test_uta_parsers_geneinfo.py

import gzip
import os
import unittest

import uta.parsers.geneinfo

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_geneinfoparser(unittest.TestCase):

    def test1(self):
        fn = os.path.join(data_dir, 'gene_info_100human.gz')
        gip = uta.parsers.geneinfo.GeneInfoParser(gzip.open(fn, "rt"))
        gi = gip.next()
        self.assertEqual(gi, {
            'Full_name_from_nomenclature_authority': 'alpha-1-B glycoprotein',
            'GeneID': '1',
            'LocusTag': '-',
            'Modification_date': '20130609',
            'Nomenclature_status': 'O',
            'Other_designations': 'alpha-1B-glycoprotein',
            'Symbol': 'A1BG',
            'Symbol_from_nomenclature_authority': 'A1BG',
            'Synonyms': 'A1B|ABG|GAB|HYST2477',
            'chromosome': '19',
            'dbXrefs': 'HGNC:5|MIM:138670|Ensembl:ENSG00000121410|HPRD:00726|Vega:OTTHUMG00000183507',
            'description': 'alpha-1-B glycoprotein',
            'map_location': '19q13.4',
            'tax_id': '9606',
            'type_of_gene': 'protein-coding'})


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>