def test_potential_target(self):
seq_file = os.path.join(self.test_folder, "seq")
gff_file = os.path.join(self.test_folder, "gff")
gen_file(seq_file, self.example.seq_file)
gen_file(gff_file, self.example.gff_file)
args = self.mock_args.mock()
args.tar_start = 2
args.tar_end = 10
args.features = ["CDS"]
pt.potential_target(gff_file, seq_file, self.test_folder, args)
data = import_data(os.path.join(self.test_folder, "aaa_target.fa"))
self.assertTrue("\n".join(data), self.example.all_result)
def test_potential_target(self):
seq_file = os.path.join(self.test_folder, "seq")
gff_file = os.path.join(self.test_folder, "gff")
gen_file(seq_file, self.example.seq_file)
gen_file(gff_file, self.example.gff_file)
args = self.mock_args.mock()
args.tar_start = 2
args.tar_end = 10
args.features = ["CDS"]
pt.potential_target(gff_file, seq_file, self.test_folder, args)
data = import_data(os.path.join(self.test_folder, "aaa_target.fa"))
self.assertTrue("\n".join(data), self.example.all_result)
def _gen_seq(self, prefixs, args_tar):
print("Generating sRNA fasta files")
for srna in os.listdir(self.srna_path):
if srna.endswith("_sRNA.gff"):
prefix = srna.replace("_sRNA.gff", "")
prefixs.append(prefix)
srna_out = os.path.join(self.srna_seq_path,
"_".join([prefix, "sRNA.fa"]))
if "all" in args_tar.query:
self.helper.get_seq(
os.path.join(self.srna_path, srna),
os.path.join(self.fasta_path, prefix + ".fa"),
srna_out)
else:
if "_".join([prefix,
"sRNA.fa"]) in os.listdir(self.srna_seq_path):
os.remove(srna_out)
self._get_specific_seq(
os.path.join(self.srna_path, srna),
os.path.join(self.fasta_path, prefix + ".fa"),
srna_out, args_tar.query)
self._sort_srna_fasta(srna_out, prefix, self.srna_seq_path)
print("Generating target fasta files")
for gff in os.listdir(self.gff_path):
if gff.endswith(".gff"):
prefix = gff.replace(".gff", "")
potential_target(os.path.join(self.gff_path, gff),
os.path.join(self.fasta_path, prefix + ".fa"),
os.path.join(self.target_seq_path), args_tar)
file_num = 1
num = 0
sub_prefix = os.path.join(self.target_seq_path,
"_".join([prefix, "target"]))
sub_out = open("_".join([sub_prefix,
str(file_num) + ".fa"]), "w")
with open((sub_prefix + ".fa"), "r") as t_f:
for line in t_f:
line = line.strip()
if line.startswith(">"):
# line = line.replace("|", "_")
num += 1
if (num == 100):
num = 0
file_num += 1
sub_out.close()
sub_out = open(
"_".join([sub_prefix,
str(file_num) + ".fa"]), "w")
sub_out.write(line + "\n")
sub_out.close()
def _gen_seq(self, prefixs, args_tar):
print("Generating sRNA fasta files")
for srna in os.listdir(self.srna_path):
if srna.endswith("_sRNA.gff"):
prefix = srna.replace("_sRNA.gff", "")
prefixs.append(prefix)
srna_out = os.path.join(self.srna_seq_path,
"_".join([prefix, "sRNA.fa"]))
if "all" in args_tar.query:
self.helper.get_seq(
os.path.join(self.srna_path, srna),
os.path.join(self.fasta_path, prefix + ".fa"),
srna_out)
else:
if "_".join([prefix, "sRNA.fa"]) in os.listdir(
self.srna_seq_path):
os.remove(srna_out)
self._get_specific_seq(
os.path.join(self.srna_path, srna),
os.path.join(self.fasta_path, prefix + ".fa"),
srna_out, args_tar.query)
self._sort_srna_fasta(srna_out, prefix, self.srna_seq_path)
print("Generating target fasta files")
for gff in os.listdir(self.gff_path):
if gff.endswith(".gff"):
prefix = gff.replace(".gff", "")
potential_target(os.path.join(self.gff_path, gff),
os.path.join(self.fasta_path, prefix + ".fa"),
os.path.join(self.target_seq_path), args_tar)
file_num = 1
num = 0
sub_prefix = os.path.join(self.target_seq_path,
"_".join([prefix, "target"]))
sub_out = open("_".join([sub_prefix, str(file_num) + ".fa"]),
"w")
with open((sub_prefix + ".fa"), "r") as t_f:
for line in t_f:
line = line.strip()
if line.startswith(">"):
# line = line.replace("|", "_")
num += 1
if (num == 100):
num = 0
file_num += 1
sub_out.close()
sub_out = open("_".join([sub_prefix,
str(file_num) + ".fa"]), "w")
sub_out.write(line + "\n")
sub_out.close()
def _gen_seq(self, prefixs, target_prefixs, args_tar):
print("Generating sRNA fasta files")
for gff in os.listdir(self.gff_path):
if gff.endswith(".gff"):
prefix = gff.replace(".gff", "")
target_prefixs.append(prefix)
detect = False
for gff in os.listdir(self.gff_path):
if gff.endswith(".gff"):
prefix = gff.replace(".gff", "")
potential_target(os.path.join(self.gff_path, gff),
os.path.join(self.fasta_path, prefix + ".fa"),
os.path.join(self.target_seq_path), args_tar,
target_prefixs)
file_num = 1
num = 0
sub_prefix = os.path.join(self.target_seq_path,
"_".join([prefix, "target"]))
if os.path.exists(sub_prefix + ".fa"):
sub_out = open(
"_".join([sub_prefix,
str(file_num) + ".fa"]), "w")
with open((sub_prefix + ".fa"), "r") as t_f:
for line in t_f:
line = line.strip()
if line.startswith(">"):
# line = line.replace("|", "_")
num += 1
if (num == 100):
num = 0
file_num += 1
sub_out.close()
sub_out = open(
"_".join(
[sub_prefix,
str(file_num) + ".fa"]), "w")
detect = True
sub_out.write(line + "\n")
sub_out.close()
else:
open(sub_prefix + ".fa", "w").close()
if not detect:
print("No assigned features can be found. "
"Please check your genome annotation. "
"And assign correct features to --target_feature.")
sys.exit()
print("Generating sRNA fasta files")
for srna in os.listdir(self.srna_path):
if srna.endswith("_sRNA.gff"):
prefix = srna.replace("_sRNA.gff", "")
prefixs.append(prefix)
srna_out = os.path.join(self.srna_seq_path,
"_".join([prefix, "sRNA.fa"]))
if "all" in args_tar.query:
self.helper.get_seq(
os.path.join(self.srna_path, srna),
os.path.join(self.fasta_path, prefix + ".fa"),
srna_out)
else:
if "_".join([prefix,
"sRNA.fa"]) in os.listdir(self.srna_seq_path):
os.remove(srna_out)
self._get_specific_seq(
os.path.join(self.srna_path, srna),
os.path.join(self.fasta_path, prefix + ".fa"),
srna_out, args_tar.query)
self._sort_srna_fasta(srna_out, prefix, self.srna_seq_path)
