def _scan_extract_rfam(self, prefixs, args_ribo):
for gff in os.listdir(self.gff_path):
if gff.endswith(".gff"):
prefix = gff.replace(".gff", "")
first_seq = os.path.join(self.tmp_files["fasta"],
prefix + ".fa")
prefixs.append(prefix)
print("extracting seq of riboswitch candidates of {0}".format(
prefix))
extract_potential_rbs(
os.path.join(self.fasta_path, prefix + ".fa"),
os.path.join(self.gff_path, gff),
os.path.join(self.tss_path, prefix + "_TSS.gff"),
os.path.join(self.tran_path, prefix + "_transcript.gff"),
first_seq, args_ribo)
print("pre-scanning of {0}".format(prefix))
first_scan_file = self._run_infernal(args_ribo, first_seq,
"txt", prefix)
sec_seq = os.path.join(self.tmp_files["fasta"],
"_".join([prefix, "regenerate.fa"]))
first_table = os.path.join(
self.tmp_files["table"],
"_".join([prefix, self.suffixs["csv"]]))
regenerate_seq(first_scan_file, first_seq,
first_table, sec_seq)
print("scanning of {0}".format(prefix))
sec_scan_file = self._run_infernal(args_ribo, sec_seq,
"re_txt", prefix)
sec_table = os.path.join(
self.tmp_files["table"],
"_".join([prefix, self.suffixs["re_csv"]]))
reextract_rbs(sec_scan_file, first_table, sec_table)
shutil.move(sec_table, first_table)
modify_table(first_table, args_ribo.output_all)
return prefixs
def _scan_extract_rfam(self, prefixs, args_ribo):
for gff in os.listdir(self.gff_path):
if gff.endswith(".gff"):
prefix = gff.replace(".gff", "")
first_seq = os.path.join(self.tmp_files["fasta"],
prefix + ".fa")
prefixs.append(prefix)
print("extracting seq of riboswitch candidates of {0}".format(
prefix))
extract_potential_rbs(
os.path.join(self.fasta_path, prefix + ".fa"),
os.path.join(self.gff_path, gff),
os.path.join(self.tss_path, prefix + "_TSS.gff"),
os.path.join(self.tran_path, prefix + "_transcript.gff"),
first_seq, args_ribo)
print("pre-scanning of {0}".format(prefix))
first_scan_file = self._run_infernal(args_ribo, first_seq,
"txt", prefix)
sec_seq = os.path.join(self.tmp_files["fasta"],
"_".join([prefix, "regenerate.fa"]))
first_table = os.path.join(
self.tmp_files["table"],
"_".join([prefix, self.suffixs["csv"]]))
regenerate_seq(first_scan_file, first_seq, first_table,
sec_seq)
print("scanning of {0}".format(prefix))
sec_scan_file = self._run_infernal(args_ribo, sec_seq,
"re_txt", prefix)
sec_table = os.path.join(
self.tmp_files["table"],
"_".join([prefix, self.suffixs["re_csv"]]))
reextract_rbs(sec_scan_file, first_table, sec_table)
shutil.move(sec_table, first_table)
modify_table(first_table, args_ribo.output_all)
return prefixs
def test_regenerate_seq(self):
out_table = os.path.join(self.test_folder, "table")
out_seq = os.path.join(self.test_folder, "seq")
align_file = os.path.join(self.test_folder, "align")
seq_file = os.path.join(self.test_folder, "ribo_seq")
gen_file(align_file, self.example.scan_file)
gen_file(seq_file, self.example.seq_file)
rr.regenerate_seq(align_file, seq_file, out_table, out_seq)
data = import_data(out_table)
self.assertEqual("\n".join(data), "riboswitch_5\tStaphylococcus_aureus_HG003\t+\tSAOUHSC_00013\t10\t16\tRF00162\t6.2e-18\t5\t12")
data = import_data(out_seq)
self.assertEqual("\n".join(data), ">riboswitch_5|Staphylococcus_aureus_HG003|+|SAOUHSC_00013|14|21\nATTATTAC")
def test_regenerate_seq(self):
out_table = os.path.join(self.test_folder, "table")
out_seq = os.path.join(self.test_folder, "seq")
align_file = os.path.join(self.test_folder, "align")
seq_file = os.path.join(self.test_folder, "ribo_seq")
gen_file(align_file, self.example.scan_file)
gen_file(seq_file, self.example.seq_file)
rr.regenerate_seq(align_file, seq_file, out_table, out_seq)
data = import_data(out_table)
self.assertEqual(
"\n".join(data),
"riboswitch_5\tStaphylococcus_aureus_HG003\t+\tSAOUHSC_00013\t10\t16\tRF00162\t6.2e-18\t5\t12"
)
data = import_data(out_seq)
self.assertEqual("\n".join(data), (
">riboswitch_5|Staphylococcus_aureus_HG003|+|SAOUHSC_00013|14|21\nATTATTAC\n"
">riboswitch_5|Staphylococcus_aureus_HG003|+|SAOUHSC_00013|14|21\nATTATTAC"
))
def _scan_extract_rfam(self, prefixs, args_ribo, tmp_files, suffixs,
feature, rfam):
'''extract the seq of candidates and scanning the candidates'''
for gff in os.listdir(self.gff_path):
if gff.endswith(".gff"):
prefix = gff.replace(".gff", "")
first_seq = os.path.join(tmp_files["fasta"],
prefix + ".fa")
prefixs.append(prefix)
print("Extracting sequences of candidates for {0}".format(
prefix))
extract_potential_rbs(
os.path.join(self.fasta_path, prefix + ".fa"),
os.path.join(self.gff_path, gff),
os.path.join(self.tss_path, prefix + "_TSS.gff"),
os.path.join(self.tran_path, prefix + "_transcript.gff"),
first_seq, args_ribo, feature)
print("Pre-scanning of {0}".format(prefix))
first_scan_file = self._run_cmscan(
args_ribo, first_seq, "txt", prefix, tmp_files,
suffixs, rfam)
sec_seq = os.path.join(tmp_files["fasta"],
"_".join([prefix, "regenerate.fa"]))
first_table = os.path.join(
tmp_files["table"],
"_".join([prefix, suffixs["csv"]]))
regenerate_seq(first_scan_file, first_seq,
first_table, sec_seq)
print("Scanning of {0}".format(prefix))
sec_scan_file = self._run_cmscan(
args_ribo, sec_seq, "re_txt", prefix, tmp_files,
suffixs, rfam)
sec_table = os.path.join(
tmp_files["table"],
"_".join([prefix, suffixs["re_csv"]]))
reextract_rbs(sec_scan_file, first_table, sec_table)
shutil.move(sec_table, first_table)
modify_table(first_table, args_ribo.output_all)
return prefixs
def _scan_extract_rfam(self, prefixs, args_ribo, tmp_files, suffixs,
feature, rfam, log):
'''extract the seq of candidates and scanning the candidates'''
for gff in os.listdir(self.gff_path):
if gff.endswith(".gff"):
prefix = gff.replace(".gff", "")
first_seq = os.path.join(tmp_files["fasta"],
prefix + ".fa")
prefixs.append(prefix)
print("Extracting sequences of candidates for {0}".format(
prefix))
if self.tss_path is not None:
tss_file = os.path.join(self.tss_path, prefix + "_TSS.gff")
else:
tss_file = None
log.write("Running extract_RBS.py to extract potential "
"sequences of riboswitches/RNA thermometers for "
"{0}.\n".format(prefix))
extract_potential_rbs(
os.path.join(self.fasta_path, prefix + ".fa"),
os.path.join(self.gff_path, gff), tss_file,
os.path.join(self.tran_path, prefix + "_transcript.gff"),
first_seq, args_ribo, feature)
log.write("\t" + first_seq + " is temporary generated.\n")
print("Pre-scanning of {0}".format(prefix))
log.write("Using Infernal to pre-scan riboswitches/RNA "
"thermometers for {0}.\n".format(prefix))
log.write("Please make sure the version of Infernal is at least 1.1.1.\n")
first_scan_file = self._run_cmscan(
args_ribo, first_seq, "txt", prefix, tmp_files,
suffixs, rfam, log)
sec_seq = os.path.join(tmp_files["fasta"],
"_".join([prefix, "regenerate.fa"]))
first_table = os.path.join(
tmp_files["table"],
"_".join([prefix, suffixs["csv"]]))
log.write("Running recompute_RBS.py to update the potential "
"sequences of riboswitches/RNA thermometers for {0} "
"based on the pre-scanning results.\n".format(prefix))
regenerate_seq(first_scan_file, first_seq,
first_table, sec_seq)
log.write("\t" + sec_seq + " is temporary generated.\n")
print("Scanning of {0}".format(prefix))
log.write("Using Infernal to scan riboswitches/RNA "
"thermometers for {0}.\n".format(prefix))
log.write("Please make sure the version of Infernal is at "
"least 1.1.1.\n")
sec_scan_file = self._run_cmscan(
args_ribo, sec_seq, "re_txt", prefix, tmp_files,
suffixs, rfam, log)
sec_table = os.path.join(
tmp_files["table"],
"_".join([prefix, suffixs["re_csv"]]))
log.write("Running recompute_RBS.py and modify_rbs_table.py "
"to generate tables for {0} "
"based on the scanning results.\n".format(prefix))
reextract_rbs(sec_scan_file, first_table, sec_table,
args_ribo.cutoff)
shutil.move(sec_table, first_table)
modify_table(first_table, args_ribo.output_all)
return prefixs
def _scan_extract_rfam(self, prefixs, args_ribo, tmp_files, suffixs,
feature, rfam, log):
'''extract the seq of candidates and scanning the candidates'''
for gff in os.listdir(self.gff_path):
if gff.endswith(".gff"):
prefix = gff.replace(".gff", "")
first_seq = os.path.join(tmp_files["fasta"], prefix + ".fa")
prefixs.append(prefix)
print("Extracting sequences of candidates for {0}".format(
prefix))
if self.tss_path is not None:
tss_file = os.path.join(self.tss_path, prefix + "_TSS.gff")
else:
tss_file = None
log.write("Running extract_RBS.py to extract potential "
"sequences of riboswitches/RNA thermometers for "
"{0}.\n".format(prefix))
extract_potential_rbs(
os.path.join(self.fasta_path, prefix + ".fa"),
os.path.join(self.gff_path, gff), tss_file,
os.path.join(self.tran_path, prefix + "_transcript.gff"),
first_seq, args_ribo, feature)
log.write("\t" + first_seq + " is temporary generated.\n")
print("Pre-scanning of {0}".format(prefix))
log.write("Using Infernal to pre-scan riboswitches/RNA "
"thermometers for {0}.\n".format(prefix))
log.write(
"Please make sure the version of Infernal is at least 1.1.1.\n"
)
first_scan_file = self._run_cmscan(args_ribo, first_seq, "txt",
prefix, tmp_files, suffixs,
rfam, log)
sec_seq = os.path.join(tmp_files["fasta"],
"_".join([prefix, "regenerate.fa"]))
first_table = os.path.join(tmp_files["table"],
"_".join([prefix, suffixs["csv"]]))
log.write(
"Running recompute_RBS.py to update the potential "
"sequences of riboswitches/RNA thermometers for {0} "
"based on the pre-scanning results.\n".format(prefix))
regenerate_seq(first_scan_file, first_seq, first_table,
sec_seq)
log.write("\t" + sec_seq + " is temporary generated.\n")
print("Scanning of {0}".format(prefix))
log.write("Using Infernal to scan riboswitches/RNA "
"thermometers for {0}.\n".format(prefix))
log.write("Please make sure the version of Infernal is at "
"least 1.1.1.\n")
sec_scan_file = self._run_cmscan(args_ribo, sec_seq, "re_txt",
prefix, tmp_files, suffixs,
rfam, log)
sec_table = os.path.join(tmp_files["table"],
"_".join([prefix, suffixs["re_csv"]]))
log.write("Running recompute_RBS.py and modify_rbs_table.py "
"to generate tables for {0} "
"based on the scanning results.\n".format(prefix))
reextract_rbs(sec_scan_file, first_table, sec_table,
args_ribo.cutoff)
shutil.move(sec_table, first_table)
modify_table(first_table, args_ribo.output_all)
return prefixs