Python strip_illumina_suffix Examples

Example #1

File: strip_illumina_suffix.py Project: martinghunt/Fastaq

def run(description):
    parser = argparse.ArgumentParser(
        description = description,
        usage = 'fastaq strip_illumina_suffix <infile> <outfile>')
    parser.add_argument('infile', help='Name of input file')
    parser.add_argument('outfile', help='Name of output file')
    options = parser.parse_args()
    tasks.strip_illumina_suffix(options.infile, options.outfile)

Example #2

File: strip_illumina_suffix.py Project: jhh130910/code-test

def run(description):
    parser = argparse.ArgumentParser(
        description=description,
        usage='fastaq strip_illumina_suffix <infile> <outfile>')
    parser.add_argument('infile', help='Name of input file')
    parser.add_argument('outfile', help='Name of output file')
    options = parser.parse_args()
    tasks.strip_illumina_suffix(options.infile, options.outfile)

Example #3

 def test_strip_illumina_suffix(self):
     '''Check illumina suffixes stripped correctly off read names'''
     tmpfile = 'tmp.stripped.fa'
     tasks.strip_illumina_suffix(
         os.path.join(data_dir, 'sequences_test_strip_illumina_suffix.fq'),
         tmpfile)
     self.assertTrue(
         filecmp.cmp(
             os.path.join(
                 data_dir,
                 'sequences_test_strip_illumina_suffix.fq.stripped'),
             tmpfile))
     os.unlink(tmpfile)

Example #4

File: tasks_test.py Project: martinghunt/Fastaq

 def test_strip_illumina_suffix(self):
     '''Check illumina suffixes stripped correctly off read names'''
     tmpfile = 'tmp.stripped.fa'
     tasks.strip_illumina_suffix(os.path.join(data_dir, 'sequences_test_strip_illumina_suffix.fq'), tmpfile)
     self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'sequences_test_strip_illumina_suffix.fq.stripped'), tmpfile))
     os.unlink(tmpfile)