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)