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)