class BlastMapperTest(unittest.TestCase):
"""
Run a number of tests using taxa id
"""
def setUp(self):
"""
connect to the database
"""
self.parsedFile = os.path.join(os.path.dirname(__file__),"blast-parsed.csv")
self.bm = BlastMapper()
def test01Summarize(self):
"""
test the summarize function
"""
summaryFile = re.sub("\.csv","",self.parsedFile)+"_summary.csv"
if os.path.exists(summaryFile):
os.remove(summaryFile)
self.bm.create_summarized(self.parsedFile,uniprot=True)
self.assertTrue(os.path.exists(summaryFile))
def test02Something(self):
"""
read in the results summary
"""
summaryFile = re.sub("\.csv","",self.parsedFile)+"_summary.csv"
bmap = self.bm.load_summary(summaryFile,taxaList=["10090"])
self.assertEqual(bmap['GG11117|c2_g1_i1'][0],'INT1_MOUSE')
self.assertEqual(bmap['GG11117|c2_g1_i1'][1],'68510')
bmap = self.bm.load_summary(summaryFile,taxaList=["10090"],trinityGene=True)
self.assertEqual(bmap['GG11117|c2_g1'][0],'INT1_MOUSE')
bmap = self.bm.load_summary(summaryFile,taxaList=["10090"],trinityGene=True,best=False)
self.assertEqual(bmap['GG11117|c2_g1'][0][0],'INT1_MOUSE')
self.assertEqual(bmap['GG11117|c2_g1'][0][4],0.0)
hitEntries = transcript2uniprot.values()
print 'hits', len(hitEntries)
print 'matched', len(blah)
#print 'results', len(results)
#for row in results:
# upEntry2Gene[str(row.uniprot_entry)] = str(row.gene_id)
#print upEntry2Gene
#sys.exit()
# ## using htsint's mapper
#upEntry2Gene,upEntry2Taxa = {},{}
#uMapper = uniprot_mapper(session,uniprotIdList=hitEntries,gene=True,taxa=True)
#for key,item in uMapper.iteritems():
# upEntry2Gene[str(key)] = str(item['gene_id'])
# upEntry2Taxa[str(key)] = str(item['taxa_id'])
#
#print list(set(upEntry2Taxa.values()))
#print len(upEntry2Gene.keys())
#
#
sys.exit()
else:
id2gene = None
## run
bm.create_summarized(parsedFilePath,
species=species,
taxaList=taxaList,
hit2gene=id2gene,
uniprot=uniprot)
