def test_namewithoutpipe_maintained(self):
self.assertEqual(internal.fix_leaky_pipes('CbirLOC12345'),
'CbirLOC12345')
def test_namewithpipe_fixed(self):
self.assertEqual(internal.fix_leaky_pipes('Cbir|LOC12345'),
'Cbir\|LOC12345')
previousseq = ""
seqdic = {} # loaded up to remove duplicate sequences
excluded_genes = config.make_a_list(args.exclude_genes)
excluded_species = config.make_a_list(args.exclude_species)
# place any sequences provided in the input into the seqdic
if args.fasta:
for defline, seq in internal.parsefasta(args.fasta):
if sequence_filter(seq, args.maxlength, args.minlength):
continue
else:
seqdic[seq] = defline
for homolog in sorted(homologlist):
# remove excluded genes before bothering to look up their sequence:
searchname = internal.fix_leaky_pipes(homolog)
if searchname in excluded_genes:
continue
if homologlist[homolog][0] in excluded_species:
continue
# extract sequences of remaining genes and add to conversion dictionary
itercount += 1
for defline, seq, spec in internal.get_gene_fastas(
genes=[searchname],
species=homologlist[homolog][0],
fastafile=None,
dbpaths=dbpaths,
specieslist=specieslist,
comment=str(homologlist[homolog][1]) + str(itercount),
def test_namewithoutpipe_maintained(self):
self.assertEqual(internal.fix_leaky_pipes('CbirLOC12345'),
'CbirLOC12345')
def test_namewithpipe_fixed(self):
self.assertEqual(internal.fix_leaky_pipes('Cbir|LOC12345'),
'Cbir\|LOC12345')
previousseq = ""
seqdic = {} # loaded up to remove duplicate sequences
excluded_genes = config.make_a_list(args.exclude_genes)
excluded_species = config.make_a_list(args.exclude_species)
# place any sequences provided in the input into the seqdic
if args.fasta:
for defline, seq in internal.parsefasta(args.fasta):
if sequence_filter(seq, args.maxlength, args.minlength):
continue
else:
seqdic[seq] = defline
for homolog in sorted(homologlist):
# remove excluded genes before bothering to look up their sequence:
searchname = internal.fix_leaky_pipes(homolog)
if searchname in excluded_genes:
continue
if homologlist[homolog][0] in excluded_species:
continue
# extract sequences of remaining genes and add to conversion dictionary
itercount += 1
for defline, seq, spec in internal.get_gene_fastas(
genes=[searchname],
species=homologlist[homolog][0],
fastafile=None,
dbpaths=dbpaths,
specieslist=specieslist,
comment=str(homologlist[homolog][1]) + str(itercount),
