def _move_and_merge_fasta(self, input_path, prefix):
all_type = os.path.join(self.tmp_folder, self.fastas["all"])
all_no_orph = os.path.join(self.tmp_folder, self.fastas["all_no_orph"])
if self.fastas["all"] in os.listdir(self.tmp_folder):
os.remove(all_type)
if self.fastas["all_no_orph"] in os.listdir(self.tmp_folder):
os.remove(all_no_orph)
shutil.copyfile(self.fastas["pri"], self.fastas["tmp_fa"])
self.helper.merge_file(self.fastas["sec"], self.fastas["tmp_fa"])
self.helper.merge_file(self.fastas["inter"], self.fastas["tmp_fa"])
self.helper.merge_file(self.fastas["anti"], self.fastas["tmp_fa"])
shutil.copyfile(self.fastas["tmp_fa"], self.fastas["tmp_all"])
self.helper.merge_file(self.fastas["orph"], self.fastas["tmp_all"])
del_repeat_fasta(self.fastas["tmp_fa"], all_no_orph)
del_repeat_fasta(self.fastas["tmp_all"], all_type)
os.remove(self.fastas["tmp_fa"])
os.remove(self.fastas["tmp_all"])
out_prefix = os.path.join(input_path, prefix)
shutil.move(self.fastas["pri"], "_".join([
out_prefix, "allgenome_primary.fa"]))
shutil.move(self.fastas["sec"], "_".join([
out_prefix, "allgenome_secondary.fa"]))
shutil.move(self.fastas["inter"], "_".join([
out_prefix, "allgenome_internal.fa"]))
shutil.move(self.fastas["anti"], "_".join([
out_prefix, "allgenome_antisense.fa"]))
shutil.move(self.fastas["orph"], "_".join([
out_prefix, "allgenome_orphan.fa"]))
shutil.move(all_type, "_".join([
out_prefix, "allgenome_all_types.fa"]))
shutil.move(all_no_orph, "_".join([
out_prefix, "allgenome_without_orphan.fa"]))
def _move_and_merge_fasta(self, input_path, prefix):
all_type = os.path.join(self.tmp_folder, self.fastas["all"])
all_no_orph = os.path.join(self.tmp_folder, self.fastas["all_no_orph"])
if self.fastas["all"] in os.listdir(self.tmp_folder):
os.remove(all_type)
if self.fastas["all_no_orph"] in os.listdir(self.tmp_folder):
os.remove(all_no_orph)
shutil.copyfile(self.fastas["pri"], self.fastas["tmp_fa"])
self.helper.merge_file(self.fastas["sec"], self.fastas["tmp_fa"])
self.helper.merge_file(self.fastas["inter"], self.fastas["tmp_fa"])
self.helper.merge_file(self.fastas["anti"], self.fastas["tmp_fa"])
shutil.copyfile(self.fastas["tmp_fa"], self.fastas["tmp_all"])
self.helper.merge_file(self.fastas["orph"], self.fastas["tmp_all"])
del_repeat_fasta(self.fastas["tmp_fa"], all_no_orph)
del_repeat_fasta(self.fastas["tmp_all"], all_type)
os.remove(self.fastas["tmp_fa"])
os.remove(self.fastas["tmp_all"])
out_prefix = os.path.join(input_path, prefix)
shutil.move(self.fastas["pri"],
"_".join([out_prefix, "allstrain_primary.fa"]))
shutil.move(self.fastas["sec"],
"_".join([out_prefix, "allstrain_secondary.fa"]))
shutil.move(self.fastas["inter"],
"_".join([out_prefix, "allstrain_internal.fa"]))
shutil.move(self.fastas["anti"],
"_".join([out_prefix, "allstrain_antisense.fa"]))
shutil.move(self.fastas["orph"],
"_".join([out_prefix, "allstrain_orphan.fa"]))
shutil.move(all_type, "_".join([out_prefix, "allstrain_all_types.fa"]))
shutil.move(all_no_orph,
"_".join([out_prefix, "allstrain_without_orphan.fa"]))