def testSingleParser_v18(self):
fastq.single_parser(open(self.ver18_single, "r"), self.left_tempfile,
fastq._illumina18, 33, 25, 18)
self.left_tempfile.seek(0)
self.assertTrue(
filecmp.cmp(self.left_tempfile.name,
"./filter_reads/ver18_single-FILTERED.fastq"))
def testSingleParser_v18(self):
fastq.single_parser(open(self.ver18_single, "r"),
self.left_tempfile,
fastq._illumina18,
33, 25, 18)
self.left_tempfile.seek(0)
self.assertTrue(filecmp.cmp(self.left_tempfile.name,
"./filter_reads/ver18_single-FILTERED.fastq"))
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))