def run(description):
parser = argparse.ArgumentParser(
description = description,
usage = 'fastaq to_mira_xml <infile> <xml_out>')
parser.add_argument('infile', help='Name of input fasta/q file')
parser.add_argument('xml_out', help='Name of output xml file')
options = parser.parse_args()
tasks.fastaq_to_mira_xml(options.infile, options.xml_out)
def test_fastaq_to_mira_xml(self):
'''check that fastaq_to_mira_xml makes the correct xml file from a fastq file'''
tmp = 'tmp.mira.xml'
tasks.fastaq_to_mira_xml(
os.path.join(data_dir, 'sequences_test_good_file.fq'), tmp)
self.assertTrue(
filecmp.cmp(
os.path.join(data_dir, 'sequences_test_good_file_mira.xml'),
tmp))
os.unlink(tmp)
def run(description):
parser = argparse.ArgumentParser(description=description, usage="fastaq to_mira_xml <infile> <xml_out>")
parser.add_argument("infile", help="Name of input fasta/q file")
parser.add_argument("xml_out", help="Name of output xml file")
options = parser.parse_args()
tasks.fastaq_to_mira_xml(options.infile, options.xml_out)
def test_fastaq_to_mira_xml(self):
'''check that fastaq_to_mira_xml makes the correct xml file from a fastq file'''
tmp = 'tmp.mira.xml'
tasks.fastaq_to_mira_xml(os.path.join(data_dir, 'sequences_test_good_file.fq'), tmp)
self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'sequences_test_good_file_mira.xml'), tmp))
os.unlink(tmp)
