test_uta_parsers_seqgene.py

import gzip
import os
import unittest

import uta.parsers.seqgene

data_dir = os.path.realpath(
    os.path.realpath(os.path.join(__file__, '../data')))

# gzip -cd misc/data/ftp.ncbi.nih.gov/gene/DATA/gene_info.gz | grep ^9606
# | head -101 | gzip -c >tests/data/gene_info_100human.gz


class Test_parsers_seqgene(unittest.TestCase):

    def test1(self):
        fn = os.path.join(data_dir, 'seq_gene_100.md.gz')
        parser = uta.parsers.seqgene.SeqGeneParser(gzip.open(fn, "rt"))
        rec = parser.next()
        self.assertEqual(rec, {
            'chr_orient': '+',
            'chr_start': '697',
            'chr_stop': '1075',
            'chromosome': '1',
            'contig': 'NW_001838563.2',
            'ctg_orient': '-',
            'ctg_start': '4805',
            'ctg_stop': '5183',
            'evidence_code': '',
            'feature_id': 'GeneID:100887749',
            'feature_name': 'MTND1P23',
            'feature_type': 'GENE',
            'group_label': 'HuRef-Primary Assembly',
            'tax_id': '9606',
            'transcript': '-'})


if __name__ == '__main__':
    unittest.main()


# <LICENSE>
# Copyright 2014 UTA Contributors (https://bitbucket.org/biocommons/uta)
##
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
##
# http://www.apache.org/licenses/LICENSE-2.0
##
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
# </LICENSE>