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test_uta_models.py
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import datetime
import unittest
import sqlalchemy
from sqlalchemy import text
import testing.postgresql
import uta
usam = uta.models
transcripts = {
'NM_000680.2': {
'seq': 'gaattccgaatcatgtgcagaatgctgaatcttcccccagccaggacgaataagacagcgcggaaaagcagattctcgtaattctggaattgcatgttgcaaggagtctcctggatcttcgcacccagcttcgggtagggagggagtccgggtcccgggctaggccagcccggcaggtggagagggtccccggcagccccgcgcgcccctggccatgtctttaatgccctgccccttcatgtggccttctgagggttcccagggctggccagggttgtttcccacccgcgcgcgcgctctcacccccagccaaacccacctggcagggctccctccagccgagaccttttgattcccggctcccgcgctcccgcctccgcgccagcccgggaggtggccctggacagccggacctcgcccggccccggctgggaccatggtgtttctctcgggaaatgcttccgacagctccaactgcacccaaccgccggcaccggtgaacatttccaaggccattctgctcggggtgatcttggggggcctcattcttttcggggtgctgggtaacatcctagtgatcctctccgtagcctgtcaccgacacctgcactcagtcacgcactactacatcgtcaacctggcggtggccgacctcctgctcacctccacggtgctgcccttctccgccatcttcgaggtcctaggctactgggccttcggcagggtcttctgcaacatctgggcggcagtggatgtgctgtgctgcaccgcgtccatcatgggcctctgcatcatctccatcgaccgctacatcggcgtgagctacccgctgcgctacccaaccatcgtcacccagaggaggggtctcatggctctgctctgcgtctgggcactctccctggtcatatccattggacccctgttcggctggaggcagccggcccccgaggacgagaccatctgccagatcaacgaggagccgggctacgtgctcttctcagcgctgggctccttctacctgcctctggccatcatcctggtcatgtactgccgcgtctacgtggtggccaagagggagagccggggcctcaagtctggcctcaagaccgacaagtcggactcggagcaagtgacgctccgcatccatcggaaaaacgccccggcaggaggcagcgggatggccagcgccaagaccaagacgcacttctcagtgaggctcctcaagttctcccgggagaagaaagcggccaaaacgctgggcatcgtggtcggctgcttcgtcctctgctggctgccttttttcttagtcatgcccattgggtctttcttccctgatttcaagccctctgaaacagtttttaaaatagtattttggctcggatatctaaacagctgcatcaaccccatcatatacccatgctccagccaagagttcaaaaaggcctttcagaatgtcttgagaatccagtgtctctgcagaaagcagtcttccaaacatgccctgggctacaccctgcacccgcccagccaggccgtggaagggcaacacaaggacatggtgcgcatccccgtgggatcaagagagaccttctacaggatctccaagacggatggcgtttgtgaatggaaatttttctcttccatgccccgtggatctgccaggattacagtgtccaaagaccaatcctcctgtaccacagcccgggtgagaagtaaaagctttttgcaggtctgctgctgtgtagggccctcaacccccagccttgacaagaaccatcaagttccaaccattaaggtccacaccatctccctcagtgagaacggggaggaagtctaggacaggaaagatgcagaggaaaggggaataatcttaggtacccaccccacttccttctcggaaggccagctcttcttggaggacaagacaggaccaatcaaagaggggacctgctgggaatggggtgggtggtagacccaactcatcaggcagcgggtagggcacagggaagagggagggtgtctcacaaccaaccagttcagaatgatacggaacagcatttccctgcagctaatgctttcttggtcactctgtgcccacttcaacgaaaaccaccatgggaaacagaatttcatgcacaatccaaaagactataaatataggattatgatttcatcatgaatattttgagcacacactctaagtttggagctatttcttgatggaagtgaggggattttattttcaggctcaacctactgacagccacatttgacatttatg',
't_starts_i': [0, 1319], 't_ends_i': [1319, 2281], 'names': ['1', '2b'],
't_cds_start_i': 436, 't_cds_end_i': 1837,
'g_strand': -1,
'g_starts_i': [26721603, 26627221], 'g_ends_i': [26722922, 26628183],
'g_cds_start_i': 26627665, 'g_cds_end_i': 26722486,
'pro_ac': 'NP_000671.2',
'translation_exceptions': [
{'start_position': 333, 'end_position': 335, 'amino_acid': 'Sec'},
{'start_position': 589, 'end_position': 589, 'amino_acid': 'TERM'},
],
},
'NM_033302.2': {
'seq': 'gaattccgaatcatgtgcagaatgctgaatcttcccccagccaggacgaataagacagcgcggaaaagcagattctcgtaattctggaattgcatgttgcaaggagtctcctggatcttcgcacccagcttcgggtagggagggagtccgggtcccgggctaggccagcccggcaggtggagagggtccccggcagccccgcgcgcccctggccatgtctttaatgccctgccccttcatgtggccttctgagggttcccagggctggccagggttgtttcccacccgcgcgcgcgctctcacccccagccaaacccacctggcagggctccctccagccgagaccttttgattcccggctcccgcgctcccgcctccgcgccagcccgggaggtggccctggacagccggacctcgcccggccccggctgggaccatggtgtttctctcgggaaatgcttccgacagctccaactgcacccaaccgccggcaccggtgaacatttccaaggccattctgctcggggtgatcttggggggcctcattcttttcggggtgctgggtaacatcctagtgatcctctccgtagcctgtcaccgacacctgcactcagtcacgcactactacatcgtcaacctggcggtggccgacctcctgctcacctccacggtgctgcccttctccgccatcttcgaggtcctaggctactgggccttcggcagggtcttctgcaacatctgggcggcagtggatgtgctgtgctgcaccgcgtccatcatgggcctctgcatcatctccatcgaccgctacatcggcgtgagctacccgctgcgctacccaaccatcgtcacccagaggaggggtctcatggctctgctctgcgtctgggcactctccctggtcatatccattggacccctgttcggctggaggcagccggcccccgaggacgagaccatctgccagatcaacgaggagccgggctacgtgctcttctcagcgctgggctccttctacctgcctctggccatcatcctggtcatgtactgccgcgtctacgtggtggccaagagggagagccggggcctcaagtctggcctcaagaccgacaagtcggactcggagcaagtgacgctccgcatccatcggaaaaacgccccggcaggaggcagcgggatggccagcgccaagaccaagacgcacttctcagtgaggctcctcaagttctcccgggagaagaaagcggccaaaacgctgggcatcgtggtcggctgcttcgtcctctgctggctgccttttttcttagtcatgcccattgggtctttcttccctgatttcaagccctctgaaacagtttttaaaatagtattttggctcggatatctaaacagctgcatcaaccccatcatatacccatgctccagccaagagttcaaaaaggcctttcagaatgtcttgagaatccagtgtctctgcagaaagcagtcttccaaacatgccctgggctacaccctgcacccgcccagccaggccgtggaagggcaacacaaggacatggtgcgcatccccgtgggatcaagagagaccttctacaggatctccaagacggatggcgtttgtgaatggaaatttttctcttccatgccccgtggatctgccaggattacagtgtccaaagaccaatcctcctgtaccacagcccggggacacacacccatgacatgaagccagcttcccgtccacgactgttgtccttactgcccaaggaaggggagcatgaaacccaccactggtcctgcgacccactgtctttggaatccaccccaggagcccaggagccttgcctgacacttggatttacttctttatcaagcatccatctgactaaggcacaaatccaacatgttactgttactgatacaggaaaaacagtaacttaaggaatgatcatgaatgcaaagggaaagaggaaaagagccttcagggacaaatagctcgattttttgtaaatcagtttcatacaacctccctcccccatttcattcttaaaagttaattgagaatcatcagccacgtgtagggtgtgag',
't_starts_i': [0, 1319, 1705], 't_ends_i': [1319, 1705, 2089], 'names': ['1', '2a', '4'],
't_cds_start_i': 436, 't_cds_end_i': 1726,
'g_strand': -1,
'g_starts_i': [26721603, 26627797, 26613912], 'g_ends_i': [26722922, 26628183, 26614296],
'g_cds_start_i': 26614275, 'g_cds_end_i': 26722486,
'pro_ac': 'NP_150645.2',
},
'NM_033303.3': {
'seq': 'gaattccgaatcatgtgcagaatgctgaatcttcccccagccaggacgaataagacagcgcggaaaagcagattctcgtaattctggaattgcatgttgcaaggagtctcctggatcttcgcacccagcttcgggtagggagggagtccgggtcccgggctaggccagcccggcaggtggagagggtccccggcagccccgcgcgcccctggccatgtctttaatgccctgccccttcatgtggccttctgagggttcccagggctggccagggttgtttcccacccgcgcgcgcgctctcacccccagccaaacccacctggcagggctccctccagccgagaccttttgattcccggctcccgcgctcccgcctccgcgccagcccgggaggtggccctggacagccggacctcgcccggccccggctgggaccatggtgtttctctcgggaaatgcttccgacagctccaactgcacccaaccgccggcaccggtgaacatttccaaggccattctgctcggggtgatcttggggggcctcattcttttcggggtgctgggtaacatcctagtgatcctctccgtagcctgtcaccgacacctgcactcagtcacgcactactacatcgtcaacctggcggtggccgacctcctgctcacctccacggtgctgcccttctccgccatcttcgaggtcctaggctactgggccttcggcagggtcttctgcaacatctgggcggcagtggatgtgctgtgctgcaccgcgtccatcatgggcctctgcatcatctccatcgaccgctacatcggcgtgagctacccgctgcgctacccaaccatcgtcacccagaggaggggtctcatggctctgctctgcgtctgggcactctccctggtcatatccattggacccctgttcggctggaggcagccggcccccgaggacgagaccatctgccagatcaacgaggagccgggctacgtgctcttctcagcgctgggctccttctacctgcctctggccatcatcctggtcatgtactgccgcgtctacgtggtggccaagagggagagccggggcctcaagtctggcctcaagaccgacaagtcggactcggagcaagtgacgctccgcatccatcggaaaaacgccccggcaggaggcagcgggatggccagcgccaagaccaagacgcacttctcagtgaggctcctcaagttctcccgggagaagaaagcggccaaaacgctgggcatcgtggtcggctgcttcgtcctctgctggctgccttttttcttagtcatgcccattgggtctttcttccctgatttcaagccctctgaaacagtttttaaaatagtattttggctcggatatctaaacagctgcatcaaccccatcatatacccatgctccagccaagagttcaaaaaggcctttcagaatgtcttgagaatccagtgtctctgcagaaagcagtcttccaaacatgccctgggctacaccctgcacccgcccagccaggccgtggaagggcaacacaaggacatggtgcgcatccccgtgggatcaagagagaccttctacaggatctccaagacggatggcgtttgtgaatggaaatttttctcttccatgccccgtggatctgccaggattacagtgtccaaagaccaatcctcctgtaccacagcccggacgaagtctcgctctgtcaccaggctggagtgcagtggcatgatcttggctcactgcaacctccgcctcccgggttcaagagattctcctgcctcagcctcccaagcagctgggactacagggatgtgccaccaggccgacgccaccaggcccagctaatttttgtatttttagtagagacggggtttcaccatgttggccaggatgatctcgatctcttgacctcatgatctgcctgcctcagcctcccaaagtgctgggattacaggcgtgagccaccgtgcccggcccaactattttttttttttatcttttttaacagtgcaatcctttctgtggatgaaatcttgctcagaagctcaatatgcaaaagaaagaaaaacagcagggctggacggatgttgggagtggggtaagaccccaaccactcagaaccacccccccaacacacacacacattctctccatggtgactggtgaggggcctctagagggtacatagtacaccatggagcacggtttaagcaccactggactacacattcttctgtggcagttatcttaccttcccatagacacccagcccatagccattggtt',
't_starts_i': [0, 1319, 1705], 't_ends_i': [1319, 1705, 2304], 'names': ['1', '2a', '5'],
't_cds_start_i': 436, 't_cds_end_i': 1864,
'g_strand': -1,
'g_starts_i': [26721603, 26627797, 26605666], 'g_ends_i': [26722922, 26628183, 26606265],
'g_cds_start_i': 26606106, 'g_cds_end_i': 26722486,
'pro_ac': 'NP_150646.3',
},
'NM_033304.2': {
'seq': 'gaattccgaatcatgtgcagaatgctgaatcttcccccagccaggacgaataagacagcgcggaaaagcagattctcgtaattctggaattgcatgttgcaaggagtctcctggatcttcgcacccagcttcgggtagggagggagtccgggtcccgggctaggccagcccggcaggtggagagggtccccggcagccccgcgcgcccctggccatgtctttaatgccctgccccttcatgtggccttctgagggttcccagggctggccagggttgtttcccacccgcgcgcgcgctctcacccccagccaaacccacctggcagggctccctccagccgagaccttttgattcccggctcccgcgctcccgcctccgcgccagcccgggaggtggccctggacagccggacctcgcccggccccggctgggaccatggtgtttctctcgggaaatgcttccgacagctccaactgcacccaaccgccggcaccggtgaacatttccaaggccattctgctcggggtgatcttggggggcctcattcttttcggggtgctgggtaacatcctagtgatcctctccgtagcctgtcaccgacacctgcactcagtcacgcactactacatcgtcaacctggcggtggccgacctcctgctcacctccacggtgctgcccttctccgccatcttcgaggtcctaggctactgggccttcggcagggtcttctgcaacatctgggcggcagtggatgtgctgtgctgcaccgcgtccatcatgggcctctgcatcatctccatcgaccgctacatcggcgtgagctacccgctgcgctacccaaccatcgtcacccagaggaggggtctcatggctctgctctgcgtctgggcactctccctggtcatatccattggacccctgttcggctggaggcagccggcccccgaggacgagaccatctgccagatcaacgaggagccgggctacgtgctcttctcagcgctgggctccttctacctgcctctggccatcatcctggtcatgtactgccgcgtctacgtggtggccaagagggagagccggggcctcaagtctggcctcaagaccgacaagtcggactcggagcaagtgacgctccgcatccatcggaaaaacgccccggcaggaggcagcgggatggccagcgccaagaccaagacgcacttctcagtgaggctcctcaagttctcccgggagaagaaagcggccaaaacgctgggcatcgtggtcggctgcttcgtcctctgctggctgccttttttcttagtcatgcccattgggtctttcttccctgatttcaagccctctgaaacagtttttaaaatagtattttggctcggatatctaaacagctgcatcaaccccatcatatacccatgctccagccaagagttcaaaaaggcctttcagaatgtcttgagaatccagtgtctctgcagaaagcagtcttccaaacatgccctgggctacaccctgcacccgcccagccaggccgtggaagggcaacacaaggacatggtgcgcatccccgtgggatcaagagagaccttctacaggatctccaagacggatggcgtttgtgaatggaaatttttctcttccatgccccgtggatctgccaggattacagtgtccaaagaccaatcctcctgtaccacagcccggaggggaatggattgtagatatttcaccaagaattgcagagagcatatcaagcatgtgaattttatgatgccaccgtggagaaagggttcagaatgctgatctccaggtagctggagacctaggcagtctgcaaatgaggagtcagctggaagctatggctatgtattatgtgacatcgcttgttcctaagtgaaaactggatatcccaaccttctggcccagtaggtttcatggttaagacctggtagtgagaacattttaggaactatttgcttgggcaggcaatttttcactct',
't_starts_i': [0, 1319, 1705], 't_ends_i': [1319, 1705, 2001], 'names': ['1', '2a', '3'],
't_cds_start_i': 436, 't_cds_end_i': 1804,
'g_strand': -1,
'g_starts_i': [26721603, 26627797, 26623370], 'g_ends_i': [26722922, 26628183, 26623666],
'g_cds_start_i': 26623567, 'g_cds_end_i': 26722486,
'pro_ac': 'NP_150647.2',
},
}
class TestUtaModels(unittest.TestCase):
@classmethod
def setUpClass(cls):
cls._postgresql = testing.postgresql.Postgresql()
engine = sqlalchemy.create_engine(cls._postgresql.url())
with engine.connect() as connection:
connection.execute(text('drop schema if exists {schema} cascade'.format(schema=usam.schema_name)))
connection.execute(text('create schema {schema}'.format(schema=usam.schema_name)))
connection.commit()
engine.dispose()
cls.session = uta.connect(cls._postgresql.url())
usam.Base.metadata.create_all(cls.session.bind.engine)
# Test data are from:
# http://www.ncbi.nlm.nih.gov/nuccore/NM_033304.2
o = usam.Origin(
name='NCBI',
descr='Testing (originally NCBI, via Eutils)',
url='http://bogus.com/',
url_ac_fmt='http://bogus.com/{ac}',
)
cls.session.add(o)
g = usam.Gene(
gene_id='148',
hgnc='ADRA1A',
symbol='ADRA1A',
maploc='8p21.2',
descr='adrenoceptor alpha 1A',
summary='''Alpha-1-adrenergic receptors (alpha-1-ARs) are
members of the G protein-coupled receptor superfamily. They
activate mitogenic responses and regulate growth and proliferation
of many cells. There are 3 alpha-1-AR subtypes: alpha-1A, -1B and
-1D, all of which signal through the Gq/11 family of G-proteins
and different subtypes show different patterns of activation. This
gene encodes alpha-1A-adrenergic receptor. Alternative splicing of
this gene generates four transcript variants, which encode four
different isoforms with distinct C-termini but having similar
ligand binding properties. [provided by RefSeq, Jul 2008]'''.replace('\n', ' ')
)
cls.session.add(g)
chr8_n = usam.Seq(
seq='',
)
cls.session.add(chr8_n)
chr8_sa_n = usam.SeqAnno(
seq=chr8_n,
origin=o,
ac='NC_000008.10',
)
cls.session.add(chr8_sa_n)
for ac, tx_info in transcripts.items():
t_seq_n = usam.Seq(
seq=tx_info['seq']
)
cls.session.add(t_seq_n)
t_sa_n = usam.SeqAnno(
seq=t_seq_n,
origin=o,
ac=ac,
)
cls.session.add(t_sa_n)
t = usam.Transcript(
ac=ac,
origin=o,
gene_id=g.gene_id,
cds_start_i=tx_info['t_cds_start_i'],
cds_end_i=tx_info['t_cds_end_i'],
cds_md5='d41d8cd98f00b204e9800998ecf8427e',
)
cls.session.add(t)
if 'translation_exceptions' in tx_info:
for te in tx_info['translation_exceptions']:
te = usam.TranslationException(tx_ac=ac, **te)
cls.session.add(te)
p = usam.AssociatedAccessions(
tx_ac=ac,
pro_ac=tx_info['pro_ac'],
origin=o.name,
)
cls.session.add(p)
# ExonSet and Exons on Transcript seq
t_es = usam.ExonSet(
tx_ac=ac,
alt_ac=ac,
alt_strand=1,
alt_aln_method='transcript',
)
cls.session.add(t_es)
for i, se in enumerate(zip(tx_info['t_starts_i'], tx_info['t_ends_i'], tx_info['names'])):
e = usam.Exon(
exon_set=t_es,
start_i=se[0],
end_i=se[1],
name=se[2],
ord=i
)
cls.session.add(e)
# ExonSet and Exons on chromosome seq
g_es = usam.ExonSet(
tx_ac=ac,
alt_ac=chr8_sa_n.ac,
alt_strand=tx_info['g_strand'],
alt_aln_method='splign',
)
cls.session.add(g_es)
for i, se in enumerate(zip(tx_info['g_starts_i'], tx_info['g_ends_i'])):
e = usam.Exon(
exon_set=g_es,
start_i=se[0],
end_i=se[1],
ord=i,
)
cls.session.add(e)
cls.session.commit()
@classmethod
def tearDownClass(cls):
cls.session.close()
# kill the database (we started it)
import signal
cls._postgresql.stop(_signal=signal.SIGKILL)
cls._postgresql.cleanup()
def test_origin(self):
all_origins = self.session.query(usam.Origin).all()
self.assertEqual(len(all_origins), 1)
o = all_origins[0]
self.assertEqual(o.name, 'NCBI')
self.assertEqual(o.url, 'http://bogus.com/')
self.assertEqual(o.url_ac_fmt, 'http://bogus.com/{ac}')
# NM_000680.2, NM_033302.2, NM_033303.3, NM_033304.2
self.assertEqual(len(o.transcripts), 4)
# self.assertEqual( len(o.dnaseqs) , 5 ) ## NC_000008.10, + transcripts
# self.assertEqual( len(o.exon_sets) , 8 ) ## 4 transcripts *
# {genomic,transcript}
def test_gene(self):
all_genes = self.session.query(usam.Gene).all()
self.assertEqual(len(all_genes), 1)
g = all_genes[0]
self.assertEqual(g.descr, u'adrenoceptor alpha 1A')
#self.assertEqual( g.maploc, u'8p21.2' )
#self.assertEqual( g.strand, -1 )
#self.assertEqual( g.strand_pm, u'-' )
#self.assertEqual( len(g.transcripts), 4 )
self.assertTrue(
g.summary.startswith('Alpha-1-adrenergic receptors (alpha-1-ARs) are'))
def test_dnaseq(self):
all_dnaseqs = self.session.query(usam.Seq).all()
self.assertEqual(len(all_dnaseqs), 5)
n = self.session.query(usam.SeqAnno).filter(
usam.SeqAnno.ac == 'NC_000008.10').one()
self.assertEqual(n.ac, u'NC_000008.10')
# self.assertTrue(len(n.exon_sets),2)
self.assertEqual(n.origin.name, 'NCBI')
#self.assertEqual(len(n.transcripts), 0)
n = self.session.query(usam.SeqAnno).filter(
usam.SeqAnno.ac == 'NM_000680.2').one()
self.assertEqual(n.ac, u'NM_000680.2')
# self.assertTrue(len(n.exon_sets),1)
self.assertEqual(n.origin.name, 'NCBI')
n = self.session.query(usam.Seq).join(usam.Seq.aliases).filter(
usam.SeqAnno.ac == 'NM_000680.2').one()
self.assertEqual(len(n.seq), 2281)
self.assertTrue(n.seq.startswith('gaattccgaa'))
self.assertTrue(n.seq.endswith('gacatttatg'))
#self.assertEqual(len(n.transcripts), 1)
def test_exon_set(self):
all_exon_sets = self.session.query(usam.Seq).all()
self.assertTrue(len(all_exon_sets), 8)
exon_sets = self.session.query(usam.ExonSet).filter(
usam.ExonSet.tx_ac == 'NM_000680.2')
# http://www.ncbi.nlm.nih.gov/nuccore/NM_000680.2
## es = [ es for es in exon_sets if es.is_primary ][0]
## self.assertEqual( (es.cds_start_i,es.cds_end_i), (436, 1837) )
## self.assertEqual( len(es.exons), 2 )
## self.assertEqual( es.is_primary, True )
## self.assertEqual( es.ref_dnaseq.ac, 'NM_000680.2' )
## self.assertEqual( es.strand, 1 )
## self.assertEqual( es.transcript.ac, 'NM_000680.2' )
# seq_gene.md.gz:
# 9606 8 26627222 26627665 - NT_167187.1 14485368 14485811 - NM_000680.2 GeneID:148 UTR GRCh37.p10-Primary Assembly NM_000680.2 -
# 9606 8 26627666 26628183 - NT_167187.1 14485812 14486329 - NP_000671.2 GeneID:148 CDS GRCh37.p10-Primary Assembly NM_000680.2 -
# 9606 8 26721604 26722486 - NT_167187.1 14579750 14580632 - NP_000671.2 GeneID:148 CDS GRCh37.p10-Primary Assembly NM_000680.2 -
# 9606 8 26722487 26722922 - NT_167187.1 14580633 14581068 - NM_000680.2 GeneID:148 UTR GRCh37.p10-Primary Assembly NM_000680.2 -
## es = [ es for es in exon_sets if not es.is_primary ][0]
## self.assertEqual( (es.cds_start_i,es.cds_end_i), (26627665, 26722486) )
## self.assertEqual( len(es.exons), 2 )
## self.assertEqual( es.is_primary, False )
## self.assertEqual( es.ref_dnaseq.ac, 'NC_000008.10' )
## self.assertEqual( es.strand, -1 )
## self.assertEqual( es.transcript.ac, 'NM_000680.2' )
def test_exon(self):
t = self.session.query(usam.Transcript).filter(
usam.Transcript.ac == 'NM_000680.2').one()
#es = [ es for es in t.exon_sets if es.is_primary ][0]
#self.assertEqual( (es.exons[0].start_i,es.exons[0].end_i) , (0,1319) )
#self.assertEqual( (es.exons[1].start_i,es.exons[1].end_i) , (1319,2281) )
def test_associated_accessions(self):
all_aa = self.session.query(usam.AssociatedAccessions).all()
self.assertEqual(len(all_aa), 4)
# check values in one row:
aa = self.session.query(usam.AssociatedAccessions).filter_by(tx_ac='NM_000680.2').one()
self.assertIsInstance(aa.associated_accession_id, int)
self.assertIsInstance(aa.added, datetime.datetime)
self.assertEqual(aa.tx_ac, 'NM_000680.2')
self.assertEqual(aa.pro_ac, 'NP_000671.2')
self.assertEqual(aa.origin, 'NCBI')
def test_associated_accessions_transcript_not_in_database(self):
"""
Should create row in associated_accessions even for transcripts not in database.
This is only the case until associated_accessions.tx_ac is converted to a transcript foreign key.
"""
p = usam.AssociatedAccessions(
tx_ac='dummy_transcript',
pro_ac='dummy_protein',
origin='dummy_origin',
)
self.session.add(p)
self.session.commit()
aa = self.session.query(usam.AssociatedAccessions).filter_by(tx_ac='dummy_transcript').one()
self.assertEqual(aa.tx_ac, 'dummy_transcript')
self.assertEqual(aa.pro_ac, 'dummy_protein')
self.assertEqual(aa.origin, 'dummy_origin')
def test_translation_exception(self):
"""
Should create rows in translation_exception table.
"""
translation_exceptions = self.session.query(usam.TranslationException).filter_by(tx_ac='NM_000680.2').all()
self.assertEqual(len(translation_exceptions), 2)
def test_translation_exception_start_not_greater_than_end(self):
"""
Should not create row in translation_exception table if start is greater than end.
"""
te = usam.TranslationException(
tx_ac='NM_033302.2',
start_position=100,
end_position=99,
amino_acid='dummy_aa',
)
self.session.add(te)
with self.assertRaises(sqlalchemy.exc.IntegrityError):
self.session.commit()
# allow session to be used after failure
self.session.rollback()
# translation exception should not exist because transaction failed
translation_exceptions = self.session.query(usam.TranslationException).filter_by(tx_ac='NM_033302.2').all()
self.assertEqual(translation_exceptions, [])
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>