def test_EMBL_CCDS_RefSeq(self):
exp = [
CodingSequence(
'CR456855', 'EMBL',
Seq(
'ATGGAGGGTCAACGCTGGCTGCCGCTGGAGGCCAATCCCGAGGTCACCAACCAGTTTCTTAAACAATTAGGTCTACATCCTAACTGGCAATTCGTTGATGTATATGGAATGGATCCTGAACTCCTTAGCATGGTACCAAGACCAGTCTGTGCAGTCTTACTTCTCTTTCCTATTACAGAAAAGTATGAAGTATTCAGAACAGAAGAGGAAGAAAAAATAAAATCTCAGGGACAAGATGTTACATCATCAGTATATTTCATGAAGCAAACAATCAGCAATGCCTGTGGAACAATTGGACTGATTCATGCTATTGCAAACAATAAAGACAAGATGCACTTTGAATCTGGATCAACCTTGAAAAAATTCCTGGAGGAATCTGTGTCAATGAGCCCTGAAGAACGAGCCAGATACCTGGAGAACTATGATGCCATCCGAGTTACTCATGAGACCAGTGCCCATGAAGGTCAGACTGAGGCACCAAGTATAGATGAGAAAGTAGATCTTCATTTTATTGCATTAGTTCATGTAGATGGGCATCTCTATGAATTAGATGGGCGGAAGCCATTTCCAATTAACCATGGTGAAACTAGTGATGAAACTTTATTAGAGGATGCCATAGAAGTTTGCAAGAAGTTTATGGAGCGCGACCCTGATGAACTAAGATTTAATGCGATTGCTCTTTCTGCAGCTTAA',
IUPACUnambiguousDNA()),
Seq(
'MEGQRWLPLEANPEVTNQFLKQLGLHPNWQFVDVYGMDPELLSMVPRPVCAVLLLFPITEKYEVFRTEEEEKIKSQGQDVTSSVYFMKQTISNACGTIGLIHAIANNKDKMHFESGSTLKKFLEESVSMSPEERARYLENYDAIRVTHETSAHEGQTEAPSIDEKVDLHFIALVHVDGHLYELDGRKPFPINHGETSDETLLEDAIEVCKKFMERDPDELRFNAIALSAA',
ExtendedIUPACProtein())),
CodingSequence(
'DQ917642', 'EMBL',
Seq(
'ATGACGGGCAATGCCGGGGAGTGGTGCCTCATGGAAAGCGACCCCGGAGTCTTCACCGAGCTCATTAAAGGATTCGGTTGCCGAGGAGCCCAAGTAGAAGAAATATGGAGTTTAGAGCCTGAGAATTTTGAAAAATTAAAGCCAGTTCATGGGCTGATTTTTCTTTTCAAGTGGCAGCCCGGAGAAGAACCAGCAGGCTCTGTGGTTCAGGACTCCCGACTTGACACGATATTTTTTGCCAAGCAGGTAATTAATAATGCTTGTGCTACTCAAGCCATAGTAAGTGTGTTATTGAACTGTACCCATCAGGATGTCCATTTAGGAGAGACATTGTCAGAGTTTAAGGAATTCTCACAAAGTTTTGATGCAGCTATGAAAGGTTTGGCCCTGAGTAATTCGGATGTGATTCGCCAAGTACACAACAGTTTCGCCAGACAGCAAATGTTTGAATTTGATGCAAAGACATCAGCAAAAGAAGAAGATGCTTTTCACTTTGTCAGTTACGTTCCTGTGAATGGAAGACTGTACGAATTAGATGGATTAAGAGAAGGACCGATCGATTTAGGTGCATGCAATCAAGATGACTGGATCAGCGCAGTGAGGCCAGTCATAGAAAAAAGGATACAAAAGTACAGTGAAGGTGAAATTCGATTTAACTTAATGGCCATTGTGTCTGACAGGAAAATGATATATGAACAGAAGATAGCAGAGTTACAAAGACAGCTTGCTGAGGAGGAACCCATGGATACAGATCAGGGTAGTAACATGTTAAGTGCTATTCAGTCAGAAGTTGCCAAAAATCAGATGCTTATTGAAGAAGAAGTACAGAAATTAAAAAGATATAAGATTGAAAACATCAGAAGGAAGCATAATTATCTGCCTTTCATTATGGAACTGTTAAAGACTTTAGCAGAACACCAGCAGTTAATACCTCTCGTAGAAAAGGCAAAAGAAAAACAGAATGCGAAGAAGGCACAGGAAACCAAATGA',
IUPACUnambiguousDNA()),
Seq(
'MTGNAGEWCLMESDPGVFTELIKGFGCRGAQVEEIWSLEPENFEKLKPVHGLIFLFKWQPGEEPAGSVVQDSRLDTIFFAKQVINNACATQAIVSVLLNCTHQDVHLGETLSEFKEFSQSFDAAMKGLALSNSDVIRQVHNSFARQQMFEFDAKTSAKEEDAFHFVSYVPVNGRLYELDGLREGPIDLGACNQDDWISAVRPVIEKRIQKYSEGEIRFNLMAIVSDRKMIYEQKIAELQRQLAEEEPMDTDQGSNMLSAIQSEVAKNQMLIEEEVQKLKRYKIENIRRKHNYLPFIMELLKTLAEHQQLIPLVEKAKEKQNAKKAQETK',
ExtendedIUPACProtein())),
CodingSequence(
'NM_001270952', 'RefSeq',
Seq(
'ATGGATCCTGAACTCCTTAGCATGGTACCAAGACCAGTCTGTGCAGTCTTACTTCTCTTTCCTATTACAGAAAAGTATGAAGTATTCAGAACAGAAGAGGAAGAAAAAATAAAATCTCAGGGACAAGATGTTACATCATCAGTATATTTCATGAAGCAAACAATCAGCAATGCCTGTGGAACAATTGGACTGATTCATGCTATTGCAAACAATAAAGACAAGATGCACTTTGAATCTGGATCAACCTTGAAAAAATTCCTGGAGGAATCTGTGTCAATGAGCCCTGAAGAACGAGCCAGATACCTGGAGAACTATGATGCCATCCGAGTTACTCATGAGACCAGTGCCCATGAAGGTCAGACTGAGGCACCAAGTATAGATGAGAAAGTAGATCTTCATTTTATTGCATTAGTTCATGTAGATGGGCATCTCTATGAATTAGATGGGCGGAAGCCATTTCCAATTAACCATGGTGAAACTAGTGATGAAACTTTATTAGAGGATGCCATAGAAGTTTGCAAGAAGTTTATGGAGCGCGACCCTGATGAACTAAGATTTAATGCGATTGCTCTTTCTGCAGCATAG',
IUPACUnambiguousDNA()),
Seq(
'MDPELLSMVPRPVCAVLLLFPITEKYEVFRTEEEEKIKSQGQDVTSSVYFMKQTISNACGTIGLIHAIANNKDKMHFESGSTLKKFLEESVSMSPEERARYLENYDAIRVTHETSAHEGQTEAPSIDEKVDLHFIALVHVDGHLYELDGRKPFPINHGETSDETLLEDAIEVCKKFMERDPDELRFNAIALSAA',
ExtendedIUPACProtein())),
CodingSequence(
'CCDS73586.1', 'CCDS',
Seq('ATGGATCCTGAACTCCTTAGCATGGTACCAAGACCAGTCTGTGCAGTCTTACTTCTCTTTCCTATTACAGAAAAGTATGAAGTATTCAGAACAGAAGAGGAAGAAAAAATAAAATCTCAGGGACAAGATGTTACATCATCAGTATATTTCATGAAGCAAACAATCAGCAATGCCTGTGGAACAATTGGACTGATTCATGCTATTGCAAACAATAAAGACAAGATGCACTTTGAATCTGGATCAACCTTGAAAAAATTCCTGGAGGAATCTGTGTCAATGAGCCCTGAAGAACGAGCCAGATACCTGGAGAACTATGATGCCATCCGAGTTACTCATGAGACCAGTGCCCATGAAGGTCAGACTGAGGCACCAAGTATAGATGAGAAAGTAGATCTTCATTTTATTGCATTAGTTCATGTAGATGGGCATCTCTATGAATTAGATGGGCGGAAGCCATTTCCAATTAACCATGGTGAAACTAGTGATGAAACTTTATTAGAGGATGCCATAGAAGTTTGCAAGAAGTTTATGGAGCGCGACCCTGATGAACTAAGATTTAATGCGATTGCTCTTTCTGCAGCATAG'
),
Seq('MDPELLSMVPRPVCAVLLLFPITEKYEVFRTEEEEKIKSQGQDVTSSVYFMKQTISNACGTIGLIHAIANNKDKMHFESGSTLKKFLEESVSMSPEERARYLENYDAIRVTHETSAHEGQTEAPSIDEKVDLHFIALVHVDGHLYELDGRKPFPINHGETSDETLLEDAIEVCKKFMERDPDELRFNAIALSAA'
)),
CodingSequence(
'CCDS86041.1', 'CCDS',
Seq('ATGACGGGCAATGCCGGGGAGTGGTGCCTCATGGAAAGCGACCCCGGGGTCTTCACCGAGCTCATTAAAGGATTCGGTTGCCGAGGAGCCCAAGTAGAAGAAATATGGAGTTTAGAGCCTGAGAATTTTGAAAAATTAAAGCCAGTTCATGGGTTAATTTTTCTTTTCAAGTGGCAGCCAGGAGAAGAACCAGCAGGCTCTGTGGTTCAGGACTCCCGACTTGACACGATATTTTTTGCTAAGCAGGTAATTAATAATGCTTGTGCTACTCAAGCCATAGTGAGTGTGTTACTGAACTGTACCCACCAGGATGTCCATTTAGGCGAGACATTATCAGAGTTTAAAGAATTTTCACAAAGTTTTGATGCAGCTATGAAAGGCTTGGCACTGAGCAATTCAGATGTGATTCGACAAGTACACAACAGTTTCGCCAGACAGCAAATGTTTGAATTTGATACGAAGACATCAGCAAAAGAAGAAGATGCTTTTCACTTTGTCAGTTATGTTCCTGTTAATGGGAGACTGTATGAATTAGATGGATTAAGAGAAGGACCGATTGATTTAGGTGCATGCAATCAAGATGATTGGATCAGTGCAGTAAGGCCTGTCATAGAAAAAAGGATACAAAAAGACGGGTTTTCACCATGTTGCCCAGGCTGGTCTCAGACTCCTGAGCTCAAGCCATCCGCCTGCCTCGACCTCCCAAAGTGGTACAGTGAAGGTGAAATTCGATTTAATTTAATGGCCATTGTGTCTGACAGAAAAATGATATATGAGCAGAAGATAGCAGAGTTACAAAGACAACTTGCAGAGGAACCCATGGATACAGATCAAGGTAATAGTATGTTAAGTGCTATTCAGTCAGAAGTTGCCAAAAATCAGATGCTTATTGAAGAAGAAGTACAGAAATTAAAAAGATACAAGATTGAGAATATCAGAAGGAAGCATAATTATCTGCCTTTCATTATGGAATTGTTAAAGACTTTAGCAGAACACCAGCAGTTAATACCACTAGTAGAAAAGGCAAAAGAAAAACAGAACGCAAAGAAAGCTCAGGAAACCAAATGA'
),
Seq('MTGNAGEWCLMESDPGVFTELIKGFGCRGAQVEEIWSLEPENFEKLKPVHGLIFLFKWQPGEEPAGSVVQDSRLDTIFFAKQVINNACATQAIVSVLLNCTHQDVHLGETLSEFKEFSQSFDAAMKGLALSNSDVIRQVHNSFARQQMFEFDTKTSAKEEDAFHFVSYVPVNGRLYELDGLREGPIDLGACNQDDWISAVRPVIEKRIQKDGFSPCCPGWSQTPELKPSACLDLPKWYSEGEIRFNLMAIVSDRKMIYEQKIAELQRQLAEEPMDTDQGNSMLSAIQSEVAKNQMLIEEEVQKLKRYKIENIRRKHNYLPFIMELLKTLAEHQQLIPLVEKAKEKQNAKKAQETK'
))
]
ids = {
'EMBL': ['CR456855.1', 'DQ917642.1'],
'RefSeq': ['NM_001270952.1'],
'CCDS': ['CCDS73586.1', 'CCDS86041.1']
}
formatter = dba.UrlFormatter()
queries = []
for database, id_list in ids.items():
queries += formatter.format(database, id_list)
loop = asyncio.get_event_loop()
fetcher = dba.Entry_fetcher()
entries = loop.run_until_complete(fetcher.fetch_all(queries))
splitter = dba.EntrySplitter()
entries = splitter.split(entries)
loop.close()
parser = dba.DnaParser()
res = parser.parse(entries)
for item in res:
self.assertTrue(item in exp)
self.assertEqual(len(exp), len(res))
def test_split_entries_EMBL(self):
xml_response = '<GBSet><GBSeq>a</GBseq><GBSeq>b</GBseq></GBSet>'
database = 'EMBL'
splitter = dba.EntrySplitter()
exp = [(database, '<GBSeq>a</GBSeq>'), (database, '<GBSeq>b</GBSeq>')]
res = splitter.split([(database, xml_response)])
self.assertEqual(res, exp)
def test_split_entries_summary(self):
xml_response = '<eSummaryResult><DocSum>a</DocSum><DocSum>b</DocSum></eSummaryResult>'
database = 'Summary'
splitter = dba.EntrySplitter()
exp = [(database, '<DocSum>a</DocSum>'),
(database, '<DocSum>b</DocSum>')]
res = splitter.split([(database, xml_response)])
self.assertEqual(res, exp)
def test_split_entries_Gene(self):
xml_response = '<Entrezgene-Set><Entrezgene>a</Entrezgene><Entrezgene>b</Entrezgene></Entrezgene-Set>'
database = 'Gene'
splitter = dba.EntrySplitter()
exp = [(database, '<Entrezgene>a</Entrezgene>'),
(database, '<Entrezgene>b</Entrezgene>')]
res = splitter.split([(database, xml_response)])
self.assertEqual(res, exp)
def test_split_entries_Uniprot(self):
xml_response = '''<uniprot>
<entry><accession>P13368</accession></entry>
<entry><accession>P13456</accession></entry>
</uniprot>'''
database = 'Uniprot'
splitter = dba.EntrySplitter()
exp = [(database, '<entry><accession>P13368</accession></entry>'),
(database, '<entry><accession>P13456</accession></entry>')]
res = splitter.split([(database, xml_response)])
self.assertEqual(res, exp)
def test_nodatabase(self):
with self.assertRaises(ValueError):
splitter = dba.EntrySplitter()
splitter.split([('NotADatabase', '')])