def run(description):
parser = argparse.ArgumentParser(
description = 'Searches for an exact match on a given string and its reverse complement, in every sequence of input sequence file. Case insensitive. Guaranteed to find all hits',
usage = 'fastaq search_for_seq [options] <infile> <outfile> <search_string>')
parser.add_argument('infile', help='Name of input file')
parser.add_argument('outfile', help='Name of outputfile. Tab-delimited output: sequence name, position, strand')
parser.add_argument('search_string', help='String to search for in the sequences')
options = parser.parse_args()
tasks.search_for_seq(options.infile, options.outfile, options.search_string)
def test_search_for_seq(self):
'''Test that sequence search finds all hits'''
tmp = 'tmp.search.fa'
tasks.search_for_seq(
os.path.join(data_dir, 'sequences_test_search_string.fa'), tmp,
'AGA')
self.assertTrue(
filecmp.cmp(
os.path.join(data_dir, 'sequences_test_search_string.fa.hits'),
tmp))
os.unlink(tmp)
def test_search_for_seq(self):
'''Test that sequence search finds all hits'''
tmp = 'tmp.search.fa'
tasks.search_for_seq(os.path.join(data_dir, 'sequences_test_search_string.fa'), tmp, 'AGA')
self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'sequences_test_search_string.fa.hits'), tmp))
os.unlink(tmp)
