def _assign_single(self,blast,db_file,best):
self.logger.info("\n# [BASTA STATUS] Assigning taxonomies ...")
(tax_lookup, map_lookup) = self._get_lookups(db_file)
taxa = []
nofo_map = []
out_fh = open(self.output, "w")
for seq_hits in futils.hit_gen(blast,self.alen,self.evalue,self.identity,self.config,self.num):
for seq in seq_hits:
self._get_tax_list(seq_hits[seq],map_lookup,tax_lookup,taxa,nofo_map)
lca = self._getLCS([x for x in taxa if x])
if self.info_file:
self._print_info(taxa,"Sequence")
self._print(out_fh,"Sequence",lca,best,taxa)
return lca
def _assign_sequence(self,blast,db_file,best):
self.logger.info("\n# [BASTA STATUS] Assigning taxonomies ...")
(tax_lookup, map_lookup) = self._get_lookups(db_file)
nofo_map = []
out_fh = open(self.output,"w")
print(self.info_file)
for seq_hits in futils.hit_gen(blast,self.alen,self.evalue,self.identity,self.config,self.num):
for seq in seq_hits:
taxa = []
self._get_tax_list(seq_hits[seq],map_lookup,tax_lookup,taxa,nofo_map)
lca = self._getLCS(taxa)
if self.info_file:
self._print_info(taxa,seq)
self._print(out_fh,seq,lca,best,taxa)
out_fh.close()
def test_hit_hash(self):
hh = fu._hit_hash(['bli',10,20,1e-7,'bla'],self.config)
self.assertEqual(hh['evalue'],1e-7)
self.assertEqual(hh['identity'],10)
self.assertEqual(hh['id'],'bla')
self.assertEqual(hh['alen'],20)
def test_get_hit_name(self):
self.assertEqual(fu._get_hit_name("something|acc.1|me myself and I"),"acc")
self.assertEqual(fu._get_hit_name("acc.1 me, myself and I"),"acc")
self.assertEqual(fu._get_hit_name("gi|123145|ref|acc.1"),"acc")
self.assertEqual(fu._get_hit_name("acc.1"),"acc")
def test_check_hit(self):
self.assertTrue(fu._check_hit(['bli',10,20,1e-7,'bla'],5,0.05,5,self.config))
self.assertFalse(fu._check_hit(['bli',4,20,1e-7,'bla'],5,0.05,5,self.config))
self.assertFalse(fu._check_hit(['bli',10,4,1e-7,'bla'],5,0.05,5,self.config))
self.assertFalse(fu._check_hit(['bli',10,20,2,'bla'],5,0.05,5,self.config))