def _merge_results(self, args_ribo, scan_folder, suffixs, tmp_files,
table_folder, stat_folder, feature_id, gff_outfolder,
feature, log):
'''merge the results from the results of two searching'''
for gff in os.listdir(args_ribo.gffs):
if gff.endswith(".gff"):
prefix = gff.replace(".gff", "")
print("Merging results of {0}".format(prefix))
pre_strain = ""
self.helper.check_make_folder(os.path.join(
scan_folder, prefix))
fh = open(os.path.join(args_ribo.gffs, gff))
log.write("Merging the results from Infernal to generate "
"tables for {0}.\n".format(prefix))
for entry in self.gff_parser.entries(fh):
if entry.seq_id != pre_strain:
if len(pre_strain) == 0:
shutil.copyfile(os.path.join(
tmp_files["table"],
"_".join([entry.seq_id, suffixs["csv"]])),
os.path.join(
table_folder,
"_".join([prefix, suffixs["csv"]])))
else:
self.helper.merge_file(os.path.join(
tmp_files["table"],
"_".join([entry.seq_id, suffixs["csv"]])),
os.path.join(
table_folder,
"_".join([prefix, suffixs["csv"]])))
shutil.copy(os.path.join(
tmp_files["scan"],
"_".join([entry.seq_id, suffixs["txt"]])),
os.path.join(scan_folder, prefix))
shutil.copy(os.path.join(
tmp_files["scan"],
"_".join([entry.seq_id, suffixs["re_txt"]])),
os.path.join(scan_folder, prefix))
pre_strain = entry.seq_id
log.write("The following files are generated.\n")
for folder in (table_folder, scan_folder):
for file_ in os.listdir(folder):
log.write("\t" + os.path.join(folder, file_) + "\n")
out_stat = os.path.join(
stat_folder,
"_".join(["stat", prefix, feature + ".txt"]))
print("Computing statistics of {0}".format(prefix))
log.write("Running ribo_gff.py to do statistics and generate "
"gff files for {0}.\n".format(prefix))
log.write("The following files are generated:\n")
out_gff = os.path.join(gff_outfolder, "_".join([
prefix, feature + ".gff"]))
stat_and_covert2gff(os.path.join(
table_folder, "_".join([prefix, suffixs["csv"]])),
feature_id, out_gff,
args_ribo.fuzzy, out_stat, feature)
log.write("\t" + out_gff + "\n")
log.write("\t" + out_stat + "\n")
fh.close()
def test_stat_and_covert2gff(self):
ribo_table = os.path.join(self.test_folder, "ribo")
rfam_table = os.path.join(self.test_folder, "rfam")
gen_file(ribo_table, self.example.table)
gen_file(rfam_table, self.example.rfam)
gff_file = os.path.join(self.test_folder, "gff")
out_stat = os.path.join(self.test_folder, "stat")
rg.stat_and_covert2gff(ribo_table, rfam_table, gff_file, 3, out_stat, "riboswitch")
data = import_data(gff_file)
self.assertEqual("\n".join(data), self.example.out_gff)
def test_stat_and_covert2gff(self):
ribo_table = os.path.join(self.test_folder, "ribo")
rfam_table = os.path.join(self.test_folder, "rfam")
gen_file(ribo_table, self.example.table)
gen_file(rfam_table, self.example.rfam)
gff_file = os.path.join(self.test_folder, "gff")
out_stat = os.path.join(self.test_folder, "stat")
rg.stat_and_covert2gff(ribo_table, rfam_table, gff_file,
3, out_stat, "riboswitch")
data = import_data(gff_file)
self.assertEqual("\n".join(data), self.example.out_gff)
def _merge_results(self, args_ribo, scan_folder, suffixs, tmp_files,
table_folder, stat_folder, feature_id, gff_outfolder,
feature):
'''merge the results from the results of two searching'''
for gff in os.listdir(args_ribo.gffs):
if gff.endswith(".gff"):
prefix = gff.replace(".gff", "")
print("Merging results of {0}".format(prefix))
pre_strain = ""
self.helper.check_make_folder(os.path.join(
scan_folder, prefix))
fh = open(os.path.join(args_ribo.gffs, gff))
for entry in self.gff_parser.entries(fh):
if entry.seq_id != pre_strain:
if len(pre_strain) == 0:
shutil.copyfile(
os.path.join(
tmp_files["table"],
"_".join([entry.seq_id, suffixs["csv"]])),
os.path.join(
table_folder,
"_".join([prefix, suffixs["csv"]])))
else:
self.helper.merge_file(
os.path.join(
tmp_files["table"],
"_".join([entry.seq_id, suffixs["csv"]])),
os.path.join(
table_folder,
"_".join([prefix, suffixs["csv"]])))
shutil.copy(
os.path.join(
tmp_files["scan"],
"_".join([entry.seq_id, suffixs["txt"]])),
os.path.join(scan_folder, prefix))
shutil.copy(
os.path.join(
tmp_files["scan"],
"_".join([entry.seq_id, suffixs["re_txt"]])),
os.path.join(scan_folder, prefix))
pre_strain = entry.seq_id
out_stat = os.path.join(
stat_folder, "_".join(["stat", prefix, feature + ".txt"]))
print("Computing statistics of {0}".format(prefix))
stat_and_covert2gff(
os.path.join(table_folder,
"_".join([prefix,
suffixs["csv"]])), feature_id,
os.path.join(gff_outfolder,
"_".join([prefix, feature + ".gff"])),
args_ribo.fuzzy, out_stat, feature)
fh.close()
def _merge_results(self, args_ribo):
for gff in os.listdir(args_ribo.gffs):
if gff.endswith(".gff"):
prefix = gff.replace(".gff", "")
print("Merge results of {0}".format(prefix))
pre_strain = ""
self.helper.check_make_folder(
os.path.join(self.scan_folder, prefix))
fh = open(os.path.join(args_ribo.gffs, gff))
for entry in self.gff_parser.entries(fh):
if entry.seq_id != pre_strain:
if len(pre_strain) == 0:
shutil.copyfile(
os.path.join(
self.tmp_files["table"], "_".join(
[entry.seq_id, self.suffixs["csv"]])),
os.path.join(
self.table_folder,
"_".join([prefix, self.suffixs["csv"]])))
else:
self.helper.merge_file(
os.path.join(
self.tmp_files["table"], "_".join(
[entry.seq_id, self.suffixs["csv"]])),
os.path.join(
self.table_folder,
"_".join([prefix, self.suffixs["csv"]])))
shutil.copy(
os.path.join(
self.tmp_files["scan"],
"_".join([entry.seq_id, self.suffixs["txt"]])),
os.path.join(self.scan_folder, prefix))
shutil.copy(
os.path.join(
self.tmp_files["scan"], "_".join(
[entry.seq_id, self.suffixs["re_txt"]])),
os.path.join(self.scan_folder, prefix))
pre_strain = entry.seq_id
out_stat = os.path.join(
self.stat_folder,
"_".join(["stat", prefix, "riboswitch.txt"]))
print("compute statistics of {0}".format(prefix))
stat_and_covert2gff(
os.path.join(self.table_folder,
"_".join([prefix, self.suffixs["csv"]])),
args_ribo.ribos_id,
os.path.join(self.gff_outfolder,
"_".join([prefix, "riboswitch.gff"])),
args_ribo.fuzzy, out_stat)
fh.close()
def _merge_results(self, args_ribo):
for gff in os.listdir(args_ribo.gffs):
if gff.endswith(".gff"):
prefix = gff.replace(".gff", "")
print("Merge results of {0}".format(prefix))
pre_strain = ""
self.helper.check_make_folder(os.path.join(
self.scan_folder, prefix))
fh = open(os.path.join(args_ribo.gffs, gff))
for entry in self.gff_parser.entries(fh):
if entry.seq_id != pre_strain:
if len(pre_strain) == 0:
shutil.copyfile(os.path.join(
self.tmp_files["table"],
"_".join([entry.seq_id, self.suffixs["csv"]])),
os.path.join(
self.table_folder,
"_".join([prefix, self.suffixs["csv"]])))
else:
self.helper.merge_file(os.path.join(
self.tmp_files["table"],
"_".join([entry.seq_id, self.suffixs["csv"]])),
os.path.join(
self.table_folder,
"_".join([prefix, self.suffixs["csv"]])))
shutil.copy(os.path.join(
self.tmp_files["scan"],
"_".join([entry.seq_id, self.suffixs["txt"]])),
os.path.join(self.scan_folder, prefix))
shutil.copy(os.path.join(
self.tmp_files["scan"],
"_".join([entry.seq_id, self.suffixs["re_txt"]])),
os.path.join(self.scan_folder, prefix))
pre_strain = entry.seq_id
out_stat = os.path.join(
self.stat_folder,
"_".join(["stat", prefix, "riboswitch.txt"]))
print("compute statistics of {0}".format(prefix))
stat_and_covert2gff(os.path.join(
self.table_folder,
"_".join([prefix, self.suffixs["csv"]])),
args_ribo.ribos_id, os.path.join(
self.gff_outfolder,
"_".join([prefix, "riboswitch.gff"])),
args_ribo.fuzzy, out_stat)
fh.close()
def _merge_results(self, args_ribo, scan_folder, suffixs, tmp_files,
table_folder, stat_folder, feature_id, gff_outfolder,
feature, log):
'''merge the results from the results of two searching'''
for gff in os.listdir(args_ribo.gffs):
if gff.endswith(".gff"):
prefix = gff.replace(".gff", "")
print("Merging results of {0}".format(prefix))
pre_strain = ""
self.helper.check_make_folder(os.path.join(
scan_folder, prefix))
fh = open(os.path.join(args_ribo.gffs, gff))
log.write("Merging the results from Infernal to generate "
"tables for {0}.\n".format(prefix))
for entry in self.gff_parser.entries(fh):
if entry.seq_id != pre_strain:
if len(pre_strain) == 0:
shutil.copyfile(
os.path.join(
tmp_files["table"],
"_".join([entry.seq_id, suffixs["csv"]])),
os.path.join(
table_folder,
"_".join([prefix, suffixs["csv"]])))
else:
self.helper.merge_file(
os.path.join(
tmp_files["table"],
"_".join([entry.seq_id, suffixs["csv"]])),
os.path.join(
table_folder,
"_".join([prefix, suffixs["csv"]])))
shutil.copy(
os.path.join(
tmp_files["scan"],
"_".join([entry.seq_id, suffixs["txt"]])),
os.path.join(scan_folder, prefix))
shutil.copy(
os.path.join(
tmp_files["scan"],
"_".join([entry.seq_id, suffixs["re_txt"]])),
os.path.join(scan_folder, prefix))
pre_strain = entry.seq_id
log.write("The following files are generated.\n")
for folder in (table_folder, scan_folder):
for file_ in os.listdir(folder):
log.write("\t" + os.path.join(folder, file_) + "\n")
out_stat = os.path.join(
stat_folder, "_".join(["stat", prefix, feature + ".txt"]))
print("Computing statistics of {0}".format(prefix))
log.write("Running ribo_gff.py to do statistics and generate "
"gff files for {0}.\n".format(prefix))
log.write("The following files are generated:\n")
out_gff = os.path.join(gff_outfolder,
"_".join([prefix, feature + ".gff"]))
stat_and_covert2gff(
os.path.join(table_folder,
"_".join([prefix, suffixs["csv"]])),
feature_id, out_gff, args_ribo.fuzzy, out_stat, feature)
log.write("\t" + out_gff + "\n")
log.write("\t" + out_stat + "\n")
fh.close()