class RATT(object):
'''annotation transfer'''
def __init__(self, args_ratt):
self.multiparser = Multiparser()
self.converter = Converter()
self.format_fixer = FormatFixer()
self.helper = Helper()
if args_ratt.ref_gbk:
self.gbk = os.path.join(args_ratt.ref_gbk, "gbk_tmp")
self.gbk_tmp = os.path.join(self.gbk, "tmp")
self.embl = os.path.join(args_ratt.ref_gbk, "embls")
if args_ratt.ref_embls:
self.embl = args_ratt.ref_embls
self.ratt_log = os.path.join(args_ratt.output_path, "ratt_log.txt")
self.tmp_files = {
"tar": os.path.join(args_ratt.tar_fastas, "tmp"),
"ref": os.path.join(args_ratt.ref_fastas, "tmp"),
"out_gff": os.path.join(args_ratt.gff_outfolder, "tmp"),
"gff": os.path.join(args_ratt.gff_outfolder, "tmp.gff"),
"ptt": os.path.join(args_ratt.gff_outfolder, "tmp.ptt"),
"rnt": os.path.join(args_ratt.gff_outfolder, "tmp.rnt")
}
def _convert_to_pttrnt(self, gffs, files):
for gff in files:
if gff.endswith(".gff"):
gff = os.path.join(gffs, gff)
filename = gff.split("/")
prefix = filename[-1][:-4]
rnt = gff[:-3] + "rnt"
ptt = gff[:-3] + "ptt"
fasta = self.helper.get_correct_file(self.tmp_files["tar"],
".fa", prefix, None, None)
if fasta:
self.converter.convert_gff2rntptt(gff, fasta, ptt, rnt,
None, None)
def _remove_files(self, args_ratt, out_gbk):
self.helper.remove_all_content(args_ratt.gff_outfolder, ".gff", "file")
self.helper.remove_all_content(args_ratt.gff_outfolder, ".ptt", "file")
self.helper.remove_all_content(args_ratt.gff_outfolder, ".rnt", "file")
self.helper.move_all_content(self.tmp_files["out_gff"],
args_ratt.gff_outfolder, None)
shutil.rmtree(self.tmp_files["out_gff"])
shutil.rmtree(self.tmp_files["tar"])
shutil.rmtree(self.tmp_files["ref"])
self.helper.remove_tmp_dir(args_ratt.tar_fastas)
self.helper.remove_tmp_dir(args_ratt.ref_fastas)
self.helper.remove_tmp_dir(args_ratt.ref_embls)
self.helper.remove_tmp_dir(args_ratt.ref_gbk)
def _convert_to_gff(self, ratt_result, args_ratt, files):
name = ratt_result.split(".")
filename = ".".join(name[1:-2]) + ".gff"
output_file = os.path.join(args_ratt.output_path, filename)
self.converter.convert_embl2gff(
os.path.join(args_ratt.output_path, ratt_result), output_file)
self.format_fixer.fix_ratt(output_file, ".".join(name[1:-2]),
"tmp_gff")
shutil.move("tmp_gff", output_file)
shutil.copy(output_file, os.path.join(args_ratt.gff_outfolder,
filename))
files.append(filename)
def _parser_embl_gbk(self, files):
self.helper.check_make_folder(self.gbk)
for file_ in files:
close = False
with open(file_, "r") as f_h:
for line in f_h:
if (line.startswith("LOCUS")):
out = open(self.gbk_tmp, "w")
datas = line.split(" ")
for data in datas:
if (len(data) != 0) and (data != "LOCUS"):
filename = ".".join([data, "gbk"])
break
elif (line.startswith("VERSION")):
datas = line.split(" ")
for data in datas:
if (len(data) != 0) and (data != "VERSION"):
new_filename = ".".join([data, "gbk"])
break
if new_filename.find(filename):
filename = new_filename
if out:
out.write(line)
if line.startswith("//"):
out.close()
close = True
shutil.move(self.gbk_tmp,
os.path.join(self.gbk, filename))
if not close:
out.close()
return self.gbk
def _convert_embl(self, ref_embls):
'''convert gbk to embl'''
detect_gbk = False
gbks = []
out_gbk = None
for embl in os.listdir(ref_embls):
if (embl.endswith(".gbk")) or (embl.endswith(".gbff")) or (
embl.endswith(".gb")):
detect_gbk = True
gbks.append(os.path.join(ref_embls, embl))
if not detect_gbk:
print("Error: Please assign proper Genebank files!")
sys.exit()
elif detect_gbk:
out_gbk = self._parser_embl_gbk(gbks)
self.converter.convert_gbk2embl(out_gbk)
self.helper.check_make_folder(self.embl)
self.helper.move_all_content(out_gbk, self.embl, [".embl"])
return out_gbk
def _run_ratt(self, args_ratt, tar, ref, out):
call([
args_ratt.ratt_path, self.embl,
os.path.join(self.tmp_files["tar"], tar + ".fa"),
args_ratt.element, args_ratt.transfer_type,
os.path.join(self.tmp_files["ref"], ref + ".fa")
],
stdout=out,
stderr=DEVNULL)
def _format_and_run(self, args_ratt):
print("Running RATT")
for pair in args_ratt.pairs:
ref = pair.split(":")[0]
tar = pair.split(":")[1]
out = open(self.ratt_log, "w+")
self._run_ratt(args_ratt, tar, ref, out)
for filename in os.listdir():
if ("final" in filename):
shutil.move(filename,
os.path.join(args_ratt.output_path, filename))
elif (args_ratt.element in filename) or (
"query" in filename) or ("Reference" in filename) or (
"Query" in filename) or ("Sequences" in filename):
if os.path.isfile(filename):
os.remove(filename)
if os.path.isdir(filename):
shutil.rmtree(filename)
out.close()
def annotation_transfer(self, args_ratt):
self.multiparser.parser_fasta(args_ratt.tar_fastas)
self.multiparser.parser_fasta(args_ratt.ref_fastas)
out_gbk = None
if args_ratt.ref_embls is None:
out_gbk = self._convert_embl(args_ratt.ref_gbk)
self._format_and_run(args_ratt)
if args_ratt.convert:
files = []
for data in os.listdir(args_ratt.output_path):
if "final.embl" in data:
self._convert_to_gff(data, args_ratt, files)
self._convert_to_pttrnt(args_ratt.gff_outfolder, files)
self.helper.check_make_folder(self.tmp_files["out_gff"])
for folder in os.listdir(args_ratt.tar_fastas):
files = []
if "_folder" in folder:
datas = folder.split("_folder")
prefix = ".".join(datas[0].split(".")[:-1])
for file_ in os.listdir(
os.path.join(args_ratt.tar_fastas, folder)):
files.append(file_[:-3])
for gff in os.listdir(args_ratt.gff_outfolder):
for file_ in files:
if (".gff" in gff) and (file_ == gff[:-4]):
self.helper.merge_file(
os.path.join(args_ratt.gff_outfolder, gff),
self.tmp_files["gff"])
if (".ptt" in gff) and (file_ == gff[:-4]):
self.helper.merge_file(
os.path.join(args_ratt.gff_outfolder, gff),
self.tmp_files["ptt"])
if (".rnt" in gff) and (file_ == gff[:-4]):
self.helper.merge_file(
os.path.join(args_ratt.gff_outfolder, gff),
self.tmp_files["rnt"])
if os.path.exists(self.tmp_files["gff"]):
shutil.move(
self.tmp_files["gff"],
os.path.join(self.tmp_files["out_gff"],
prefix + ".gff"))
shutil.move(
self.tmp_files["ptt"],
os.path.join(self.tmp_files["out_gff"],
prefix + ".ptt"))
shutil.move(
self.tmp_files["rnt"],
os.path.join(self.tmp_files["out_gff"],
prefix + ".rnt"))
else:
print("Error: Please check your fasta or "
"annotation files, they should only contain "
"the query genome. And make sure your RATT can "
"work properly (check $ANNOgesic/output/"
"annotation_transfer/ratt_log.txt).")
self._remove_files(args_ratt, out_gbk)
class RATT(object):
'''annotation transfer'''
def __init__(self, args_ratt):
self.multiparser = Multiparser()
self.converter = Converter()
self.format_fixer = FormatFixer()
self.helper = Helper()
if args_ratt.ref_gbk:
self.gbk = os.path.join(args_ratt.ref_gbk, "gbk_tmp")
self.gbk_tmp = os.path.join(self.gbk, "tmp")
self.embl = os.path.join(args_ratt.ref_gbk, "embls")
if args_ratt.ref_embls:
self.embl = args_ratt.ref_embls
self.ratt_log = os.path.join(args_ratt.output_path, "ratt_log.txt")
self.tmp_files = {
"tar": os.path.join(args_ratt.tar_fastas, "tmp"),
"ref": os.path.join(args_ratt.ref_fastas, "tmp"),
"out_gff": os.path.join(args_ratt.gff_outfolder, "tmp"),
"gff": os.path.join(args_ratt.gff_outfolder, "tmp.gff"),
"ptt": os.path.join(args_ratt.gff_outfolder, "tmp.ptt"),
"rnt": os.path.join(args_ratt.gff_outfolder, "tmp.rnt")
}
def _convert_to_pttrnt(self, gffs, files, log):
for gff in files:
if gff.endswith(".gff"):
gff = os.path.join(gffs, gff)
filename = gff.split("/")
prefix = filename[-1][:-4]
rnt = gff[:-3] + "rnt"
ptt = gff[:-3] + "ptt"
fasta = self.helper.get_correct_file(self.tmp_files["tar"],
".fa", prefix, None, None)
if fasta:
self.converter.convert_gff2rntptt(gff, fasta, ptt, rnt,
None, None)
log.write("\t" + ptt + " is generated.\n")
log.write("\t" + rnt + " is generated.\n")
def _remove_files(self, args_ratt, out_gbk, log):
self.helper.remove_all_content(args_ratt.gff_outfolder, ".gff", "file")
self.helper.remove_all_content(args_ratt.gff_outfolder, ".ptt", "file")
self.helper.remove_all_content(args_ratt.gff_outfolder, ".rnt", "file")
log.write("Moving the final output files to {0}.\n".format(
args_ratt.gff_outfolder))
self.helper.move_all_content(self.tmp_files["out_gff"],
args_ratt.gff_outfolder, None)
log.write("Remove the temperary files.\n")
shutil.rmtree(self.tmp_files["out_gff"])
shutil.rmtree(self.tmp_files["tar"])
shutil.rmtree(self.tmp_files["ref"])
self.helper.remove_tmp_dir(args_ratt.tar_fastas)
self.helper.remove_tmp_dir(args_ratt.ref_fastas)
self.helper.remove_tmp_dir(args_ratt.ref_embls)
self.helper.remove_tmp_dir(args_ratt.ref_gbk)
def _convert_to_gff(self, ratt_result, args_ratt, files, log):
name = ratt_result.split(".")
filename = ".".join(name[1:-2]) + ".gff"
output_file = os.path.join(args_ratt.output_path, filename)
self.converter.convert_embl2gff(
os.path.join(args_ratt.output_path, ratt_result), output_file)
self.format_fixer.fix_ratt(output_file, ".".join(name[1:-2]),
"tmp_gff")
shutil.move("tmp_gff", output_file)
shutil.copy(output_file, os.path.join(args_ratt.gff_outfolder,
filename))
log.write("\t" + os.path.join(args_ratt.gff_outfolder, filename) +
" is generated.\n")
files.append(filename)
def _parser_embl_gbk(self, files):
self.helper.check_make_folder(self.gbk)
for file_ in files:
close = False
with open(file_, "r") as f_h:
for line in f_h:
if (line.startswith("LOCUS")):
out = open(self.gbk_tmp, "w")
datas = line.split(" ")
for data in datas:
if (len(data) != 0) and (data != "LOCUS"):
filename = ".".join([data.strip(), "gbk"])
break
elif (line.startswith("VERSION")):
datas = line.split(" ")
for data in datas:
if (len(data) != 0) and (data != "VERSION"):
new_filename = ".".join([data.strip(), "gbk"])
break
if new_filename.find(filename):
filename = new_filename
if out:
out.write(line)
if line.startswith("//"):
out.close()
close = True
shutil.move(self.gbk_tmp,
os.path.join(self.gbk, filename))
if not close:
out.close()
return self.gbk
def _convert_embl(self, ref_embls, log):
'''convert gbk to embl'''
detect_gbk = False
gbks = []
out_gbk = None
for embl in os.listdir(ref_embls):
if (embl.endswith(".gbk")) or (embl.endswith(".gbff")) or (
embl.endswith(".gb")):
detect_gbk = True
gbks.append(os.path.join(ref_embls, embl))
if not detect_gbk:
log.write(
"--related_gbk_files is assigned, but not gbk files are detected.\n"
"The gbk file names need to be ended at .gbk, .gb, or .gbff. \n"
)
print("Error: Please assign proper Genebank files!")
sys.exit()
elif detect_gbk:
out_gbk = self._parser_embl_gbk(gbks)
log.write(
"Running converter.py to convert gbk file to embl format.\n")
self.converter.convert_gbk2embl(out_gbk)
self.helper.check_make_folder(self.embl)
self.helper.move_all_content(out_gbk, self.embl, [".embl"])
log.write("\t" + self.embl +
" is generated and the embl files are stored in it.\n")
return out_gbk
def _run_ratt(self, args_ratt, tar, ref, out, log):
if (not os.path.exists(self.embl)) or (not os.path.exists(
os.path.join(self.tmp_files["tar"], tar + ".fa"))) or (
not os.path.exists(
os.path.join(self.tmp_files["ref"], ref + ".fa"))):
print("Error: Please check --compare_pair, the strain names "
"should be the same as the strain names in fasta, "
"genbank or embl files!")
log.write(
"The strain names in --compare_pair should be the same "
"as the strain names in fasta, genbank, or embl files.\n")
sys.exit()
log.write("Make sure your RATT version is at least 1.64.\n")
log.write("If the RATT can not run properly, please check the "
"RATT_HOME and PAGIT_HOME is assigned correctly.\n")
log.write(" ".join([
args_ratt.ratt_path, self.embl,
os.path.join(self.tmp_files["tar"], tar +
".fa"), args_ratt.element, args_ratt.transfer_type,
os.path.join(self.tmp_files["ref"], ref + ".fa")
]) + "\n")
call([
args_ratt.ratt_path, self.embl,
os.path.join(self.tmp_files["tar"], tar + ".fa"),
args_ratt.element, args_ratt.transfer_type,
os.path.join(self.tmp_files["ref"], ref + ".fa")
],
stdout=out,
stderr=DEVNULL)
log.write("Done!\n")
def _format_and_run(self, args_ratt, log):
print("Running RATT")
for pair in args_ratt.pairs:
ref = pair.split(":")[0]
tar = pair.split(":")[1]
out = open(self.ratt_log, "w+")
self._run_ratt(args_ratt, tar, ref, out, log)
log.write("The following files are generatd:\n")
for filename in os.listdir():
if ("final" in filename):
log.write("\t" + filename + "\n")
shutil.move(filename,
os.path.join(args_ratt.output_path, filename))
elif (args_ratt.element in filename) or (
"query" in filename) or ("Reference" in filename) or (
"Query" in filename) or ("Sequences" in filename):
log.write("\t" + filename + "\n")
if os.path.isfile(filename):
os.remove(filename)
if os.path.isdir(filename):
shutil.rmtree(filename)
out.close()
def annotation_transfer(self, args_ratt, log):
self.multiparser.parser_fasta(args_ratt.tar_fastas)
self.multiparser.parser_fasta(args_ratt.ref_fastas)
out_gbk = None
if args_ratt.ref_embls is None:
out_gbk = self._convert_embl(args_ratt.ref_gbki, log)
self._format_and_run(args_ratt, log)
files = []
for data in os.listdir(args_ratt.output_path):
if "final.embl" in data:
log.write(
"Running converter.py to convert embl "
"files in {0} to gff, ptt, and rnt format.\n".format(data))
self._convert_to_gff(data, args_ratt, files, log)
self._convert_to_pttrnt(args_ratt.gff_outfolder, files, log)
self.helper.check_make_folder(self.tmp_files["out_gff"])
log.write("Merging the output of {0}.\n".format(data))
for folder in os.listdir(args_ratt.tar_fastas):
files = []
if "_folder" in folder:
datas = folder.split("_folder")
prefix = ".".join(datas[0].split(".")[:-1])
for file_ in os.listdir(
os.path.join(args_ratt.tar_fastas, folder)):
files.append(file_[:-3])
for gff in os.listdir(args_ratt.gff_outfolder):
for file_ in files:
if (".gff" in gff) and (file_ == gff[:-4]):
self.helper.merge_file(
os.path.join(args_ratt.gff_outfolder, gff),
self.tmp_files["gff"])
if (".ptt" in gff) and (file_ == gff[:-4]):
self.helper.merge_file(
os.path.join(args_ratt.gff_outfolder, gff),
self.tmp_files["ptt"])
if (".rnt" in gff) and (file_ == gff[:-4]):
self.helper.merge_file(
os.path.join(args_ratt.gff_outfolder, gff),
self.tmp_files["rnt"])
if os.path.exists(self.tmp_files["gff"]):
shutil.move(
self.tmp_files["gff"],
os.path.join(self.tmp_files["out_gff"],
prefix + ".gff"))
shutil.move(
self.tmp_files["ptt"],
os.path.join(self.tmp_files["out_gff"],
prefix + ".ptt"))
shutil.move(
self.tmp_files["rnt"],
os.path.join(self.tmp_files["out_gff"],
prefix + ".rnt"))
else:
print("Error: Please check your fasta or "
"annotation files, they should only contain "
"the query genome. And make sure your RATT can "
"work properly (check $ANNOgesic/output/"
"annotation_transfer/ratt_log.txt).")
log.write("Please check your fasta or "
"annotation files, they should only contain "
"the query genome. And make sure your RATT can "
"work properly (check $ANNOgesic/output/"
"annotation_transfer/ratt_log.txt).\n")
self._remove_files(args_ratt, out_gbk, log)
class RATT(object):
def __init__(self, args_ratt):
self.multiparser = Multiparser()
self.converter = Converter()
self.format_fixer = FormatFixer()
self.helper = Helper()
self.gbk = os.path.join(args_ratt.ref_embls, "gbk_tmp")
self.gbk_tmp = os.path.join(self.gbk, "tmp")
self.embl = os.path.join(args_ratt.ref_embls, "embls")
self.ratt_log = os.path.join(args_ratt.output_path, "ratt_log.txt")
self.tmp_files = {"tar": os.path.join(args_ratt.tar_fastas, "tmp"),
"ref": os.path.join(args_ratt.ref_fastas, "tmp"),
"out_gff": os.path.join(args_ratt.gff_outfolder,
"tmp"),
"gff": os.path.join(args_ratt.gff_outfolder,
"tmp.gff"),
"ptt": os.path.join(args_ratt.gff_outfolder,
"tmp.ptt"),
"rnt": os.path.join(args_ratt.gff_outfolder,
"tmp.rnt")}
def _convert_to_pttrnt(self, gffs, files):
for gff in files:
if gff.endswith(".gff"):
gff = os.path.join(gffs, gff)
filename = gff.split("/")
prefix = filename[-1][:-4]
rnt = gff[:-3] + "rnt"
ptt = gff[:-3] + "ptt"
fasta = self.helper.get_correct_file(self.tmp_files["tar"],
".fa", prefix, None, None)
if fasta:
self.converter.convert_gff2rntptt(gff, fasta, ptt, rnt,
None, None)
def _remove_files(self, args_ratt, out_gbk):
self.helper.remove_all_content(args_ratt.gff_outfolder, ".gff", "file")
self.helper.remove_all_content(args_ratt.gff_outfolder, ".ptt", "file")
self.helper.remove_all_content(args_ratt.gff_outfolder, ".rnt", "file")
self.helper.move_all_content(self.tmp_files["out_gff"],
args_ratt.gff_outfolder, None)
shutil.rmtree(self.tmp_files["out_gff"])
shutil.rmtree(self.tmp_files["tar"])
shutil.rmtree(self.tmp_files["ref"])
shutil.rmtree(self.embl)
self.helper.remove_all_content(args_ratt.tar_fastas, "_folder", "dir")
self.helper.remove_all_content(args_ratt.ref_fastas, "_folder", "dir")
if out_gbk:
shutil.rmtree(out_gbk)
def _convert_to_gff(self, ratt_result, args_ratt, files):
name = ratt_result.split(".")
filename = ".".join(name[1:-2]) + ".gff"
output_file = os.path.join(args_ratt.output_path, filename)
self.converter.convert_embl2gff(
os.path.join(args_ratt.output_path, ratt_result), output_file)
self.format_fixer.fix_ratt(output_file, ".".join(name[1:-2]),
"tmp_gff")
shutil.move("tmp_gff", output_file)
shutil.copy(output_file, os.path.join(args_ratt.gff_outfolder,
filename))
files.append(filename)
def _parser_embl_gbk(self, files):
self.helper.check_make_folder(self.gbk)
for file_ in files:
close = False
with open(file_, "r") as f_h:
for line in f_h:
if (line.startswith("LOCUS")):
out = open(self.gbk_tmp, "w")
datas = line.split(" ")
for data in datas:
if (len(data) != 0) and (data != "LOCUS"):
filename = ".".join([data, "gbk"])
break
elif (line.startswith("VERSION")):
datas = line.split(" ")
for data in datas:
if (len(data) != 0) and (data != "VERSION"):
new_filename = ".".join([data, "gbk"])
break
if new_filename.find(filename):
filename = new_filename
if out:
out.write(line)
if line.startswith("//"):
out.close()
close = True
shutil.move(self.gbk_tmp,
os.path.join(self.gbk, filename))
if not close:
out.close()
return self.gbk
def _convert_embl(self, ref_embls):
detect_gbk = False
gbks = []
out_gbk = None
for embl in os.listdir(ref_embls):
if embl.endswith(".gbk"):
detect_gbk = True
gbks.append(os.path.join(ref_embls, embl))
if not detect_gbk:
print("Error: please assign proper folder for Genebank file!!!")
sys.exit()
elif detect_gbk:
out_gbk = self._parser_embl_gbk(gbks)
self.converter.convert_gbk2embl(out_gbk)
self.helper.check_make_folder(self.embl)
self.helper.move_all_content(out_gbk, self.embl, [".embl"])
return out_gbk
def _run_ratt(self, args_ratt, tar, ref, out):
call([args_ratt.ratt_path, self.embl,
os.path.join(self.tmp_files["tar"], tar + ".fa"),
args_ratt.element, args_ratt.transfer_type,
os.path.join(self.tmp_files["ref"], ref + ".fa")],
stdout=out, stderr=DEVNULL)
def _format_and_run(self, args_ratt):
print("Running RATT...")
for pair in args_ratt.pairs:
ref = pair.split(":")[0]
tar = pair.split(":")[1]
out = open(self.ratt_log, "w+")
print(tar)
self._run_ratt(args_ratt, tar, ref, out)
for filename in os.listdir():
if ("final" in filename):
shutil.move(filename, os.path.join(args_ratt.output_path,
filename))
elif (args_ratt.element in filename) or (
"query" in filename) or (
"Reference" in filename) or (
"Query" in filename) or (
"Sequences" in filename):
if os.path.isfile(filename):
os.remove(filename)
if os.path.isdir(filename):
shutil.rmtree(filename)
out.close()
def annotation_transfer(self, args_ratt):
self.multiparser.parser_fasta(args_ratt.tar_fastas)
self.multiparser.parser_fasta(args_ratt.ref_fastas)
out_gbk = self._convert_embl(args_ratt.ref_embls)
self._format_and_run(args_ratt)
if args_ratt.convert:
files = []
for data in os.listdir(args_ratt.output_path):
if "final.embl" in data:
self._convert_to_gff(data, args_ratt, files)
self._convert_to_pttrnt(args_ratt.gff_outfolder, files)
self.helper.check_make_folder(self.tmp_files["out_gff"])
for folder in os.listdir(args_ratt.tar_fastas):
files = []
if "_folder" in folder:
datas = folder.split("_folder")
prefix = datas[0][:-3]
for file_ in os.listdir(os.path.join(args_ratt.tar_fastas,
folder)):
files.append(file_[:-3])
for gff in os.listdir(args_ratt.gff_outfolder):
for file_ in files:
if (".gff" in gff) and (file_ == gff[:-4]):
self.helper.merge_file(os.path.join(
args_ratt.gff_outfolder, gff),
self.tmp_files["gff"])
if (".ptt" in gff) and (file_ == gff[:-4]):
self.helper.merge_file(os.path.join(
args_ratt.gff_outfolder, gff),
self.tmp_files["ptt"])
if (".rnt" in gff) and (file_ == gff[:-4]):
self.helper.merge_file(os.path.join(
args_ratt.gff_outfolder, gff),
self.tmp_files["rnt"])
shutil.move(self.tmp_files["gff"], os.path.join(
self.tmp_files["out_gff"], prefix + ".gff"))
shutil.move(self.tmp_files["ptt"], os.path.join(
self.tmp_files["out_gff"], prefix + ".ptt"))
shutil.move(self.tmp_files["rnt"], os.path.join(
self.tmp_files["out_gff"], prefix + ".rnt"))
self._remove_files(args_ratt, out_gbk)
class RATT(object):
'''annotation transfer'''
def __init__(self, args_ratt):
self.multiparser = Multiparser()
self.converter = Converter()
self.format_fixer = FormatFixer()
self.helper = Helper()
if args_ratt.ref_gbk:
self.gbk = os.path.join(args_ratt.ref_gbk, "gbk_tmp")
self.gbk_tmp = os.path.join(self.gbk, "tmp")
self.embl = os.path.join(args_ratt.ref_gbk, "embls")
if args_ratt.ref_embls:
self.embl = args_ratt.ref_embls
self.ratt_log = os.path.join(args_ratt.output_path, "ratt_log.txt")
self.tmp_files = {"tar": os.path.join(args_ratt.tar_fastas, "tmp"),
"ref": os.path.join(args_ratt.ref_fastas, "tmp"),
"out_gff": os.path.join(args_ratt.gff_outfolder,
"tmp"),
"gff": os.path.join(args_ratt.gff_outfolder,
"tmp.gff"),
"ptt": os.path.join(args_ratt.gff_outfolder,
"tmp.ptt"),
"rnt": os.path.join(args_ratt.gff_outfolder,
"tmp.rnt")}
def _convert_to_pttrnt(self, gffs, files, log):
for gff in files:
if gff.endswith(".gff"):
gff = os.path.join(gffs, gff)
filename = gff.split("/")
prefix = filename[-1][:-4]
rnt = gff[:-3] + "rnt"
ptt = gff[:-3] + "ptt"
fasta = self.helper.get_correct_file(self.tmp_files["tar"],
".fa", prefix, None, None)
if fasta:
self.converter.convert_gff2rntptt(gff, fasta, ptt, rnt,
None, None)
log.write("\t" + ptt + " is generated.\n")
log.write("\t" + rnt + " is generated.\n")
def _remove_files(self, args_ratt, out_gbk, log):
self.helper.remove_all_content(args_ratt.gff_outfolder, ".gff", "file")
self.helper.remove_all_content(args_ratt.gff_outfolder, ".ptt", "file")
self.helper.remove_all_content(args_ratt.gff_outfolder, ".rnt", "file")
log.write("Moving the final output files to {0}.\n".format(args_ratt.gff_outfolder))
self.helper.move_all_content(self.tmp_files["out_gff"],
args_ratt.gff_outfolder, None)
log.write("Remove the temperary files.\n")
shutil.rmtree(self.tmp_files["out_gff"])
shutil.rmtree(self.tmp_files["tar"])
shutil.rmtree(self.tmp_files["ref"])
self.helper.remove_tmp_dir(args_ratt.tar_fastas)
self.helper.remove_tmp_dir(args_ratt.ref_fastas)
self.helper.remove_tmp_dir(args_ratt.ref_embls)
self.helper.remove_tmp_dir(args_ratt.ref_gbk)
def _convert_to_gff(self, ratt_result, args_ratt, files, log):
name = ratt_result.split(".")
filename = ".".join(name[1:-2]) + ".gff"
output_file = os.path.join(args_ratt.output_path, filename)
self.converter.convert_embl2gff(
os.path.join(args_ratt.output_path, ratt_result), output_file)
self.format_fixer.fix_ratt(output_file, ".".join(name[1:-2]),
"tmp_gff")
shutil.move("tmp_gff", output_file)
shutil.copy(output_file, os.path.join(args_ratt.gff_outfolder,
filename))
log.write("\t" + os.path.join(args_ratt.gff_outfolder, filename) +
" is generated.\n")
files.append(filename)
def _parser_embl_gbk(self, files):
self.helper.check_make_folder(self.gbk)
for file_ in files:
close = False
with open(file_, "r") as f_h:
for line in f_h:
if (line.startswith("LOCUS")):
out = open(self.gbk_tmp, "w")
datas = line.split(" ")
for data in datas:
if (len(data) != 0) and (data != "LOCUS"):
filename = ".".join([data.strip(), "gbk"])
break
elif (line.startswith("VERSION")):
datas = line.split(" ")
for data in datas:
if (len(data) != 0) and (data != "VERSION"):
new_filename = ".".join([data.strip(), "gbk"])
break
if new_filename.find(filename):
filename = new_filename
if out:
out.write(line)
if line.startswith("//"):
out.close()
close = True
shutil.move(self.gbk_tmp,
os.path.join(self.gbk, filename))
if not close:
out.close()
return self.gbk
def _convert_embl(self, ref_embls, log):
'''convert gbk to embl'''
detect_gbk = False
gbks = []
out_gbk = None
for embl in os.listdir(ref_embls):
if (embl.endswith(".gbk")) or (
embl.endswith(".gbff")) or (
embl.endswith(".gb")):
detect_gbk = True
gbks.append(os.path.join(ref_embls, embl))
if not detect_gbk:
log.write("--related_gbk_files is assigned, but not gbk files are detected.\n"
"The gbk file names need to be ended at .gbk, .gb, or .gbff. \n")
print("Error: Please assign proper Genebank files!")
sys.exit()
elif detect_gbk:
out_gbk = self._parser_embl_gbk(gbks)
log.write("Running converter.py to convert gbk file to embl format.\n")
self.converter.convert_gbk2embl(out_gbk)
self.helper.check_make_folder(self.embl)
self.helper.move_all_content(out_gbk, self.embl, [".embl"])
log.write("\t" + self.embl + " is generated and the embl files are stored in it.\n")
return out_gbk
def _run_ratt(self, args_ratt, tar, ref, out, log):
if (not os.path.exists(self.embl)) or (
not os.path.exists(os.path.join(
self.tmp_files["tar"], tar + ".fa"))) or (
not os.path.exists(os.path.join(
self.tmp_files["ref"], ref + ".fa"))):
print("Error: Please check --compare_pair, the strain names "
"should be the same as the strain names in fasta, "
"genbank or embl files!")
log.write("The strain names in --compare_pair should be the same "
"as the strain names in fasta, genbank, or embl files.\n")
sys.exit()
log.write("Make sure your RATT version is at least 1.64.\n")
log.write("If the RATT can not run properly, please check the "
"RATT_HOME and PAGIT_HOME is assigned correctly.\n")
log.write(" ".join([args_ratt.ratt_path, self.embl,
os.path.join(self.tmp_files["tar"], tar + ".fa"),
args_ratt.element, args_ratt.transfer_type,
os.path.join(self.tmp_files["ref"], ref + ".fa")]) + "\n")
call([args_ratt.ratt_path, self.embl,
os.path.join(self.tmp_files["tar"], tar + ".fa"),
args_ratt.element, args_ratt.transfer_type,
os.path.join(self.tmp_files["ref"], ref + ".fa")],
stdout=out, stderr=DEVNULL)
log.write("Done!\n")
def _format_and_run(self, args_ratt, log):
print("Running RATT")
for pair in args_ratt.pairs:
ref = pair.split(":")[0]
tar = pair.split(":")[1]
out = open(self.ratt_log, "w+")
self._run_ratt(args_ratt, tar, ref, out, log)
log.write("The following files are generatd:\n")
for filename in os.listdir():
if ("final" in filename):
log.write("\t" + filename + "\n")
shutil.move(filename, os.path.join(args_ratt.output_path,
filename))
elif (args_ratt.element in filename) or (
"query" in filename) or (
"Reference" in filename) or (
"Query" in filename) or (
"Sequences" in filename):
log.write("\t" + filename + "\n")
if os.path.isfile(filename):
os.remove(filename)
if os.path.isdir(filename):
shutil.rmtree(filename)
out.close()
def annotation_transfer(self, args_ratt, log):
self.multiparser.parser_fasta(args_ratt.tar_fastas)
self.multiparser.parser_fasta(args_ratt.ref_fastas)
out_gbk = None
if args_ratt.ref_embls is None:
out_gbk = self._convert_embl(args_ratt.ref_gbki, log)
self._format_and_run(args_ratt, log)
files = []
for data in os.listdir(args_ratt.output_path):
if "final.embl" in data:
log.write("Running converter.py to convert embl "
"files in {0} to gff, ptt, and rnt format.\n".format(data))
self._convert_to_gff(data, args_ratt, files, log)
self._convert_to_pttrnt(args_ratt.gff_outfolder, files, log)
self.helper.check_make_folder(self.tmp_files["out_gff"])
log.write("Merging the output of {0}.\n".format(data))
for folder in os.listdir(args_ratt.tar_fastas):
files = []
if "_folder" in folder:
datas = folder.split("_folder")
prefix = ".".join(datas[0].split(".")[:-1])
for file_ in os.listdir(os.path.join(args_ratt.tar_fastas,
folder)):
files.append(file_[:-3])
for gff in os.listdir(args_ratt.gff_outfolder):
for file_ in files:
if (".gff" in gff) and (file_ == gff[:-4]):
self.helper.merge_file(os.path.join(
args_ratt.gff_outfolder, gff),
self.tmp_files["gff"])
if (".ptt" in gff) and (file_ == gff[:-4]):
self.helper.merge_file(os.path.join(
args_ratt.gff_outfolder, gff),
self.tmp_files["ptt"])
if (".rnt" in gff) and (file_ == gff[:-4]):
self.helper.merge_file(os.path.join(
args_ratt.gff_outfolder, gff),
self.tmp_files["rnt"])
if os.path.exists(self.tmp_files["gff"]):
shutil.move(self.tmp_files["gff"], os.path.join(
self.tmp_files["out_gff"], prefix + ".gff"))
shutil.move(self.tmp_files["ptt"], os.path.join(
self.tmp_files["out_gff"], prefix + ".ptt"))
shutil.move(self.tmp_files["rnt"], os.path.join(
self.tmp_files["out_gff"], prefix + ".rnt"))
else:
print("Error: Please check your fasta or "
"annotation files, they should only contain "
"the query genome. And make sure your RATT can "
"work properly (check $ANNOgesic/output/"
"annotation_transfer/ratt_log.txt).")
log.write("Please check your fasta or "
"annotation files, they should only contain "
"the query genome. And make sure your RATT can "
"work properly (check $ANNOgesic/output/"
"annotation_transfer/ratt_log.txt).\n")
self._remove_files(args_ratt, out_gbk, log)
