def _gen_table(self, output_folder, prefixs, combine, program, log):
'''generate the promoter table'''
log.write("Running gen_promoter_table.py to generate promoter "
"table which is useful for sRNA prediction.\n")
log.write("The following files are generated:\n")
if combine:
strains = prefixs + ["allfasta"]
else:
strains = prefixs
for strain in strains:
tss_file = os.path.join(self.tss_path, strain + "_TSS.gff")
if (program.lower() == "both") or (
program.lower() == "meme"):
for folder in os.listdir(os.path.join(output_folder,
strain, "MEME")):
csv_file = os.path.join(output_folder, strain,
"MEME", folder, "meme.csv")
gen_promoter_table(os.path.join(output_folder, strain,
"MEME", folder, "meme.txt"),
csv_file, tss_file, "meme")
log.write("\t" + csv_file + "\n")
if (program.lower() == "both") or (
program.lower() == "glam2"):
for folder in os.listdir(os.path.join(output_folder,
strain, "GLAM2")):
csv_file = os.path.join(output_folder, strain,
"GLAM2", folder, "glam2.csv")
gen_promoter_table(os.path.join(output_folder, strain,
"GLAM2", folder, "glam2.txt"),
csv_file, tss_file, "glam2")
log.write("\t" + csv_file + "\n")
def _gen_table(self, output_folder, prefixs, combine, program, log):
'''generate the promoter table'''
log.write("Running gen_promoter_table.py to generate promoter "
"table which is useful for sRNA prediction.\n")
log.write("The following files are generated:\n")
if combine:
strains = prefixs + ["allfasta"]
else:
strains = prefixs
for strain in strains:
tss_file = os.path.join(self.tss_path, strain + "_TSS.gff")
if (program.lower() == "both") or (
program.lower() == "meme"):
for folder in os.listdir(os.path.join(output_folder,
strain, "MEME")):
csv_file = os.path.join(output_folder, strain,
"MEME", folder, "meme.csv")
gen_promoter_table(os.path.join(output_folder, strain,
"MEME", folder, "meme.txt"),
csv_file, tss_file, "meme")
log.write("\t" + csv_file + "\n")
if (program.lower() == "both") or (
program.lower() == "glam2"):
for folder in os.listdir(os.path.join(output_folder,
strain, "GLAM2")):
csv_file = os.path.join(output_folder, strain,
"GLAM2", folder, "glam2.csv")
gen_promoter_table(os.path.join(output_folder, strain,
"GLAM2", folder, "glam2.txt"),
csv_file, tss_file, "glam2")
log.write("\t" + csv_file + "\n")
def _gen_table(self, output_folder, prefixs, combine, program):
'''generate the promoter table'''
if combine:
strains = prefixs + ["allfasta"]
else:
strains = prefixs
for strain in strains:
tss_file = os.path.join(self.tss_path, strain + "_TSS.gff")
if (program.lower() == "both") or (
program.lower() == "meme"):
for folder in os.listdir(os.path.join(output_folder,
strain, "MEME")):
gen_promoter_table(os.path.join(output_folder, strain,
"MEME", folder, "meme.txt"),
os.path.join(output_folder, strain,
"MEME", folder, "meme.csv"), tss_file,
"meme")
if (program.lower() == "both") or (
program.lower() == "glam2"):
for folder in os.listdir(os.path.join(output_folder,
strain, "GLAM2")):
gen_promoter_table(os.path.join(output_folder, strain,
"GLAM2", folder, "glam2.txt"),
os.path.join(output_folder, strain,
"GLAM2", folder, "glam2.csv"),
tss_file, "glam2")
def _gen_table(self, output_folder, prefixs, combine):
if combine:
strains = prefixs + ["allfasta"]
else:
strains = prefixs
for strain in strains:
for folder in os.listdir(os.path.join(output_folder, strain)):
tss_file = os.path.join(self.tss_path, strain + "_TSS.gff")
gen_promoter_table(
os.path.join(output_folder, strain, folder, "meme.txt"),
os.path.join(output_folder, strain, folder, "meme.csv"),
tss_file)
def _gen_table(self, output_folder, prefixs, combine):
if combine:
strains = prefixs + ["allfasta"]
else:
strains = prefixs
for strain in strains:
for folder in os.listdir(os.path.join(output_folder, strain)):
tss_file = os.path.join(self.tss_path, strain + "_TSS.gff")
gen_promoter_table(os.path.join(output_folder, strain,
folder, "meme.txt"),
os.path.join(output_folder, strain,
folder, "meme.csv"), tss_file)