def run(description):
parser = argparse.ArgumentParser(
description = description,
usage = 'fastaq fasta_to_fastq <fasta in> <qual in> <fastq out>')
parser.add_argument('fasta', help='Name of input FASTA file', metavar='fasta in')
parser.add_argument('qual', help='Name of input quality scores file', metavar='qual in')
parser.add_argument('outfile', help='Name of output FASTQ file', metavar='fastq out')
options = parser.parse_args()
tasks.fasta_to_fastq(options.fasta, options.qual, options.outfile)
def test_fasta_to_fastq(self):
'''Check fasta_to_fastq converts files as expected'''
tasks.fasta_to_fastq(os.path.join(data_dir, 'sequences_test.fa'),
os.path.join(data_dir, 'sequences_test.fa.qual'),
'tmp.fq')
self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'sequences_test.fasta_to_fastq.fq'), 'tmp.fq'))
with self.assertRaises(tasks.Error):
tasks.fasta_to_fastq(os.path.join(data_dir, 'sequences_test.fa'),
os.path.join(data_dir, 'sequences_test.fa.qual.bad'),
'tmp.fq')
os.unlink('tmp.fq')
def test_fasta_to_fastq(self):
'''Check fasta_to_fastq converts files as expected'''
tasks.fasta_to_fastq(os.path.join(data_dir, 'sequences_test.fa'),
os.path.join(data_dir, 'sequences_test.fa.qual'),
'tmp.fq')
self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'sequences_test.fasta_to_fastq.fq'), 'tmp.fq'))
with self.assertRaises(tasks.Error):
tasks.fasta_to_fastq(os.path.join(data_dir, 'sequences_test.fa'),
os.path.join(data_dir, 'sequences_test.fa.qual.bad'),
'tmp.fq')
os.unlink('tmp.fq')
def run(description):
parser = argparse.ArgumentParser(
description=description,
usage='fastaq fasta_to_fastq <fasta in> <qual in> <fastq out>')
parser.add_argument('fasta',
help='Name of input FASTA file',
metavar='fasta in')
parser.add_argument('qual',
help='Name of input quality scores file',
metavar='qual in')
parser.add_argument('outfile',
help='Name of output FASTQ file',
metavar='fastq out')
options = parser.parse_args()
tasks.fasta_to_fastq(options.fasta, options.qual, options.outfile)
