def test_get_intergenic(self):
out_file = os.path.join(self.test_folder, "out")
gff_file = os.path.join(self.test_folder, "anno.gff")
tran_file = os.path.join(self.test_folder, "tran.gff")
gen_file(gff_file, self.example.gff_file)
gen_file(tran_file, self.example.tran_file)
si.get_intergenic(gff_file, tran_file, out_file, True, False)
datas = import_data(out_file)
self.assertEqual("\n".join(datas), self.example.out_file)
def test_get_intergenic(self):
out_file = os.path.join(self.test_folder, "out")
gff_file = os.path.join(self.test_folder, "anno.gff")
tran_file = os.path.join(self.test_folder, "tran.gff")
gen_file(gff_file, self.example.gff_file)
gen_file(tran_file, self.example.tran_file)
si.get_intergenic(gff_file, tran_file, out_file, True, False)
datas = import_data(out_file)
self.assertEqual("\n".join(datas), self.example.out_file)
def _compare_tran_cds(self, args_sorf):
'''compare transcript and CDS to find the intergenic region'''
prefixs = []
for gff in os.listdir(args_sorf.gffs):
if gff.endswith(".gff"):
prefix = gff.replace(".gff", "")
prefixs.append(prefix)
print("Comparing transcript and CDS of {0}".format(prefix))
get_intergenic(os.path.join(args_sorf.gffs, gff),
os.path.join(self.tran_path,
"_".join([prefix, "transcript.gff"])),
os.path.join(args_sorf.out_folder,
"_".join([prefix, "inter.gff"])),
args_sorf.utr_detect, args_sorf.hypo)
return prefixs
def _compare_tran_cds(self, args_sorf, log):
'''compare transcript and CDS to find the intergenic region'''
prefixs = []
log.write("Running sORF_intergenic.py to extract the sequences of "
"potential sORFs\n")
for gff in os.listdir(args_sorf.gffs):
if gff.endswith(".gff"):
prefix = gff.replace(".gff", "")
prefixs.append(prefix)
print("Comparing transcripts and CDSs of {0}".format(prefix))
get_intergenic(os.path.join(args_sorf.gffs, gff),
os.path.join(self.tran_path,
"_".join([prefix, "transcript.gff"])),
os.path.join(args_sorf.out_folder,
"_".join([prefix, "inter.gff"])),
args_sorf.utr_detect, args_sorf.hypo,
args_sorf.extend_5, args_sorf.extend_3)
log.write("\t" + os.path.join(args_sorf.out_folder,
"_".join([prefix, "inter.gff"])) +
" is generated to temporary store the sequences.\n")
return prefixs
def _compare_tran_cds(self, args_sorf, log):
'''compare transcript and CDS to find the intergenic region'''
prefixs = []
log.write("Running sORF_intergenic.py to extract the sequences of "
"potential sORFs\n")
for gff in os.listdir(args_sorf.gffs):
if gff.endswith(".gff"):
prefix = gff.replace(".gff", "")
prefixs.append(prefix)
print("Comparing transcripts and CDSs of {0}".format(prefix))
get_intergenic(
os.path.join(args_sorf.gffs, gff),
os.path.join(self.tran_path,
"_".join([prefix, "transcript.gff"])),
os.path.join(args_sorf.out_folder,
"_".join([prefix, "inter.gff"])),
args_sorf.utr_detect, args_sorf.hypo, args_sorf.extend_5,
args_sorf.extend_3)
log.write("\t" + os.path.join(args_sorf.out_folder, "_".join(
[prefix, "inter.gff"])) +
" is generated to temporary store the sequences.\n")
return prefixs