def test_capillary_to_pairs(self): '''Check that capillary reads file converted to paired and unpaired''' tmp_prefix = 'tmp.cap_to_pairs' tasks.capillary_to_pairs( os.path.join(data_dir, 'sequences_test_cap_to_read_pairs.fa'), tmp_prefix) # sequences have been hashed, so could be in any order in # output files. So need to check contents of files are OK d_correct_paired = {} d_correct_unpaired = {} tasks.file_to_dict( os.path.join(data_dir, 'sequences_test_cap_to_read_pairs.fa.paired.gz'), d_correct_paired) tasks.file_to_dict( os.path.join(data_dir, 'sequences_test_cap_to_read_pairs.fa.unpaired.gz'), d_correct_unpaired) d_test_paired = {} d_test_unpaired = {} tasks.file_to_dict(tmp_prefix + '.paired.gz', d_test_paired) tasks.file_to_dict(tmp_prefix + '.unpaired.gz', d_test_unpaired) self.assertDictEqual(d_test_paired, d_correct_paired) self.assertDictEqual(d_test_unpaired, d_correct_unpaired) os.unlink(tmp_prefix + '.paired.gz') os.unlink(tmp_prefix + '.unpaired.gz')
def run(description): parser = argparse.ArgumentParser( description="Given a file of capillary reads, makes an interleaved file of read pairs (where more than read from same ligation, takes the longest read) and a file of unpaired reads. Replaces the .p1k/.q1k part of read names to denote fwd/rev reads with /1 and /2", usage="fastaq capillary_to_pairs <infile> <outfiles prefix>", ) parser.add_argument("infile", help="Name of input fasta/q file") parser.add_argument("outprefix", help="Prefix of output files", metavar="outfiles prefix") options = parser.parse_args() tasks.capillary_to_pairs(options.infile, options.outprefix)
def run(description): parser = argparse.ArgumentParser( description= 'Given a file of capillary reads, makes an interleaved file of read pairs (where more than read from same ligation, takes the longest read) and a file of unpaired reads. Replaces the .p1k/.q1k part of read names to denote fwd/rev reads with /1 and /2', usage='fastaq capillary_to_pairs <infile> <outfiles prefix>') parser.add_argument('infile', help='Name of input fasta/q file') parser.add_argument('outprefix', help='Prefix of output files', metavar='outfiles prefix') options = parser.parse_args() tasks.capillary_to_pairs(options.infile, options.outprefix)
def test_capillary_to_pairs(self): '''Check that capillary reads file converted to paired and unpaired''' tmp_prefix = 'tmp.cap_to_pairs' tasks.capillary_to_pairs(os.path.join(data_dir, 'sequences_test_cap_to_read_pairs.fa'), tmp_prefix) # sequences have been hashed, so could be in any order in # output files. So need to check contents of files are OK d_correct_paired = {} d_correct_unpaired = {} tasks.file_to_dict(os.path.join(data_dir, 'sequences_test_cap_to_read_pairs.fa.paired.gz'), d_correct_paired) tasks.file_to_dict(os.path.join(data_dir, 'sequences_test_cap_to_read_pairs.fa.unpaired.gz'), d_correct_unpaired) d_test_paired = {} d_test_unpaired = {} tasks.file_to_dict(tmp_prefix + '.paired.gz', d_test_paired) tasks.file_to_dict(tmp_prefix + '.unpaired.gz', d_test_unpaired) self.assertDictEqual(d_test_paired, d_correct_paired) self.assertDictEqual(d_test_unpaired, d_correct_unpaired) os.unlink(tmp_prefix + '.paired.gz') os.unlink(tmp_prefix + '.unpaired.gz')