Пример #1
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def run(description):
    parser = argparse.ArgumentParser(
        description = 'Creates a file of contigs from a file of scaffolds - i.e. breaks at every gap in the input',
        usage = 'fastaq scaffolds_to_contigs [options] <infile> <outfile>')
    parser.add_argument('--number_contigs', action='store_true', help='Use this to enumerate contig names 1,2,3,... within each scaffold')
    parser.add_argument('infile', help='Name of input file')
    parser.add_argument('outfile', help='Name of output contigs file')
    options = parser.parse_args()
    tasks.scaffolds_to_contigs(options.infile, options.outfile, number_contigs=options.number_contigs)
Пример #2
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 def test_scaffolds_to_contigs(self):
     '''Test scaffolds_to_contigs'''
     tmp = 'tmp.contigs.fa'
     tasks.scaffolds_to_contigs(
         os.path.join(data_dir, 'utils_test_scaffolds.fa'), tmp)
     self.assertTrue(
         filecmp.cmp(
             os.path.join(data_dir,
                          'utils_test_scaffolds.fa.to_contigs.fa'), tmp))
     os.unlink(tmp)
Пример #3
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 def test_scaffolds_to_contigs_number_contigs(self):
     '''Test scaffolds_to_contigs with contig numbering'''
     tmp = 'tmp.contigs.fa'
     tasks.scaffolds_to_contigs(os.path.join(data_dir,
                                             'utils_test_scaffolds.fa'),
                                tmp,
                                number_contigs=True)
     self.assertTrue(
         filecmp.cmp(
             os.path.join(
                 data_dir,
                 'utils_test_scaffolds.fa.to_contigs.number_contigs.fa'),
             tmp))
     os.unlink(tmp)
Пример #4
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def run(description):
    parser = argparse.ArgumentParser(
        description=
        'Creates a file of contigs from a file of scaffolds - i.e. breaks at every gap in the input',
        usage='fastaq scaffolds_to_contigs [options] <infile> <outfile>')
    parser.add_argument(
        '--number_contigs',
        action='store_true',
        help='Use this to enumerate contig names 1,2,3,... within each scaffold'
    )
    parser.add_argument('infile', help='Name of input file')
    parser.add_argument('outfile', help='Name of output contigs file')
    options = parser.parse_args()
    tasks.scaffolds_to_contigs(options.infile,
                               options.outfile,
                               number_contigs=options.number_contigs)
Пример #5
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 def test_scaffolds_to_contigs_number_contigs(self):
     '''Test scaffolds_to_contigs with contig numbering'''
     tmp = 'tmp.contigs.fa'
     tasks.scaffolds_to_contigs(os.path.join(data_dir, 'utils_test_scaffolds.fa'), tmp, number_contigs=True)
     self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'utils_test_scaffolds.fa.to_contigs.number_contigs.fa'), tmp))
     os.unlink(tmp)
Пример #6
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 def test_scaffolds_to_contigs(self):
     '''Test scaffolds_to_contigs'''
     tmp = 'tmp.contigs.fa'
     tasks.scaffolds_to_contigs(os.path.join(data_dir, 'utils_test_scaffolds.fa'), tmp)
     self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'utils_test_scaffolds.fa.to_contigs.fa'), tmp))
     os.unlink(tmp)