def ribos(self):
"""riboswitch and RNA thermometer prediction"""
print("Running riboswitch and RNA thermometer prediction")
self.check_multi_files(
[self._args.annotation_files, self._args.fasta_files,
self._args.tss_files, self._args.transcript_files],
["--annotation_files", "--fasta_files", "--tss_files",
"--transcript_files"])
if (self._args.program == "both"):
self.check_file([self._args.riboswitch_id_file, self._args.rfam_path],
["--riboswitch_id_file", "--rfam_path"], True)
self.check_file([self._args.rna_thermometer_id_file,
self._args.rfam_path],
["--rna_thermometer_id_file", "--rfam_path"], True)
project_creator.create_subfolders(
self._paths.required_folders("riboswitch"))
project_creator.create_subfolders(
self._paths.required_folders("thermometer"))
ribos_path = self._paths.ribos_output_folder
thermo_path = self._paths.thermo_output_folder
elif (self._args.program == "thermometer"):
self.check_file([self._args.rna_thermometer_id_file,
self._args.rfam_path],
["--thermometer_id_file", "--rfam_path"], True)
project_creator.create_subfolders(
self._paths.required_folders("thermometer"))
ribos_path = None
thermo_path = self._paths.thermo_output_folder
elif (self._args.program == "riboswitch"):
self.check_file([self._args.riboswitch_id_file, self._args.rfam_path],
["--riboswitch_id_file", "--rfam_path"], True)
project_creator.create_subfolders(
self._paths.required_folders("riboswitch"))
ribos_path = self._paths.ribos_output_folder
thermo_path = None
else:
print("Error: Please assign \"thermometer\", \"riboswitch\" "
"or \"both\" in --program!")
sys.exit()
self._args.cmscan_path = self.check_execute_file(self._args.cmscan_path)
self._args.cmpress_path = self.check_execute_file(self._args.cmpress_path)
args_ribo = self.args_container.container_ribos(
self._args.program, self._args.rna_thermometer_id_file,
self._args.cmscan_path, self._args.cmpress_path,
self._args.riboswitch_id_file,
self._args.annotation_files, self._args.fasta_files,
self._args.tss_files, self._args.transcript_files,
self._args.rfam_path, ribos_path,
thermo_path, self._args.e_value,
self._args.output_all, self._paths.database_folder,
self._args.tolerance, self._args.start_codon,
self._args.min_dist_rbs, self._args.max_dist_rbs,
self._args.tolerance_rbs, self._args.utr_length)
ribos = Ribos(args_ribo)
ribos.run_ribos(args_ribo)
def ribos(self):
"""riboswitch and RNA thermometer prediction"""
print("Running riboswitch and RNA thermometer prediction...")
self.check_folder([self._args.gff_path, self._args.fasta_path,
self._args.tss_path, self._args.transcript_path])
if (self._args.program == "both"):
self.check_file([self._args.riboswitch_ID, self._args.Rfam],
["--riboswitch_ID", "--Rfam"], True)
self.check_file([self._args.RNA_thermometer_ID, self._args.Rfam],
["--RNA_thermometer_ID", "--Rfam"], True)
project_creator.create_subfolders(
self._paths.required_folders("riboswitch"))
project_creator.create_subfolders(
self._paths.required_folders("thermometer"))
ribos_path = self._paths.ribos_output_folder
thermo_path = self._paths.thermo_output_folder
elif (self._args.program == "thermometer"):
self.check_file([self._args.RNA_thermometer_ID, self._args.Rfam],
["--thermometer_ID", "--Rfam"], True)
project_creator.create_subfolders(
self._paths.required_folders("thermometer"))
ribos_path = None
thermo_path = self._paths.thermo_output_folder
elif (self._args.program == "riboswitch"):
self.check_file([self._args.riboswitch_ID, self._args.Rfam],
["--riboswitch_ID", "--Rfam"], True)
project_creator.create_subfolders(
self._paths.required_folders("riboswitch"))
ribos_path = self._paths.ribos_output_folder
thermo_path = None
else:
print("Error: Please assign \"thermometer\", \"riboswitch\" "
"or \"both\" in --program!!")
sys.exit()
args_ribo = self.args_container.container_ribos(
self._args.program, self._args.RNA_thermometer_ID,
self._args.infernal_path, self._args.riboswitch_ID,
self._args.gff_path, self._args.fasta_path,
self._args.tss_path, self._args.transcript_path,
self._args.Rfam, ribos_path,
thermo_path, self._args.e_value,
self._args.output_all, self._paths.database_folder,
self._args.fuzzy, self._args.start_codon,
self._args.min_dist_rbs, self._args.max_dist_rbs,
self._args.fuzzy_rbs, self._args.UTR_length)
ribos = Ribos(args_ribo)
ribos.run_ribos(args_ribo)
def setUp(self):
self.example = Example()
self.mock_args = MockClass()
self.mock = Mock_func()
self.test_folder = "test_folder"
self.gffs = os.path.join(self.test_folder, "gffs")
self.fastas = os.path.join(self.test_folder, "fastas")
self.out_folder = os.path.join(self.test_folder, "output")
self.database = os.path.join(self.test_folder, "database")
self.seq_path = os.path.join(self.test_folder, "seqs")
self.tables = os.path.join(self.out_folder, "tables")
self.stat = os.path.join(self.out_folder, "statistics")
self.scan = os.path.join(self.test_folder, "scan")
self.tsss = os.path.join(self.test_folder, "tsss")
self.trans = os.path.join(self.test_folder, "trans")
self.out_gff = os.path.join(self.out_folder, "gffs")
if (not os.path.exists(self.test_folder)):
os.mkdir(self.test_folder)
os.mkdir(self.tsss)
os.mkdir(os.path.join(self.tsss, "tmp"))
os.mkdir(self.trans)
os.mkdir(os.path.join(self.trans, "tmp"))
os.mkdir(self.gffs)
os.mkdir(os.path.join(self.gffs, "tmp"))
os.mkdir(self.fastas)
os.mkdir(os.path.join(self.fastas, "tmp"))
os.mkdir(self.out_folder)
os.mkdir(self.database)
os.mkdir(self.seq_path)
os.mkdir(os.path.join(self.out_folder, "tmp_table"))
os.mkdir(os.path.join(self.out_folder, "tmp_scan"))
os.mkdir(os.path.join(self.out_folder, "tmp_fasta"))
os.mkdir(os.path.join(self.out_folder, "scan_Rfam"))
os.mkdir(self.tables)
os.mkdir(self.scan)
os.mkdir(self.stat)
os.mkdir(self.out_gff)
args = self.mock_args.mock()
args.gffs = self.gffs
args.fastas = self.fastas
args.ribos_out_folder = self.out_folder
args.database = self.database
args.tsss = self.tsss
args.trans = self.trans
args.program = 'riboswtich'
self.ribo = Ribos(args)
def ribos(self):
"""riboswitch prediction"""
print("Running riboswitch prediction...")
self.check_folder([self._args.gff_path, self._args.fasta_path,
self._args.tss_path, self._args.transcript_path])
self.check_file([self._args.riboswitch_ID, self._args.Rfam],
["--riboswitch_ID", "--Rfam"], True)
project_creator.create_subfolders(
self._paths.required_folders("riboswitch"))
args_ribo = self.args_container.container_ribos(
self._args.infernal_path, self._args.riboswitch_ID,
self._args.gff_path, self._args.fasta_path,
self._args.tss_path, self._args.transcript_path,
self._args.Rfam, self._paths.ribos_output_folder,
self._args.e_value,
self._args.output_all, self._paths.database_folder,
self._args.fuzzy, self._args.start_codon,
self._args.min_dist_rbs, self._args.max_dist_rbs,
self._args.fuzzy_rbs, self._args.UTR_length)
ribos = Ribos(args_ribo)
ribos.run_ribos(args_ribo)
def ribos(self):
"""riboswitch prediction"""
print("Running riboswitch prediction...")
self.check_folder([
self._args.gff_path, self._args.fasta_path, self._args.tss_path,
self._args.transcript_path
])
self.check_file([self._args.riboswitch_ID, self._args.Rfam],
["--riboswitch_ID", "--Rfam"], True)
project_creator.create_subfolders(
self._paths.required_folders("riboswitch"))
args_ribo = self.args_container.container_ribos(
self._args.infernal_path, self._args.riboswitch_ID,
self._args.gff_path, self._args.fasta_path, self._args.tss_path,
self._args.transcript_path, self._args.Rfam,
self._paths.ribos_output_folder, self._args.e_value,
self._args.output_all, self._paths.database_folder,
self._args.fuzzy, self._args.start_codon, self._args.min_dist_rbs,
self._args.max_dist_rbs, self._args.fuzzy_rbs,
self._args.UTR_length)
ribos = Ribos(args_ribo)
ribos.run_ribos(args_ribo)
def setUp(self):
self.example = Example()
self.mock_args = MockClass()
self.mock = Mock_func()
self.test_folder = "test_folder"
self.gffs = os.path.join(self.test_folder, "gffs")
self.fastas = os.path.join(self.test_folder, "fastas")
self.out_folder = os.path.join(self.test_folder, "output")
self.database = os.path.join(self.test_folder, "database")
self.seq_path = os.path.join(self.test_folder, "seqs")
self.tables = os.path.join(self.out_folder, "tables")
self.stat = os.path.join(self.out_folder, "statistics")
self.scan = os.path.join(self.test_folder, "scan")
self.tsss = os.path.join(self.test_folder, "tsss")
self.trans = os.path.join(self.test_folder, "trans")
self.out_gff = os.path.join(self.out_folder, "gffs")
if (not os.path.exists(self.test_folder)):
os.mkdir(self.test_folder)
os.mkdir(self.tsss)
os.mkdir(os.path.join(self.tsss, "tmp"))
os.mkdir(self.trans)
os.mkdir(os.path.join(self.trans, "tmp"))
os.mkdir(self.gffs)
os.mkdir(os.path.join(self.gffs, "tmp"))
os.mkdir(self.fastas)
os.mkdir(os.path.join(self.fastas, "tmp"))
os.mkdir(self.out_folder)
os.mkdir(self.database)
os.mkdir(self.seq_path)
os.mkdir(os.path.join(self.out_folder, "tmp_table"))
os.mkdir(os.path.join(self.out_folder, "tmp_scan"))
os.mkdir(os.path.join(self.out_folder, "tmp_fasta"))
os.mkdir(os.path.join(self.out_folder, "scan_Rfam"))
os.mkdir(self.tables)
os.mkdir(self.scan)
os.mkdir(self.stat)
os.mkdir(self.out_gff)
args = self.mock_args.mock()
args.gffs = self.gffs
args.fastas = self.fastas
args.ribos_out_folder = self.out_folder
args.database = self.database
args.tsss = self.tsss
args.trans = self.trans
args.program = 'riboswtich'
self.ribo = Ribos(args)
class TestRibos(unittest.TestCase):
def setUp(self):
self.example = Example()
self.mock_args = MockClass()
self.mock = Mock_func()
self.test_folder = "test_folder"
self.gffs = os.path.join(self.test_folder, "gffs")
self.fastas = os.path.join(self.test_folder, "fastas")
self.out_folder = os.path.join(self.test_folder, "output")
self.database = os.path.join(self.test_folder, "database")
self.seq_path = os.path.join(self.test_folder, "seqs")
self.tables = os.path.join(self.out_folder, "tables")
self.stat = os.path.join(self.out_folder, "statistics")
self.scan = os.path.join(self.test_folder, "scan")
self.tsss = os.path.join(self.test_folder, "tsss")
self.trans = os.path.join(self.test_folder, "trans")
self.out_gff = os.path.join(self.out_folder, "gffs")
if (not os.path.exists(self.test_folder)):
os.mkdir(self.test_folder)
os.mkdir(self.tsss)
os.mkdir(os.path.join(self.tsss, "tmp"))
os.mkdir(self.trans)
os.mkdir(os.path.join(self.trans, "tmp"))
os.mkdir(self.gffs)
os.mkdir(os.path.join(self.gffs, "tmp"))
os.mkdir(self.fastas)
os.mkdir(os.path.join(self.fastas, "tmp"))
os.mkdir(self.out_folder)
os.mkdir(self.database)
os.mkdir(self.seq_path)
os.mkdir(os.path.join(self.out_folder, "tmp_table"))
os.mkdir(os.path.join(self.out_folder, "tmp_scan"))
os.mkdir(os.path.join(self.out_folder, "tmp_fasta"))
os.mkdir(os.path.join(self.out_folder, "scan_Rfam"))
os.mkdir(self.tables)
os.mkdir(self.scan)
os.mkdir(self.stat)
os.mkdir(self.out_gff)
args = self.mock_args.mock()
args.gffs = self.gffs
args.fastas = self.fastas
args.ribos_out_folder = self.out_folder
args.database = self.database
args.tsss = self.tsss
args.trans = self.trans
args.program = 'riboswtich'
self.ribo = Ribos(args)
def tearDown(self):
if os.path.exists(self.test_folder):
shutil.rmtree(self.test_folder)
def test_scan_extract_rfam(self):
self.ribo._run_cmscan = self.mock.mock_run_cmscan
rb.modify_table = self.mock.mock_modify_table
rb.regenerate_seq = self.mock.mock_regenerate_seq
rb.reextract_rbs = self.mock.mock_reextract_rbs
prefixs = []
gen_file(os.path.join(self.gffs, "tmp/test.gff"),
self.example.gff_file)
gen_file(os.path.join(self.fastas, "tmp/test.fa"),
self.example.fasta_file)
gen_file(os.path.join(self.seq_path, "test.fa"),
self.example.fasta_file)
gen_file(os.path.join(self.tsss, "tmp/test_TSS.gff"),
self.example.tss_file)
gen_file(os.path.join(self.trans, "tmp/test_transcript.gff"),
self.example.tran_file)
gen_file(os.path.join(self.out_folder, "tmp_fasta", "test.fa"),
self.example.fasta_file)
args = self.mock_args.mock()
args.start_codons = ["ATG"]
args.fastas = self.fastas
args.out_folder = self.out_folder
args.gffs = self.gffs
args.fuzzy = 5
args.fuzzy_rbs = 2
args.utr = True
args.output_all = "test"
tmp_files = {
"fasta": os.path.join(self.out_folder, "tmp_fasta"),
"scan": "tmp_scan",
"table": os.path.join(self.out_folder, "tmp_table")
}
rfam = "Rfam_.cm"
suffixs = {
"csv": "test.csv",
"txt": "test_prescan.txt",
"re_txt": "test_scan.txt",
"re_csv": "test_scan.csv"
}
self.ribo._scan_extract_rfam(prefixs, args, tmp_files, suffixs, "test",
rfam)
self.assertListEqual(prefixs, ["test"])
self.assertTrue(
os.path.exists(
os.path.join(self.out_folder, "tmp_fasta",
"test_regenerate.fa")))
def test_merge_results(self):
rb.stat_and_covert2gff = self.mock.mock_stat_and_covert2gff
gen_file(os.path.join(self.gffs, "test.gff"), self.example.gff_file)
gen_file(
os.path.join(self.out_folder, "tmp_table/test_riboswitch.csv"),
self.example.table)
gen_file(
os.path.join(self.out_folder,
"tmp_scan/test_riboswitch_prescan.txt"),
self.example.rescan_file)
gen_file(
os.path.join(self.out_folder, "tmp_scan/test_riboswitch_scan.txt"),
self.example.rescan_file)
gen_file(os.path.join(self.test_folder, "ids"), self.example.ids)
gen_file(os.path.join(self.tables, "test_riboswitch.csv"),
self.example.table)
gen_file('test_folder/output/tmp_table/test_test_scan.csv', "test")
gen_file(
os.path.join("test_folder/output", "tmp_fasta",
"test_regenerate.fa"), "test")
gen_file('test_folder/output/tmp_scan/test_test_prescan.txt', "test")
gen_file('test_folder/output/tmp_scan/test_test_scan.txt', "test")
if not os.path.exists('test_folder/output/tmp_table/test_test.csv'):
gen_file('test_folder/output/tmp_table/test_test.csv', "test")
args = self.mock_args.mock()
args.start_codons = ["ATG"]
args.fastas = self.fastas
args.out_folder = self.out_folder
args.gffs = self.gffs
args.ribos_id = os.path.join(self.test_folder, "ids")
args.fuzzy = 3
suffixs = {
"csv": "test.csv",
"txt": "test_prescan.txt",
"re_txt": "test_scan.txt",
"re_csv": "test_scan.csv"
}
tmp_files = {
"fasta": os.path.join(self.out_folder, "tmp_fasta"),
"scan": os.path.join(self.out_folder, "tmp_scan"),
"table": os.path.join(self.out_folder, "tmp_table")
}
rfam = "Rfam_.cm"
self.ribo._merge_results(args, os.path.join(self.out_folder,
"tmp_scan"), suffixs,
tmp_files,
os.path.join(self.out_folder, "tmp_scan"),
os.path.join(self.out_folder, "scan_Rfam"),
os.path.join(self.out_folder, "scan_Rfam"),
os.path.join(self.out_folder,
"gffs"), "riboswitch")
class TestRibos(unittest.TestCase):
def setUp(self):
self.example = Example()
self.mock_args = MockClass()
self.mock = Mock_func()
self.test_folder = "test_folder"
self.gffs = os.path.join(self.test_folder, "gffs")
self.fastas = os.path.join(self.test_folder, "fastas")
self.out_folder = os.path.join(self.test_folder, "output")
self.database = os.path.join(self.test_folder, "database")
self.seq_path = os.path.join(self.test_folder, "seqs")
self.tables = os.path.join(self.out_folder, "tables")
self.stat = os.path.join(self.out_folder, "statistics")
self.scan = os.path.join(self.test_folder, "scan")
self.tsss = os.path.join(self.test_folder, "tsss")
self.trans = os.path.join(self.test_folder, "trans")
self.out_gff = os.path.join(self.out_folder, "gffs")
if (not os.path.exists(self.test_folder)):
os.mkdir(self.test_folder)
os.mkdir(self.tsss)
os.mkdir(os.path.join(self.tsss, "tmp"))
os.mkdir(self.trans)
os.mkdir(os.path.join(self.trans, "tmp"))
os.mkdir(self.gffs)
os.mkdir(os.path.join(self.gffs, "tmp"))
os.mkdir(self.fastas)
os.mkdir(os.path.join(self.fastas, "tmp"))
os.mkdir(self.out_folder)
os.mkdir(self.database)
os.mkdir(self.seq_path)
os.mkdir(os.path.join(self.out_folder, "tmp_table"))
os.mkdir(os.path.join(self.out_folder, "tmp_scan"))
os.mkdir(os.path.join(self.out_folder, "tmp_fasta"))
os.mkdir(os.path.join(self.out_folder, "scan_Rfam"))
os.mkdir(self.tables)
os.mkdir(self.scan)
os.mkdir(self.stat)
os.mkdir(self.out_gff)
args = self.mock_args.mock()
args.gffs = self.gffs
args.fastas = self.fastas
args.out_folder = self.out_folder
args.database = self.database
args.tsss = self.tsss
args.trans = self.trans
self.ribo = Ribos(args)
def tearDown(self):
if os.path.exists(self.test_folder):
shutil.rmtree(self.test_folder)
def test_scan_extract_rfam(self):
self.ribo._run_infernal = self.mock.mock_run_infernal
rb.modify_table = self.mock.mock_modify_table
prefixs = []
gen_file(os.path.join(self.gffs, "tmp/test.gff"), self.example.gff_file)
gen_file(os.path.join(self.fastas, "tmp/test.fa"), self.example.fasta_file)
gen_file(os.path.join(self.seq_path, "test.fa"), self.example.fasta_file)
gen_file(os.path.join(self.tsss, "tmp/test_TSS.gff"), self.example.tss_file)
gen_file(os.path.join(self.trans, "tmp/test_transcript.gff"), self.example.tran_file)
gen_file(os.path.join(self.out_folder, "tmp_fasta", "test.fa"), self.example.fasta_file)
args = self.mock_args.mock()
args.start_codons = ["ATG"]
args.fastas = self.fastas
args.out_folder = self.out_folder
args.gffs = self.gffs
args.fuzzy = 5
args.fuzzy_rbs = 2
args.utr = True
args.output_all = "test"
self.ribo._scan_extract_rfam(prefixs, args)
self.assertListEqual(prefixs, ["test"])
self.assertTrue(os.path.exists(os.path.join(self.out_folder, "tmp_fasta", "test_regenerate.fa")))
def test_merge_results(self):
gen_file(os.path.join(self.gffs, "test.gff"), self.example.gff_file)
gen_file(os.path.join(self.out_folder, "tmp_table/test_riboswitch.csv"), self.example.table)
gen_file(os.path.join(self.out_folder, "tmp_scan/test_riboswitch_prescan.txt"), self.example.rescan_file)
gen_file(os.path.join(self.out_folder, "tmp_scan/test_riboswitch_scan.txt"), self.example.rescan_file)
gen_file(os.path.join(self.test_folder, "ids"), self.example.ids)
gen_file(os.path.join(self.tables, "test_riboswitch.csv"), self.example.table)
args = self.mock_args.mock()
args.start_codons = ["ATG"]
args.fastas = self.fastas
args.out_folder = self.out_folder
args.gffs = self.gffs
args.ribos_id = os.path.join(self.test_folder, "ids")
args.fuzzy = 3
self.ribo._merge_results(args)
class TestRibos(unittest.TestCase):
def setUp(self):
self.example = Example()
self.mock_args = MockClass()
self.mock = Mock_func()
self.test_folder = "test_folder"
self.gffs = os.path.join(self.test_folder, "gffs")
self.fastas = os.path.join(self.test_folder, "fastas")
self.out_folder = os.path.join(self.test_folder, "output")
self.database = os.path.join(self.test_folder, "database")
self.seq_path = os.path.join(self.test_folder, "seqs")
self.tables = os.path.join(self.out_folder, "tables")
self.stat = os.path.join(self.out_folder, "statistics")
self.scan = os.path.join(self.test_folder, "scan")
self.tsss = os.path.join(self.test_folder, "tsss")
self.trans = os.path.join(self.test_folder, "trans")
self.out_gff = os.path.join(self.out_folder, "gffs")
if (not os.path.exists(self.test_folder)):
os.mkdir(self.test_folder)
os.mkdir(self.tsss)
os.mkdir(os.path.join(self.tsss, "tmp"))
os.mkdir(self.trans)
os.mkdir(os.path.join(self.trans, "tmp"))
os.mkdir(self.gffs)
os.mkdir(os.path.join(self.gffs, "tmp"))
os.mkdir(self.fastas)
os.mkdir(os.path.join(self.fastas, "tmp"))
os.mkdir(self.out_folder)
os.mkdir(self.database)
os.mkdir(self.seq_path)
os.mkdir(os.path.join(self.out_folder, "tmp_table"))
os.mkdir(os.path.join(self.out_folder, "tmp_scan"))
os.mkdir(os.path.join(self.out_folder, "tmp_fasta"))
os.mkdir(os.path.join(self.out_folder, "scan_Rfam"))
os.mkdir(self.tables)
os.mkdir(self.scan)
os.mkdir(self.stat)
os.mkdir(self.out_gff)
args = self.mock_args.mock()
args.gffs = self.gffs
args.fastas = self.fastas
args.ribos_out_folder = self.out_folder
args.database = self.database
args.tsss = self.tsss
args.trans = self.trans
args.program = 'riboswtich'
self.ribo = Ribos(args)
def tearDown(self):
if os.path.exists(self.test_folder):
shutil.rmtree(self.test_folder)
def test_scan_extract_rfam(self):
self.ribo._run_cmscan = self.mock.mock_run_cmscan
rb.modify_table = self.mock.mock_modify_table
rb.regenerate_seq = self.mock.mock_regenerate_seq
rb.reextract_rbs = self.mock.mock_reextract_rbs
prefixs = []
gen_file(os.path.join(self.gffs, "tmp/test.gff"),
self.example.gff_file)
gen_file(os.path.join(self.fastas, "tmp/test.fa"),
self.example.fasta_file)
gen_file(os.path.join(self.seq_path, "test.fa"),
self.example.fasta_file)
gen_file(os.path.join(self.tsss, "tmp/test_TSS.gff"),
self.example.tss_file)
gen_file(os.path.join(self.trans, "tmp/test_transcript.gff"),
self.example.tran_file)
gen_file(os.path.join(self.out_folder, "tmp_fasta", "test.fa"),
self.example.fasta_file)
args = self.mock_args.mock()
args.start_codons = ["ATG"]
args.fastas = self.fastas
args.out_folder = self.out_folder
args.gffs = self.gffs
args.fuzzy = 5
args.fuzzy_rbs = 2
args.utr = True
args.without_rbs = False
args.rbs_seq = ["AGGAGG"]
args.output_all = "test"
args.cutoff = "e_0.01"
tmp_files = {"fasta": os.path.join(self.out_folder, "tmp_fasta"),
"scan": "tmp_scan",
"table": os.path.join(self.out_folder, "tmp_table")}
rfam = "Rfam_.cm"
suffixs = {"csv": "test.csv",
"txt": "test_prescan.txt",
"re_txt": "test_scan.txt",
"re_csv": "test_scan.csv"}
log = open(os.path.join(self.test_folder, "test.log"), "w")
self.ribo._scan_extract_rfam(prefixs, args, tmp_files,
suffixs, "test", rfam, log)
self.assertListEqual(prefixs, ["test"])
self.assertTrue(os.path.exists(os.path.join(
self.out_folder, "tmp_fasta", "test_regenerate.fa")))
def test_merge_results(self):
rb.stat_and_covert2gff = self.mock.mock_stat_and_covert2gff
gen_file(os.path.join(self.gffs, "test.gff"), self.example.gff_file)
gen_file(os.path.join(
self.out_folder, "tmp_table/test_riboswitch.csv"),
self.example.table)
gen_file(os.path.join(
self.out_folder, "tmp_scan/test_riboswitch_prescan.txt"),
self.example.rescan_file)
gen_file(os.path.join(
self.out_folder, "tmp_scan/test_riboswitch_scan.txt"),
self.example.rescan_file)
gen_file(os.path.join(
self.test_folder, "ids"), self.example.ids)
gen_file(os.path.join(
self.tables, "test_riboswitch.csv"), self.example.table)
gen_file('test_folder/output/tmp_table/test_test_scan.csv', "test")
gen_file(os.path.join("test_folder/output", "tmp_fasta",
"test_regenerate.fa"), "test")
gen_file('test_folder/output/tmp_scan/test_test_prescan.txt', "test")
gen_file('test_folder/output/tmp_scan/test_test_scan.txt', "test")
if not os.path.exists('test_folder/output/tmp_table/test_test.csv'):
gen_file('test_folder/output/tmp_table/test_test.csv', "test")
args = self.mock_args.mock()
args.start_codons = ["ATG"]
args.fastas = self.fastas
args.out_folder = self.out_folder
args.gffs = self.gffs
args.ribos_id = os.path.join(self.test_folder, "ids")
args.fuzzy = 3
suffixs = {"csv": "test.csv",
"txt": "test_prescan.txt",
"re_txt": "test_scan.txt",
"re_csv": "test_scan.csv"}
tmp_files = {"fasta": os.path.join(self.out_folder, "tmp_fasta"),
"scan": os.path.join(self.out_folder, "tmp_scan"),
"table": os.path.join(self.out_folder, "tmp_table")}
rfam = "Rfam_.cm"
log = open(os.path.join(self.test_folder, "test.log"), "w")
self.ribo._merge_results(
args, os.path.join(self.out_folder, "tmp_scan"), suffixs,
tmp_files, os.path.join(self.out_folder, "tmp_scan"),
os.path.join(self.out_folder, "scan_Rfam"),
os.path.join(self.out_folder, "scan_Rfam"),
os.path.join(self.out_folder, "gffs"), "riboswitch", log)