def test_Gene_format_list_of_ids(self):
id_ = ['7347', '50933']
url = f'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=Gene&id={",".join(id_)}&retmode=xml&email={self.email}&tool=ccd.rhpc.nki.nl'
exp = [('Gene', url)]
formatter = dba.UrlFormatter()
res = formatter.format('Gene', id_)
self.assertEqual(res, exp)
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_EMBL_format_list_of_ids(self):
id_ = ['CR456855.1', 'GBYX01232236.1']
url = f'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id={",".join(id_)}&retmode=xml&rettype=gb&email={self.email}&tool=ccd.rhpc.nki.nl'
exp = [('EMBL', url)]
formatter = dba.UrlFormatter()
res = formatter.format('EMBL', id_)
self.assertEqual(res, exp)
def test_uniprot_no_format(self):
formatter = dba.UrlFormatter()
with self.assertRaises(ValueError):
formatter.format('Uniprot', 'q9uj41') # no format
with self.assertRaises(ValueError):
formatter.format('Uniprot', 'q9uj41',
format_='notvalid') # unsupported format
def test_RefSeq_format_list_of_ids(self):
id_ = ['NM_001270952.1', 'NM_006002.4']
url = f'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id={",".join(id_)}&retmode=xml&rettype=gb&email={self.email}&tool=ccd.rhpc.nki.nl'
exp = [('RefSeq', url)]
formatter = dba.UrlFormatter()
res = formatter.format('RefSeq', id_)
self.assertEqual(res, exp)
def test_uniprot_all_formats(self):
id_ = 'q9uj41'
formatter = dba.UrlFormatter()
for format_ in ['xml', 'fasta', 'html']:
url = f'https://www.uniprot.org/uniprot/{id_}.{format_}'
exp = [('Uniprot', url)]
res = formatter.format('Uniprot', id_, format_=format_)
self.assertEqual(res, exp)
def test_RefSeq_single_id(self):
id_ = 'NM_001270952.1'
exp = [(
'RefSeq',
f'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id={id_}&retmode=xml&rettype=gb&email={self.email}&tool=ccd.rhpc.nki.nl'
)]
formatter = dba.UrlFormatter()
res = formatter.format('RefSeq', id_)
self.assertEqual(res, exp)
def test_Gene_format_single_id(self):
id_ = '7347'
exp = [(
'Gene',
f'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=Gene&id={id_}&retmode=xml&email={self.email}&tool=ccd.rhpc.nki.nl'
)]
formatter = dba.UrlFormatter()
res = formatter.format('Gene', id_)
self.assertEqual(res, exp)
def test_CCDS_single_id(self):
id_ = 'CCDS73586.1'
exp = [(
'CCDS',
f'https://www.ncbi.nlm.nih.gov/projects/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&DATA={id_}&ORGANISM=0&BUILDS=CURRENTBUILDS'
)]
formatter = dba.UrlFormatter()
res = formatter.format('CCDS', id_)
self.assertEqual(res, exp)
def test_CCDS_format_list_of_ids(self):
id_list = ['CCDS73586.1', 'CCDS86041.1']
urls = [
f'https://www.ncbi.nlm.nih.gov/projects/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&DATA={id_}&ORGANISM=0&BUILDS=CURRENTBUILDS'
for id_ in id_list
]
exp = [('CCDS', url) for url in urls]
formatter = dba.UrlFormatter()
res = formatter.format('CCDS', id_list)
self.assertEqual(res, exp)
def test_correct_functioning(self):
loop = asyncio.get_event_loop()
parser = dba.GeneParser()
uf = dba.UrlFormatter()
fetcher = dba.Entry_fetcher()
query = uf.format('Gene', '27342')
res = loop.run_until_complete(fetcher.fetch_all(query))
xml_soup = BeautifulSoup(res[0][1], 'xml')
exp = ['CCDS69308.1', 'CCDS5535.1', 'CCDS75610.1']
self.assertEqual(exp.sort(),
parser.get_crossreferences(xml_soup).sort())
def test_uniprot_batch(self):
formatter = dba.UrlFormatter()
id_list = ['q9uj41', 'Q15287', 'Q96RL1']
formats = ['xml', 'html', 'fasta'] # batch added below
for f in formats:
exp = [(
'Uniprot',
f'https://www.uniprot.org/uploadlists?query=q9uj41 Q15287 Q96RL1&from=ACC+ID&to=ACC&format={f}'
)]
res = formatter.format('Uniprot', id_list, format_=f'batch_{f}')
self.assertEqual(res, exp)
def test_format_for_summary(self):
query1 = ('EMBL', ['CR456855.1', 'DQ917642.1']) # list of ids
query2 = ('RefSeq', 'NM_001270952.1') # single id
exp = [
('Summary',
'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=nuccore&id=CR456855.1,DQ917642.1'
),
('Summary',
'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=nuccore&id=NM_001270952.1'
)
]
formatter = dba.UrlFormatter()
res = formatter.format_for_summary(*query1)
res += formatter.format_for_summary(*query2)
self.assertEqual(exp, res)
def _fetch_data(self, database, id_list):
loop = asyncio.get_event_loop()
uf = dba.UrlFormatter()
fetcher = dba.Entry_fetcher()
query = uf.format(database, id_list)
return loop.run_until_complete(fetcher.fetch_all(query))
def test_invalid_database(self):
formatter = dba.UrlFormatter()
with self.assertRaises(ValueError):
formatter.format('NotADatabase', ['id1', 'id2'])
with self.assertRaises(ValueError):
formatter.format_for_summary('NotADatabase', ['id1', 'id2'])