Python to_boulderio Examples

Example #1

File: to_boulderio.py Project: martinghunt/Fastaq

def run(description):
    parser = argparse.ArgumentParser(
        description = 'Converts input sequence file into "Boulder-IO" format, which is used by primer3',
        usage = 'fastaq to_boulderio <infile> <outfile>')
    parser.add_argument('infile', help='Name of input file')
    parser.add_argument('outfile', help='Name of output files')
    options = parser.parse_args()
    tasks.to_boulderio(options.infile, options.outfile)

Example #2

File: to_boulderio.py Project: jhh130910/code-test

def run(description):
    parser = argparse.ArgumentParser(
        description=
        'Converts input sequence file into "Boulder-IO" format, which is used by primer3',
        usage='fastaq to_boulderio <infile> <outfile>')
    parser.add_argument('infile', help='Name of input file')
    parser.add_argument('outfile', help='Name of output files')
    options = parser.parse_args()
    tasks.to_boulderio(options.infile, options.outfile)

Example #3

File: tasks_test.py Project: jhh130910/code-test

 def test_to_boulderio(self):
     '''Test task to_boulderio'''
     tmpfile = 'tmp.boulder'
     tasks.to_boulderio(
         os.path.join(data_dir, 'tasks_test_to_boulderio.in.fa'), tmpfile)
     self.assertTrue(
         filecmp.cmp(os.path.join(data_dir,
                                  'tasks_test_to_boulderio.out.boulder'),
                     tmpfile,
                     shallow=False))
     os.unlink(tmpfile)

Example #4

File: tasks_test.py Project: martinghunt/Fastaq

 def test_to_boulderio(self):
     '''Test task to_boulderio'''
     tmpfile = 'tmp.boulder'
     tasks.to_boulderio(os.path.join(data_dir, 'tasks_test_to_boulderio.in.fa'), tmpfile)
     self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'tasks_test_to_boulderio.out.boulder'), tmpfile, shallow=False))
     os.unlink(tmpfile)