class TestConverter(unittest.TestCase):
def setUp(self):
self.converter = Converter()
self.example = Example()
self.converter.gff3parser = Mock_gff3_parser
self.converter._print_rntptt_title = Mock_func().print_rntptt_title
self.converter.tsspredator = Mock_TSSPredatorReader()
self.converter._read_file = Mock_func().mock_read_file
self.gff_file = self.example.gff_file
self.ptt_out = self.example.ptt_out
self.rnt_out = self.example.rnt_out
self.srna_out = self.example.srna_out
self.embl_file = self.example.embl_file
self.embl_out = self.example.embl_out
self.multi_embl = self.example.multi_embl
self.gff_out = self.example.gff_out
self.mastertable = self.example.mastertable
self.tss_file = self.example.tss_file
self.fasta_file = self.example.fasta_file
self.transterm = self.example.transterm
self.term_file = self.example.term_file
self.circ_file = self.example.circrna_table
self.circ_all = self.example.circrna_all
self.circ_best = self.example.circrna_best
self.test_folder = "test_folder"
self.mock_args = MockClass()
if (not os.path.exists(self.test_folder)):
os.mkdir(self.test_folder)
def tearDown(self):
if os.path.exists(self.test_folder):
shutil.rmtree(self.test_folder)
def test_print_rntptt_file(self):
cdss = []
genes = []
rnas = []
gff_dict = Example().gff_dict
for gff in gff_dict:
if gff["feature"] == "gene":
genes.append(self.converter.gff3parser.entries(self, gff))
elif gff["feature"] == "CDS":
cdss.append(self.converter.gff3parser.entries(self, gff))
elif gff["feature"] == "tRNA":
rnas.append(self.converter.gff3parser.entries(self, gff))
out_p = StringIO()
out_r = StringIO()
self.converter._print_rntptt_file(out_p, cdss, genes)
self.converter._print_rntptt_file(out_r, rnas, genes)
self.assertEqual(out_p.getvalue().split("\n")[:-1],
self.example.ptt_out_list)
self.assertEqual(out_r.getvalue().split("\n")[:-1],
self.example.rnt_out_list)
out_p.close()
out_r.close()
def test_srna2pttrnt(self):
srna_input_file = os.path.join(self.test_folder, "srna.gff")
srna_output_file = os.path.join(self.test_folder, "srna.out")
with open(srna_input_file, "w") as fh:
fh.write(self.gff_file)
srnas = []
self.converter._srna2rntptt(srna_input_file, srna_output_file, srnas,
1234567)
datas = import_data(srna_output_file)
self.assertEqual(set(datas), set(self.srna_out.split("\n")))
def test_multi_embl_pos(self):
embls = []
for line in self.embl_file.split("\n"):
datas = self.converter._multi_embl_pos(line.strip())
if datas != "Wrong":
embls.append(datas)
for index in range(0, 7):
self.assertDictEqual(embls[index], self.embl_out[index])
for index in range(0, 2):
self.assertDictEqual(embls[-1]["pos"][index],
self.multi_embl[index])
def test_parser_embl_data(self):
embl_file = os.path.join(self.test_folder, "test.embl")
embl_out = os.path.join(self.test_folder, "test.embl_out")
out = StringIO()
with open(embl_file, "w") as eh:
for line in self.embl_file.split("\n"):
eh.write(line + "\n")
info = self.converter._parser_embl_data(embl_file, out)
datas = out.getvalue().split("\n")
self.assertEqual(set(datas[:-1]), set(self.gff_out.split("\n")))
self.assertEqual(info[0], "NC_007795.1")
for index in range(0, 2):
self.assertDictEqual(info[1]["pos"][index], self.multi_embl[index])
out.close()
def test_multi_tss_class(self):
nums = {"tss": 0, "tss_uni": 0, "class": 1}
utrs = {"total": [], "pri": [], "sec": []}
tss_features = {"tss_types": [], "locus_tags": [], "utr_lengths": []}
tss_index = defaultdict(lambda: 0)
master_file = os.path.join(self.test_folder, "test.tsv")
fh = StringIO(self.mastertable)
for tss in self.converter.tsspredator.entries(fh):
self.converter._multi_tss_class(tss, tss_index, tss_features, nums,
utrs)
fh.close()
self.assertDictEqual(nums, {'tss_uni': 0, 'class': 5, 'tss': 2})
def test_convert_mastertable2gff(self):
master_file = os.path.join(self.test_folder, "test.tsv")
with open(master_file, "w") as th:
th.write(self.mastertable)
out_gff = os.path.join(self.test_folder, "test.tsv_out")
self.converter.convert_mastertable2gff(master_file, "ANNOgesic", "TSS",
"aaa", out_gff)
datas = import_data(out_gff)
self.assertEqual(set(datas), set(self.tss_file.split("\n")))
def test_convert_gff2rntptt(self):
srna_input_file = os.path.join(self.test_folder, "srna.gff")
srna_output_file = os.path.join(self.test_folder, "srna.out")
gff_file = os.path.join(self.test_folder, "test.gff")
rnt_file = os.path.join(self.test_folder, "test.rnt")
ptt_file = os.path.join(self.test_folder, "test.ptt")
fasta_file = os.path.join(self.test_folder, "test.fa")
with open(srna_input_file, "w") as fh:
fh.write(self.gff_file)
with open(gff_file, "w") as fh:
fh.write(self.gff_file)
with open(fasta_file, "w") as fh:
fh.write(self.fasta_file)
self.converter.convert_gff2rntptt(gff_file, fasta_file, ptt_file,
rnt_file, srna_input_file,
srna_output_file)
self.assertTrue(srna_output_file)
self.assertTrue(rnt_file)
self.assertTrue(ptt_file)
def test_convert_embl2gff(self):
embl_file = os.path.join(self.test_folder, "test.embl")
gff_file = os.path.join(self.test_folder, "test.embl_out")
with open(embl_file, "w") as eh:
for line in self.embl_file.split("\n"):
eh.write(line + "\n")
self.converter.convert_embl2gff(embl_file, gff_file)
datas = import_data(gff_file)
self.assertEqual(set(datas[1:-2]), set(self.gff_out.split("\n")))
def test_convert_transtermhp2gff(self):
transterm_file = os.path.join(self.test_folder,
"test_best_terminator_after_gene.bag")
gff_file = os.path.join(self.test_folder, "transterm.gff")
with open(transterm_file, "w") as th:
th.write(self.transterm)
self.converter.convert_transtermhp2gff(transterm_file, gff_file)
datas = import_data(gff_file)
self.assertEqual(set(datas), set(self.term_file.split("\n")))
def get_info(datas):
f_datas = []
for data in datas:
if not data.startswith("#"):
f_datas.append("\t".join(data.split("\t")[:8]))
return f_datas
def test_convert_circ2gff(self):
circ_file = os.path.join(self.test_folder, "circ.csv")
out_all = os.path.join(self.test_folder, "all.gff")
out_filter = os.path.join(self.test_folder, "best.gff")
with open(circ_file, "w") as ch:
ch.write(self.circ_file)
args = self.mock_args.mock()
args.start_ratio = 0.5
args.end_ratio = 0.5
args.support = 5
self.converter.convert_circ2gff(circ_file, args, out_all, out_filter)
datas = import_data(out_all)
f_datas = []
for data in datas:
if not data.startswith("#"):
f_datas.append("\t".join(data.split("\t")[:8]))
c_datas = []
for data in self.circ_all.split("\n"):
if not data.startswith("#"):
c_datas.append("\t".join(data.split("\t")[:8]))
self.assertListEqual(f_datas, c_datas)
datas = import_data(out_filter)
f_datas = []
for data in datas:
if not data.startswith("#"):
f_datas.append("\t".join(data.split("\t")[:8]))
c_datas = []
for data in self.circ_best.split("\n"):
if not data.startswith("#"):
c_datas.append("\t".join(data.split("\t")[:8]))
self.assertListEqual(f_datas, c_datas)
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):
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)
class TestConverter(unittest.TestCase):
def setUp(self):
self.converter = Converter()
self.example = Example()
self.converter.gff3parser = Mock_gff3_parser
self.converter._print_rntptt_title = Mock_func().print_rntptt_title
self.converter.tsspredator = Mock_TSSPredatorReader()
self.converter._read_file = Mock_func().mock_read_file
self.gff_file = self.example.gff_file
self.ptt_out = self.example.ptt_out
self.rnt_out = self.example.rnt_out
self.srna_out = self.example.srna_out
self.embl_file = self.example.embl_file
self.embl_out = self.example.embl_out
self.multi_embl = self.example.multi_embl
self.gff_out = self.example.gff_out
self.mastertable = self.example.mastertable
self.tss_file = self.example.tss_file
self.fasta_file = self.example.fasta_file
self.transterm = self.example.transterm
self.term_file = self.example.term_file
self.circ_file = self.example.circrna_table
self.circ_all = self.example.circrna_all
self.circ_best = self.example.circrna_best
self.test_folder = "test_folder"
self.mock_args = MockClass()
if (not os.path.exists(self.test_folder)):
os.mkdir(self.test_folder)
def tearDown(self):
if os.path.exists(self.test_folder):
shutil.rmtree(self.test_folder)
def test_print_rntptt_file(self):
cdss = []
genes = []
rnas = []
gff_dict = Example().gff_dict
for gff in gff_dict:
if gff["feature"] == "gene":
genes.append(self.converter.gff3parser.entries(self, gff))
elif gff["feature"] == "CDS":
cdss.append(self.converter.gff3parser.entries(self, gff))
elif gff["feature"] == "tRNA":
rnas.append(self.converter.gff3parser.entries(self, gff))
out_p = StringIO()
out_r = StringIO()
self.converter._print_rntptt_file(out_p, cdss, genes)
self.converter._print_rntptt_file(out_r, rnas, genes)
self.assertEqual(out_p.getvalue().split("\n")[:-1],
self.example.ptt_out_list)
self.assertEqual(out_r.getvalue().split("\n")[:-1],
self.example.rnt_out_list)
out_p.close()
out_r.close()
def test_srna2pttrnt(self):
srna_input_file = os.path.join(self.test_folder, "srna.gff")
srna_output_file = os.path.join(self.test_folder, "srna.out")
with open(srna_input_file, "w") as fh:
fh.write(self.gff_file)
srnas = []
self.converter._srna2rntptt(srna_input_file, srna_output_file,
srnas, 1234567)
datas = import_data(srna_output_file)
self.assertEqual(set(datas), set(self.srna_out.split("\n")))
def test_multi_embl_pos(self):
embls = []
for line in self.embl_file.split("\n"):
datas = self.converter._multi_embl_pos(line.strip())
if datas != "Wrong":
embls.append(datas)
for index in range(0, 7):
self.assertDictEqual(embls[index], self.embl_out[index])
for index in range(0, 2):
self.assertDictEqual(embls[-1]["pos"][index],
self.multi_embl[index])
def test_parser_embl_data(self):
embl_file = os.path.join(self.test_folder, "test.embl")
embl_out = os.path.join(self.test_folder, "test.embl_out")
out = StringIO()
with open(embl_file, "w") as eh:
for line in self.embl_file.split("\n"):
eh.write(line + "\n")
info = self.converter._parser_embl_data(embl_file, out)
datas = out.getvalue().split("\n")
self.assertEqual(set(datas[:-1]), set(self.gff_out.split("\n")))
self.assertEqual(info[0], "NC_007795.1")
for index in range(0, 2):
self.assertDictEqual(info[1]["pos"][index], self.multi_embl[index])
out.close()
def test_multi_tss_class(self):
nums = {"tss": 0, "tss_uni": 0, "class": 1}
utrs = {"total": [], "pri": [], "sec": []}
tss_features = {"tss_types": [], "locus_tags": [], "utr_lengths": []}
tss_index = defaultdict(lambda: 0)
master_file = os.path.join(self.test_folder, "test.tsv")
fh = StringIO(self.mastertable)
for tss in self.converter.tsspredator.entries(fh):
self.converter._multi_tss_class(
tss, tss_index, tss_features, nums, utrs)
fh.close()
self.assertDictEqual(nums, {'tss_uni': 0, 'class': 5, 'tss': 2})
def test_convert_mastertable2gff(self):
master_file = os.path.join(self.test_folder, "test.tsv")
with open(master_file, "w") as th:
th.write(self.mastertable)
out_gff = os.path.join(self.test_folder, "test.tsv_out")
self.converter.convert_mastertable2gff(master_file, "ANNOgesic", "TSS",
"aaa", out_gff)
datas = import_data(out_gff)
self.assertEqual(set(datas), set(self.tss_file.split("\n")))
def test_convert_gff2rntptt(self):
srna_input_file = os.path.join(self.test_folder, "srna.gff")
srna_output_file = os.path.join(self.test_folder, "srna.out")
gff_file = os.path.join(self.test_folder, "test.gff")
rnt_file = os.path.join(self.test_folder, "test.rnt")
ptt_file = os.path.join(self.test_folder, "test.ptt")
fasta_file = os.path.join(self.test_folder, "test.fa")
with open(srna_input_file, "w") as fh:
fh.write(self.gff_file)
with open(gff_file, "w") as fh:
fh.write(self.gff_file)
with open(fasta_file, "w") as fh:
fh.write(self.fasta_file)
self.converter.convert_gff2rntptt(
gff_file, fasta_file, ptt_file, rnt_file,
srna_input_file, srna_output_file)
self.assertTrue(srna_output_file)
self.assertTrue(rnt_file)
self.assertTrue(ptt_file)
def test_convert_embl2gff(self):
embl_file = os.path.join(self.test_folder, "test.embl")
gff_file = os.path.join(self.test_folder, "test.embl_out")
with open(embl_file, "w") as eh:
for line in self.embl_file.split("\n"):
eh.write(line + "\n")
self.converter.convert_embl2gff(embl_file, gff_file)
datas = import_data(gff_file)
self.assertEqual(set(datas[1:-2]), set(self.gff_out.split("\n")))
def test_convert_transtermhp2gff(self):
transterm_file = os.path.join(
self.test_folder, "test_best_terminator_after_gene.bag")
gff_file = os.path.join(self.test_folder, "transterm.gff")
with open(transterm_file, "w") as th:
th.write(self.transterm)
self.converter.convert_transtermhp2gff(transterm_file, gff_file)
datas = import_data(gff_file)
self.assertEqual(set(datas), set(self.term_file.split("\n")))
def get_info(datas):
f_datas = []
for data in datas:
if not data.startswith("#"):
f_datas.append("\t".join(data.split("\t")[:8]))
return f_datas
def test_convert_circ2gff(self):
circ_file = os.path.join(self.test_folder, "circ.csv")
out_all = os.path.join(self.test_folder, "all.gff")
out_filter = os.path.join(self.test_folder, "best.gff")
with open(circ_file, "w") as ch:
ch.write(self.circ_file)
args = self.mock_args.mock()
args.start_ratio = 0.5
args.end_ratio = 0.5
args.support = 5
self.converter.convert_circ2gff(circ_file, args, out_all, out_filter)
datas = import_data(out_all)
f_datas = []
for data in datas:
if not data.startswith("#"):
f_datas.append("\t".join(data.split("\t")[:8]))
c_datas = []
for data in self.circ_all.split("\n"):
if not data.startswith("#"):
c_datas.append("\t".join(data.split("\t")[:8]))
self.assertListEqual(f_datas, c_datas)
datas = import_data(out_filter)
f_datas = []
for data in datas:
if not data.startswith("#"):
f_datas.append("\t".join(data.split("\t")[:8]))
c_datas = []
for data in self.circ_best.split("\n"):
if not data.startswith("#"):
c_datas.append("\t".join(data.split("\t")[:8]))
self.assertListEqual(f_datas, c_datas)
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)