def setUp(self):
self.mock = Mock_func()
self.mock_args = MockClass()
self.test_folder = "test_folder"
self.tsss = "test_folder/tsss"
self.srnas = "test_folder/sRNA"
self.out = "test_folder/output"
self.trans = "test_folder/trans"
self.fastas = "test_folder/fastas"
self.tex = "test_folder/tex"
self.frag = "test_folder/frag"
self.gffs = "test_folder/gffs"
if (not os.path.exists(self.test_folder)):
os.mkdir(self.test_folder)
os.mkdir(self.tsss)
os.mkdir(self.out)
os.mkdir(self.trans)
os.mkdir(self.fastas)
os.mkdir(self.tex)
os.mkdir(self.frag)
os.mkdir(self.srnas)
os.mkdir(self.gffs)
args = self.mock_args.mock()
args.tsss = self.tsss
args.srnas = self.srnas
args.out_folder = self.out
args.trans = self.trans
args.fastas = self.fastas
self.sorf = sORFDetection(args)
def sorf_detection(self):
"""sORF_detection."""
print("Running sORF prediction")
self.check_multi_files(
[self._args.transcript_files, self._args.annotation_files,
self._args.fasta_files, self._args.srna_files,
self._args.tss_files],
["--transcript_files", "--annotation_files",
"--fasta_files", "--srna_files", "--tss_files"])
project_creator.create_subfolders(
self._paths.required_folders("sorf"))
args_sorf = self.args_container.container_sorf(
self._paths.sorf_folder, self._args.utr_derived_sorf,
self._args.transcript_files,
self._args.annotation_files,
self._args.tss_files, self._args.utr_length,
self._args.min_length, self._args.max_length,
self._args.cutoff_intergenic_coverage,
self._args.cutoff_antisense_coverage,
self._args.cutoff_5utr_coverage,
self._args.cutoff_3utr_coverage,
self._args.cutoff_intercds_coverage,
self._args.fasta_files, self._args.tex_notex_libs,
self._args.frag_libs, self._args.tex_notex,
self._args.replicate_tex, self._args.replicate_frag,
self._args.table_best, self._args.srna_files,
self._args.start_codon, self._args.stop_codon,
self._args.cutoff_base_coverage, self._args.tolerance_rbs,
self._args.rbs_not_after_tss, self._args.print_all_combination,
self._args.best_no_srna, self._args.best_no_tss,
self._args.ignore_hypothetical_protein,
self._args.min_rbs_distance, self._args.max_rbs_distance,
self._args.tolerance_3end, self._args.tolerance_5end)
sorf = sORFDetection(args_sorf)
sorf.run_sorf_detection(args_sorf)
def sorf_detection(self):
"""sORF_detection."""
print("Running sORF prediction...")
self.check_folder([self._args.transcript_assembly_folder,
self._args.annotation_folder,
self._args.fasta_folder])
self.check_no_require_folder([
self._args.sRNA_folder, self._args.TSS_folder])
project_creator.create_subfolders(
self._paths.required_folders("sorf"))
args_sorf = self.args_container.container_sorf(
self._paths.sorf_folder, self._args.UTR_derived_sORF,
self._args.transcript_assembly_folder,
self._args.annotation_folder,
self._args.TSS_folder, self._args.utr_length,
self._args.min_length, self._args.max_length,
self._args.tex_wig_folder, self._args.frag_wig_folder,
self._args.cutoff_intergenic_coverage,
self._args.cutoff_antisense_coverage,
self._args.cutoff_5utr_coverage,
self._args.cutoff_3utr_coverage,
self._args.cutoff_interCDS_coverage,
self._args.fasta_folder, self._args.tex_notex_libs,
self._args.frag_libs, self._args.tex_notex,
self._args.replicates_tex, self._args.replicates_frag,
self._args.table_best, self._args.sRNA_folder,
self._args.start_codon, self._args.stop_codon,
self._args.cutoff_background, self._args.fuzzy_rbs,
self._args.rbs_not_after_TSS, self._args.print_all_combination,
self._args.best_no_sRNA, self._args.best_no_TSS,
self._args.ignore_hypothetical_protein,
self._args.min_rbs_distance, self._args.max_rbs_distance)
sorf = sORFDetection(args_sorf)
sorf.run_sorf_detection(args_sorf)
def setUp(self):
self.mock = Mock_func()
self.mock_args = MockClass()
self.test_folder = "test_folder"
self.tsss = "test_folder/tsss"
self.srnas = "test_folder/sRNA"
self.out = "test_folder/output"
self.trans = "test_folder/trans"
self.fastas = "test_folder/fastas"
self.tex = "test_folder/tex"
self.frag = "test_folder/frag"
self.gffs = "test_folder/gffs"
if (not os.path.exists(self.test_folder)):
os.mkdir(self.test_folder)
os.mkdir(self.tsss)
os.mkdir(self.out)
os.mkdir(self.trans)
os.mkdir(self.fastas)
os.mkdir(self.tex)
os.mkdir(self.frag)
os.mkdir(self.srnas)
os.mkdir(self.gffs)
args = self.mock_args.mock()
args.tsss = self.tsss
args.srnas = self.srnas
args.out_folder = self.out
args.trans = self.trans
args.fastas = self.fastas
self.sorf = sORFDetection(args)
def sorf_detection(self):
"""sORF_detection."""
print("Running sORF prediction...")
self.check_folder([
self._args.transcript_assembly_folder,
self._args.annotation_folder, self._args.fasta_folder
])
self.check_no_require_folder(
[self._args.sRNA_folder, self._args.TSS_folder])
project_creator.create_subfolders(self._paths.required_folders("sorf"))
args_sorf = self.args_container.container_sorf(
self._paths.sorf_folder, self._args.UTR_derived_sORF,
self._args.transcript_assembly_folder,
self._args.annotation_folder, self._args.TSS_folder,
self._args.utr_length, self._args.min_length,
self._args.max_length, self._args.tex_wig_folder,
self._args.frag_wig_folder, self._args.cutoff_intergenic_coverage,
self._args.cutoff_antisense_coverage,
self._args.cutoff_5utr_coverage, self._args.cutoff_3utr_coverage,
self._args.cutoff_interCDS_coverage, self._args.fasta_folder,
self._args.tex_notex_libs, self._args.frag_libs,
self._args.tex_notex, self._args.replicates_tex,
self._args.replicates_frag, self._args.table_best,
self._args.sRNA_folder, self._args.start_codon,
self._args.stop_codon, self._args.cutoff_background,
self._args.fuzzy_rbs, self._args.rbs_not_after_TSS,
self._args.print_all_combination, self._args.best_no_sRNA,
self._args.best_no_TSS, self._args.ignore_hypothetical_protein,
self._args.min_rbs_distance, self._args.max_rbs_distance)
sorf = sORFDetection(args_sorf)
sorf.run_sorf_detection(args_sorf)