def test_gbk(self):
log = open(os.path.join(self.test_folder, "test.log"), "w")
g_h = open(os.path.join(self.test_folder, "test.gbk"), "w")
g_h.write(self.example.gbk_file)
g_h.close()
get_input.get_file(None, self.test_folder, "gbk", log)
self.assertTrue("NC_007795.1.gbk" in os.listdir(self.test_folder))
log.close()
def test_fasta(self):
log = open(os.path.join(self.test_folder, "test.log"), "w")
f_h = open(os.path.join(self.test_folder, "test.fasta"), "w")
f_h.write(self.example.fasta_file)
f_h.close()
get_input.get_file(None, self.test_folder, "fna", log)
self.assertTrue("aa.fa" in os.listdir(self.test_folder))
log.close()
def test_gff(self):
log = open(os.path.join(self.test_folder, "test.log"), "w")
g_h = open(os.path.join(self.test_folder, "test.gff"), "w")
g_h.write(self.example.gff_file)
g_h.close()
get_input.get_file(None, self.test_folder, "gff", log)
self.assertTrue("ddd.gff" in os.listdir(self.test_folder))
log.close()
def test_gbk(self):
log = open(os.path.join(self.test_folder, "test.log"), "w")
g_h = open(os.path.join(self.test_folder, "test.gbk"), "w")
g_h.write(self.example.gbk_file)
g_h.close()
get_input.get_file(None, self.test_folder, "gbk", log)
self.assertTrue("NC_007795.1.gbk" in os.listdir(self.test_folder))
log.close()
def test_gff(self):
log = open(os.path.join(self.test_folder, "test.log"), "w")
g_h = open(os.path.join(self.test_folder, "test.gff"), "w")
g_h.write(self.example.gff_file)
g_h.close()
get_input.get_file(None, self.test_folder, "gff", log)
self.assertTrue("ddd.gff" in os.listdir(self.test_folder))
log.close()
def test_fasta(self):
log = open(os.path.join(self.test_folder, "test.log"), "w")
f_h = open(os.path.join(self.test_folder, "test.fasta"), "w")
f_h.write(self.example.fasta_file)
f_h.close()
get_input.get_file(None, self.test_folder, "fna", log)
self.assertTrue("aa.fa" in os.listdir(self.test_folder))
log.close()
def get_input(self):
"""Download required files from website."""
print("Running get input files")
if self._args.ftp_path is None:
print("Error: Please assign the path for downloading the data!")
sys.exit()
annotation_folder = self._paths.ref_annotation_folder
fasta_folder = self._paths.ref_fasta_folder
self.helper.check_make_folder(self._paths.ref_annotation_folder)
self.helper.check_make_folder(self._paths.ref_fasta_folder)
if self._args.ref_gff is True:
get_file(self._args.ftp_path, self._paths.ref_annotation_folder,
"gff")
get_file(self._args.ftp_path, self._paths.ref_annotation_folder,
"_genomic.gff.gz")
if self._args.ref_fasta is True:
get_file(self._args.ftp_path, self._paths.ref_fasta_folder,
"fna")
get_file(self._args.ftp_path, self._paths.ref_fasta_folder,
"_genomic.fna.gz")
if self._args.ref_gbk is True:
get_file(self._args.ftp_path, self._paths.ref_annotation_folder,
"gbk")
get_file(self._args.ftp_path, self._paths.ref_annotation_folder,
"gbff")
get_file(self._args.ftp_path, self._paths.ref_annotation_folder,
"_genomic.gbff.gz")
if self._args.ref_ptt is True:
get_file(self._args.ftp_path, self._paths.ref_annotation_folder,
"ptt")
if self._args.ref_rnt is True:
get_file(self._args.ftp_path, self._paths.ref_annotation_folder,
"rnt")
if self._args.convert_embl is True:
annotation_files = os.listdir(self._paths.ref_annotation_folder)
if len(annotation_files) == 0:
sys.stdout.write("No gff files!!\n")
else:
Converter().convert_gbk2embl(self._paths.ref_annotation_folder)
def get_input(self):
"""Download required files from website."""
print("Running get input files...")
if self._args.FTP_path is None:
print("Error: Please assign the path for downloading the data!!")
sys.exit()
if self._args.for_target:
annotation_folder = self._paths.tar_annotation_folder
fasta_folder = self._paths.tar_fasta_folder
else:
annotation_folder = self._paths.ref_annotation_folder
fasta_folder = self._paths.ref_fasta_folder
self.helper.check_make_folder(annotation_folder)
self.helper.check_make_folder(fasta_folder)
if self._args.ref_gff is True:
get_file(self._args.FTP_path, annotation_folder,
"gff", self._args.for_target)
get_file(self._args.FTP_path, annotation_folder,
"_genomic.gff.gz", self._args.for_target)
if self._args.ref_fasta is True:
get_file(self._args.FTP_path, fasta_folder,
"fna", self._args.for_target)
get_file(self._args.FTP_path, fasta_folder,
"_genomic.fna.gz", self._args.for_target)
if self._args.ref_gbk is True:
get_file(self._args.FTP_path, annotation_folder,
"gbk", self._args.for_target)
get_file(self._args.FTP_path, annotation_folder,
"gbff", self._args.for_target)
get_file(self._args.FTP_path, annotation_folder,
"_genomic.gbff.gz", self._args.for_target)
if self._args.ref_ptt is True:
get_file(self._args.FTP_path, annotation_folder,
"ptt", self._args.for_target)
if self._args.ref_rnt is True:
get_file(self._args.FTP_path, annotation_folder,
"rnt", self._args.for_target)
if self._args.convert_embl is True:
annotation_files = os.listdir(annotation_folder)
if len(annotation_files) == 0:
sys.stdout.write("No gbk files!!\n")
else:
Converter().convert_gbk2embl(annotation_folder)