" +
"permissions.")
truncate_reverse_primer(fasta_fp, mapping_fp, output_dir, truncate_option,
primer_mismatches)
def test_truncate_reverse_primer(self):
""" Overall module functionality test """
truncate_reverse_primer(self.fasta_fp, self.mapping_fp,
self.output_dir, truncate_option='truncate_only', primer_mismatches=2)
output_log_fp = open(join(self.output_dir,
"rev_primer_truncation.log"), "U")
actual_log_lines = [line.strip() for line in output_log_fp]
# Because filepaths used are recorded, need the tmp filepaths
expected_log_lines = ['Details for removal of reverse primers',
'Original fasta filepath: %s' % self.fasta_fp,
'Total seqs in fasta: 6',
'Mapping filepath: %s' % self.mapping_fp,
'Truncation option: truncate_only',
'Mismatches allowed: 2',
'Total seqs written: 5',
'SampleIDs not found: 0',
'Reverse primers not found: 0']
self.assertEqual(actual_log_lines, expected_log_lines)
expected_fna_fp = basename(self.fasta_fp.replace('.fna', '')) +\
"_rev_primer_truncated.fna"
fasta_fp = open(join(self.output_dir, expected_fna_fp), "U")
actual_fasta_output = [line.strip() for line in fasta_fp]
self.assertEqual(actual_fasta_output,
self.expected_truncation_default_settings.strip().split('\n'))
def main():
option_parser, opts, args =\
parse_command_line_parameters(**script_info)
fasta_fp = opts.fasta_fp
mapping_fp = opts.mapping_fp
output_dir = opts.output_dir
truncate_option = opts.truncate_option
primer_mismatches = int(opts.primer_mismatches)
create_dir(output_dir)
if truncate_option not in ['truncate_only', 'truncate_remove']:
raise ValueError('-z option must be either truncate_only or ' +
'truncate_remove')
try:
fasta_f = open(fasta_fp, "U")
fasta_f.close()
except IOError:
raise IOError("Unable to open fasta file, please check path/" +
"permissions.")
try:
mapping_f = open(fasta_fp, "U")
mapping_f.close()
except IOError:
raise IOError("Unable to open mapping file, please check path/" +
"permissions.")
truncate_reverse_primer(fasta_fp, mapping_fp, output_dir, truncate_option,
primer_mismatches)
def test_truncate_reverse_primer(self):
""" Overall module functionality test """
truncate_reverse_primer(self.fasta_fp, self.mapping_fp,
self.output_dir, truncate_option='truncate_only', primer_mismatches=2)
output_log_fp = open(join(self.output_dir,
"rev_primer_truncation.log"), "U")
actual_log_lines = [line.strip() for line in output_log_fp]
# Because filepaths used are recorded, need the tmp filepaths
expected_log_lines = ['Details for removal of reverse primers',
'Original fasta filepath: %s' % self.fasta_fp,
'Total seqs in fasta: 6',
'Mapping filepath: %s' % self.mapping_fp,
'Truncation option: truncate_only',
'Mismatches allowed: 2',
'Total seqs written: 5',
'SampleIDs not found: 0',
'Reverse primers not found: 0']
self.assertEqual(actual_log_lines, expected_log_lines)
expected_fna_fp = basename(self.fasta_fp.replace('.fna', '')) +\
"_rev_primer_truncated.fna"
fasta_fp = open(join(self.output_dir, expected_fna_fp), "U")
actual_fasta_output = [line.strip() for line in fasta_fp]
self.assertEqual(actual_fasta_output,
self.expected_truncation_default_settings.strip().split('\n'))