def test_combine(self):
cft.Gff3Parser = Mock_Gff_parser
output_file = os.path.join(self.test_folder, "test.out")
frag_file = os.path.join(self.test_folder, "frag.gff")
tex_file = os.path.join(self.test_folder, "tex.gff")
with open(frag_file, "w") as fh:
fh.write("frag")
with open(tex_file, "w") as th:
th.write("tex")
cft.combine(frag_file, tex_file, 5, output_file)
trans = []
outs, attributes_out = extract_info(output_file, "file")
refs, attributes_ref = extract_info(self.example.out_tran, "string")
self.assertEqual(set(outs), set(refs[1:]))
def test_combine(self):
cft.Gff3Parser = Mock_Gff_parser
output_file = os.path.join(self.test_folder, "test.out")
frag_file = os.path.join(self.test_folder, "frag.gff")
tex_file = os.path.join(self.test_folder, "tex.gff")
with open(frag_file, "w") as fh:
fh.write("frag")
with open(tex_file, "w") as th:
th.write("tex")
cft.combine(frag_file, tex_file, 5, output_file)
trans = []
outs, attributes_out = extract_info(output_file, "file")
refs, attributes_ref = extract_info(self.example.out_tran, "string")
self.assertEqual(set(outs), set(refs[1:]))
def _for_two_wigs(self, strains, args_tran, log):
'''merge the results of fragemented and tex treated libs'''
if (args_tran.frag_wigs is not None) and (
args_tran.tex_wigs is not None):
log.write("Running combine_frag_tex.py to merge the results from "
"fragmented libs and dRNA-Seq libs.\n")
print("Merging fragmented and tex treated ones")
for strain in strains:
frag_gff = os.path.join(self.gff_outfolder,
"_".join([strain, self.frag]))
tex_gff = os.path.join(self.gff_outfolder,
"_".join([strain, self.tex]))
final_gff = os.path.join(self.gff_outfolder,
"_".join([strain, self.endfix_tran]))
for gff in os.listdir(self.gff_outfolder):
if "_transcript_" in gff:
filename = gff.split("_transcript_")
if (strain == filename[0]) and (
"tex_notex.gff" == filename[1]):
tex_file = gff
elif (strain == filename[0]) and (
"fragment.gff" == filename[1]):
frag_file = gff
combine(os.path.join(self.gff_outfolder, frag_file),
os.path.join(self.gff_outfolder, tex_file),
args_tran.tolerance,
os.path.join(self.gff_outfolder,
"_".join([strain, self.endfix_tran])))
os.remove(frag_gff)
os.remove(tex_gff)
log.write("\t" + final_gff + " is generated.\n")
else:
if args_tran.frag_wigs is not None:
for strain in strains:
frag_gff = os.path.join(
self.gff_outfolder, "_".join([strain, self.frag]))
final_gff = os.path.join(
self.gff_outfolder,
"_".join([strain, self.endfix_tran]))
shutil.move(frag_gff, final_gff)
log.write("\t" + final_gff + " is generated.\n")
elif args_tran.tex_wigs is not None:
for strain in strains:
tex_gff = os.path.join(
self.gff_outfolder, "_".join([strain, self.tex]))
final_gff = os.path.join(
self.gff_outfolder,
"_".join([strain, self.endfix_tran]))
shutil.move(tex_gff, final_gff)
log.write("\t" + final_gff + " is generated.\n")
def _for_two_wigs(self, strains, args_tran):
'''merge the results of fragemented and tex treated libs'''
if (args_tran.frag_wigs is not None) and (args_tran.tex_wigs
is not None):
print("Merging fragment and tex treat one")
for strain in strains:
frag_gff = os.path.join(self.gff_outfolder,
"_".join([strain, self.frag]))
tex_gff = os.path.join(self.gff_outfolder,
"_".join([strain, self.tex]))
final_gff = os.path.join(self.gff_outfolder,
"_".join([strain, self.endfix_tran]))
for gff in os.listdir(self.gff_outfolder):
if "_transcript_" in gff:
filename = gff.split("_transcript_")
if (strain == filename[0]) and ("tex_notex.gff"
== filename[1]):
tex_file = gff
elif (strain == filename[0]) and ("fragment.gff"
== filename[1]):
frag_file = gff
combine(
os.path.join(self.gff_outfolder, frag_file),
os.path.join(self.gff_outfolder, tex_file),
args_tran.tolerance,
os.path.join(self.gff_outfolder,
"_".join([strain, self.endfix_tran])))
os.remove(frag_gff)
os.remove(tex_gff)
else:
if args_tran.frag_wigs is not None:
for strain in strains:
frag_gff = os.path.join(self.gff_outfolder,
"_".join([strain, self.frag]))
final_gff = os.path.join(
self.gff_outfolder,
"_".join([strain, self.endfix_tran]))
shutil.move(frag_gff, final_gff)
elif args_tran.tex_wigs is not None:
for strain in strains:
tex_gff = os.path.join(self.gff_outfolder,
"_".join([strain, self.tex]))
final_gff = os.path.join(
self.gff_outfolder,
"_".join([strain, self.endfix_tran]))
shutil.move(tex_gff, final_gff)
def _for_two_wigs(self, strains, args_tran):
if (args_tran.frag_wigs is not None) and (
args_tran.tex_wigs is not None):
print("merge fragment and tex treat one ....")
for strain in strains:
frag_gff = os.path.join(self.gff_outfolder,
"_".join([strain, self.frag]))
tex_gff = os.path.join(self.gff_outfolder,
"_".join([strain, self.tex]))
final_gff = os.path.join(self.gff_outfolder,
"_".join([strain, self.endfix_tran]))
for gff in os.listdir(self.gff_outfolder):
if "transcript_assembly" in gff:
filename = gff.split("_transcript_assembly_")
if (strain == filename[0]) and (
"tex_notex.gff" == filename[1]):
tex_file = gff
elif (strain == filename[0]) and (
"fragment.gff" == filename[1]):
frag_file = gff
combine(os.path.join(self.gff_outfolder, frag_file),
os.path.join(self.gff_outfolder, tex_file),
args_tran.tolerance,
os.path.join(self.gff_outfolder,
"_".join([strain, self.endfix_tran])))
os.remove(frag_gff)
os.remove(tex_gff)
else:
if args_tran.frag_wigs is not None:
for strain in strains:
frag_gff = os.path.join(
self.gff_outfolder, "_".join([strain, self.frag]))
final_gff = os.path.join(
self.gff_outfolder,
"_".join([strain, self.endfix_tran]))
shutil.move(frag_gff, final_gff)
elif args_tran.tex_wigs is not None:
for strain in strains:
tex_gff = os.path.join(
self.gff_outfolder, "_".join([strain, self.tex]))
final_gff = os.path.join(
self.gff_outfolder,
"_".join([strain, self.endfix_tran]))
shutil.move(tex_gff, final_gff)