def testFASTQVersion(self):
# version 1.4 tests
result = fastq.fastq_version(self.ver14_pe_good)
self.assertEqual(result, fastq.ILLUMINA_V14)
result = fastq.fastq_version(self.ver14_pe_bad)
self.assertEqual(result, fastq.ILLUMINA_V14)
result = fastq.fastq_version(self.ver14_pe_mixed)
self.assertEqual(result, fastq.ILLUMINA_V14)
result = fastq.fastq_version(self.ver14_pe_unordered)
self.assertEqual(result, fastq.ILLUMINA_V14)
result = fastq.fastq_version(self.ver14_single)
self.assertEqual(result, fastq.ILLUMINA_V14)
self.assertRaises(ValueError,
fastq.fastq_version,
self.ver14_bad_metadata)
# version 1.8 tests
result = fastq.fastq_version(self.ver18_pe_good)
self.assertEqual(result, fastq.ILLUMINA_V18)
result = fastq.fastq_version(self.ver18_pe_bad)
self.assertEqual(result, fastq.ILLUMINA_V18)
result = fastq.fastq_version(self.ver18_pe_mixed)
self.assertEqual(result, fastq.ILLUMINA_V18)
result = fastq.fastq_version(self.ver18_pe_unordered)
self.assertEqual(result, fastq.ILLUMINA_V18)
result = fastq.fastq_version(self.ver18_single)
self.assertEqual(result, fastq.ILLUMINA_V18)
self.assertRaises(ValueError,
fastq.fastq_version,
self.ver18_bad_metadata)
def testFASTQVersion(self):
# version 1.4 tests
result = fastq.fastq_version(self.ver14_pe_good)
self.assertEqual(result, fastq.ILLUMINA_V14)
result = fastq.fastq_version(self.ver14_pe_bad)
self.assertEqual(result, fastq.ILLUMINA_V14)
result = fastq.fastq_version(self.ver14_pe_mixed)
self.assertEqual(result, fastq.ILLUMINA_V14)
result = fastq.fastq_version(self.ver14_pe_unordered)
self.assertEqual(result, fastq.ILLUMINA_V14)
result = fastq.fastq_version(self.ver14_single)
self.assertEqual(result, fastq.ILLUMINA_V14)
self.assertRaises(ValueError, fastq.fastq_version,
self.ver14_bad_metadata)
# version 1.8 tests
result = fastq.fastq_version(self.ver18_pe_good)
self.assertEqual(result, fastq.ILLUMINA_V18)
result = fastq.fastq_version(self.ver18_pe_bad)
self.assertEqual(result, fastq.ILLUMINA_V18)
result = fastq.fastq_version(self.ver18_pe_mixed)
self.assertEqual(result, fastq.ILLUMINA_V18)
result = fastq.fastq_version(self.ver18_pe_unordered)
self.assertEqual(result, fastq.ILLUMINA_V18)
result = fastq.fastq_version(self.ver18_single)
self.assertEqual(result, fastq.ILLUMINA_V18)
self.assertRaises(ValueError, fastq.fastq_version,
self.ver18_bad_metadata)
def main():
parse_options(sys.argv[1:])
fastq_ver = fastq.fastq_version(args[0])
fastq_readlen = fastq.fastq_readlen(args[0])
callback_func = fastq.fastq_ver_to_callback(fastq_ver)
phred_offset = fastq.fastq_ver_to_phred(fastq_ver)
if not os.path.exists(options.output_dir):
os.mkdir(options.output_dir)
stripped_fname = ".".join(os.path.basename(args[0]).split(".")[:-1])
if options.paired_end:
left_out = os.path.join(options.output_dir,
stripped_fname + "-left.fastq")
right_out = os.path.join(options.output_dir,
stripped_fname + "-right.fastq")
orphan_out = os.path.join(options.output_dir,
stripped_fname + "-orphans.fastq")
if options.split_sorted:
parser_func = fastq.split_paired_parser
else:
parser_func = fastq.paired_parser
parser_func(open(args[0], "r"),
open(left_out, "w+"),
open(right_out, "w+"),
open(orphan_out, "w+"),
callback_func,
phred_offset,
25,
int(fastq_readlen / 2))
else:
filtered_out = os.path.join(options.output_dir,
stripped_fname + "-filtered.fastq")
fastq.single_parser(open(args[0], "r"),
open(filtered_out, "w+"),
callback_func,
phred_offset,
25,
int(fastq_readlen / 2))
def main():
parse_options(sys.argv[1:])
fastq_ver = fastq.fastq_version(args[0])
fastq_readlen = fastq.fastq_readlen(args[0])
callback_func = fastq.fastq_ver_to_callback(fastq_ver)
phred_offset = fastq.fastq_ver_to_phred(fastq_ver)
if not os.path.exists(options.output_dir):
os.mkdir(options.output_dir)
stripped_fname = ".".join(os.path.basename(args[0]).split(".")[:-1])
if options.paired_end:
left_out = os.path.join(options.output_dir,
stripped_fname + "-left.fastq")
right_out = os.path.join(options.output_dir,
stripped_fname + "-right.fastq")
orphan_out = os.path.join(options.output_dir,
stripped_fname + "-orphans.fastq")
if options.split_sorted:
parser_func = fastq.split_paired_parser
else:
parser_func = fastq.paired_parser
parser_func(open(args[0], "r"), open(left_out, "w+"),
open(right_out, "w+"), open(orphan_out, "w+"),
callback_func, phred_offset, 25, int(fastq_readlen / 2))
else:
filtered_out = os.path.join(options.output_dir,
stripped_fname + "-filtered.fastq")
fastq.single_parser(open(args[0], "r"), open(filtered_out, "w+"),
callback_func, phred_offset, 25,
int(fastq_readlen / 2))
