def srna_detection(self):
"""sRNA_detection."""
print("Running sRNA prediction...")
self.check_folder([self._args.annotation_folder,
self._args.transcript_assembly_folder])
self.check_no_require_folder([
self._args.fasta_folder, self._args.sORF,
self._args.terminator_folder, self._args.tex_wig_folder,
self._args.frag_wig_folder, self._args.processing_site_folder])
self.check_file([self._args.promoter_table],
["--promoter_table"], False)
if self._args.UTR_derived_sRNA:
self.check_folder([self._args.TSS_folder])
else:
self.check_no_require_folder([self._args.TSS_folder])
project_creator.create_subfolders(self._paths.required_folders("srna"))
args_srna = self.args_container.container_srna(
self._args.Vienna_folder, self._args.Vienna_utils,
self._args.blast_plus_folder,
self._args.ps2pdf14_path, self._paths.srna_folder,
self._args.UTR_derived_sRNA, self._args.annotation_folder,
self._args.TSS_folder, self._args.transcript_assembly_folder,
self._args.TSS_intergenic_fuzzy, self._args.TSS_5UTR_fuzzy,
self._args.TSS_3UTR_fuzzy, self._args.TSS_interCDS_fuzzy,
self._args.filter_info, self._args.tex_wig_folder,
self._args.frag_wig_folder, self._args.processing_site_folder,
self._args.fasta_folder, self._args.mountain_plot,
self._args.nr_format, self._args.srna_format,
self._args.sRNA_database_path, self._args.nr_database_path,
self._args.cutoff_energy,
self._args.run_intergenic_TEX_coverage,
self._args.run_intergenic_noTEX_coverage,
self._args.run_intergenic_fragmented_coverage,
self._args.run_break_transcript,
self._args.run_antisense_TEX_coverage,
self._args.run_antisense_noTEX_coverage,
self._args.run_antisense_fragmented_coverage,
self._args.run_utr_TEX_coverage,
self._args.run_utr_noTEX_coverage,
self._args.run_utr_fragmented_coverage,
self._args.max_length, self._args.min_length,
self._args.tex_notex_libs, self._args.frag_libs,
self._args.replicates_tex, self._args.replicates_frag,
self._args.tex_notex, self._args.blast_e_nr,
self._args.blast_e_srna, self._args.detect_sRNA_in_CDS,
self._args.table_best, self._args.decrease_intergenic_antisense,
self._args.decrease_utr, self._args.fuzzy_intergenic_antisense,
self._args.fuzzy_utr, self._args.cutoff_nr_hit,
self._args.sORF,
self._args.overlap_percent_CDS,
self._args.terminator_folder,
self._args.terminator_fuzzy_in_sRNA,
self._args.terminator_fuzzy_out_sRNA,
self._args.ignore_hypothetical_protein, self._args.TSS_source,
self._args.min_utr_coverage, self._args.promoter_table,
self._args.ranking_time_promoter, self._args.promoter_name)
srna = sRNADetection(args_srna)
srna.run_srna_detection(args_srna)
def setUp(self):
self.mock_args = MockClass()
self.example = Example()
self.mock = Mock_func()
self.test_folder = "test_folder"
self.gffs = "test_folder/gffs"
self.tsss = "test_folder/tsss"
self.sorf = "test_folder/sORF"
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.pros = "test_folder/pros"
self.terms = "test_folder/terms"
if (not os.path.exists(self.test_folder)):
os.mkdir(self.test_folder)
os.mkdir(self.gffs)
os.mkdir(self.tsss)
os.mkdir(os.path.join(self.tsss, "tmp"))
os.mkdir(self.out)
os.mkdir(self.trans)
os.mkdir(os.path.join(self.trans, "tmp"))
os.mkdir(self.fastas)
os.mkdir(os.path.join(self.fastas, "tmp"))
os.mkdir(self.tex)
os.mkdir(self.frag)
os.mkdir(self.pros)
os.mkdir(os.path.join(self.pros, "tmp"))
os.mkdir(self.sorf)
os.mkdir(os.path.join(self.sorf, "tmp"))
os.mkdir(self.terms)
args = self.mock_args.mock()
args.tss_folder = self.tsss
args.pro_folder = self.pros
args.out_folder = self.out
args.sorf_file = self.sorf
args.fastas = self.fastas
args.trans = self.trans
args.terms = self.terms
self.srna = sRNADetection(args)
def srna_detection(self):
"""sRNA_detection."""
print("Running sRNA prediction")
self.check_multi_files(
[self._args.annotation_files, self._args.transcript_files,
self._args.fasta_files, self._args.sorf_files,
self._args.terminator_files, self._args.promoter_tables,
self._args.processing_site_files],
["--annotation_files", "--transcript_files",
"--fasta_files", "--sorf_files", "--terminator_files",
"--promoter_tables", "--processing_site_files"])
for info in self._args.filter_info:
if "sec_str" == info:
if not self._args.compute_sec_structures:
print("Error: --compute_sec_structures is not switch on, "
"but sec_str is still in --filter_info.")
sys.exit()
self._check_filter_input(
self._args.fasta_files, "fasta file", "sec_str")
for prop in ("rnafold_path", "relplot_path",
"mountain_path"):
setattr(self._args, prop,
self.check_execute_file(getattr(self._args, prop)))
elif ("blast_nr" == info) or (
"blast_srna"== info):
for prop in ("blastn_path", "blastx_path", "makeblastdb_path"):
setattr(self._args, prop,
self.check_execute_file(getattr(self._args, prop)))
if ("blast_nr" == info):
self._check_database(self._args.nr_database_path,
"--nr_database_path", "blast_nr")
if ("blast_srna" == info):
self._check_database(self._args.srna_database_path,
"--srna_database_path", "blast_srna")
elif "sorf" == info:
self._check_filter_input(
self._args.sorf_files, "sORF", "sorf")
elif "term" == info:
self._check_filter_input(self._args.terminator_files,
"terminator", "term")
elif "promoter" == info:
self._check_filter_input(self._args.promoter_tables,
"Promoter", "promoter")
elif "tss" == info:
self._check_filter_input(self._args.tss_files,
"TSS", "tss")
else:
if "none" != info.lower():
print("Error: Please check the --filter_info, "
"invalid value was assigned!")
sys.exit()
if self._args.utr_derived_srna:
if self._args.tss_files is None:
print("Error: The TSS has to be provided "
"if you want to compute UTR-derived sRNA!")
sys.exit()
if self._args.search_poly_u != 0:
if self._args.fasta_files is None:
print("Error: The fasta files have to be provided "
"if you want to extend 3'end of sRNA by "
"searching poly U tail!")
sys.exit()
project_creator.create_subfolders(self._paths.required_folders("srna"))
args_srna = self.args_container.container_srna(
self._args.rnafold_path, self._args.relplot_path,
self._args.mountain_path, self._args.blastn_path,
self._args.blastx_path, self._args.makeblastdb_path,
self._paths.srna_folder, self._args.utr_derived_srna,
self._args.annotation_files, self._args.tss_files,
self._args.transcript_files,
self._args.tss_intergenic_antisense_tolerance,
self._args.tss_5utr_tolerance, self._args.tss_3utr_tolerance,
self._args.tss_intercds_tolerance, self._args.filter_info,
self._args.processing_site_files, self._args.fasta_files,
self._args.mountain_plot, self._args.nr_format,
self._args.srna_format, self._args.srna_database_path,
self._args.nr_database_path, self._args.cutoff_energy,
self._args.parallel_blast,
self._args.min_intergenic_tex_coverage,
self._args.min_intergenic_notex_coverage,
self._args.min_intergenic_fragmented_coverage,
self._args.min_complete_5utr_transcript_coverage,
self._args.min_antisense_tex_coverage,
self._args.min_antisense_notex_coverage,
self._args.min_antisense_fragmented_coverage,
self._args.min_utr_tex_coverage,
self._args.min_utr_notex_coverage,
self._args.min_utr_fragmented_coverage,
self._args.max_length, self._args.min_length,
self._args.tex_notex_libs, self._args.frag_libs,
self._args.replicate_tex, self._args.replicate_frag,
self._args.tex_notex, self._args.blast_e_nr,
self._args.blast_e_srna, self._args.detect_srna_in_cds,
self._args.table_best, self._args.decrease_intergenic_antisense,
self._args.decrease_utr, self._args.tolerance_intergenic_antisense,
self._args.tolerance_utr, self._args.cutoff_nr_hit,
self._args.sorf_files, self._args.overlap_percent_cds,
self._args.terminator_files,
self._args.terminator_tolerance_in_srna,
self._args.terminator_tolerance_out_srna,
self._args.ignore_hypothetical_protein, self._args.tss_source,
self._args.min_all_utr_coverage, self._args.promoter_tables,
self._args.ranking_time_promoter, self._args.promoter_names,
self._args.compute_sec_structures, self._args.search_poly_u,
self._args.min_u_poly_u, self._args.mutation_poly_u)
srna = sRNADetection(args_srna)
srna.run_srna_detection(args_srna)
def srna_detection(self):
"""sRNA_detection."""
print("Running sRNA prediction...")
self.check_folder([self._args.annotation_folder,
self._args.transcript_assembly_folder])
self.check_no_require_folder([self._args.fasta_folder,
self._args.sORF,
self._args.terminator_folder])
self.check_file([self._args.promoter_table],
["--promoter_table"], False)
if self._args.UTR_derived_sRNA:
self.check_folder([self._args.TSS_folder,
self._args.processing_site_folder])
else:
self.check_no_require_folder([self._args.TSS_folder,
self._args.processing_site_folder])
project_creator.create_subfolders(self._paths.required_folders("srna"))
args_srna = self.args_container.container_srna(
self._args.Vienna_folder, self._args.Vienna_utils,
self._args.blast_plus_folder,
self._args.ps2pdf14_path, self._paths.srna_folder,
self._args.UTR_derived_sRNA, self._args.annotation_folder,
self._args.TSS_folder, self._args.transcript_assembly_folder,
self._args.TSS_intergenic_fuzzy, self._args.TSS_5UTR_fuzzy,
self._args.TSS_3UTR_fuzzy, self._args.TSS_interCDS_fuzzy,
self._args.import_info, self._args.tex_wig_folder,
self._args.frag_wig_folder, self._args.processing_site_folder,
self._args.fasta_folder, self._args.mountain_plot,
self._args.nr_format, self._args.srna_format,
self._args.sRNA_database_path, self._args.nr_database_path,
self._args.cutoff_energy,
self._args.run_intergenic_TEX_coverage,
self._args.run_intergenic_noTEX_coverage,
self._args.run_intergenic_fragmented_coverage,
self._args.run_antisense_TEX_coverage,
self._args.run_antisense_noTEX_coverage,
self._args.run_antisense_fragmented_coverage,
self._args.intergenic_tolerance,
self._args.run_utr_TEX_coverage,
self._args.run_utr_noTEX_coverage,
self._args.run_utr_fragmented_coverage,
self._args.max_length, self._args.min_length,
self._args.tex_notex_libs, self._args.frag_libs,
self._args.replicates_tex, self._args.replicates_frag,
self._args.tex_notex, self._args.blast_e_nr,
self._args.blast_e_srna, self._args.detect_sRNA_in_CDS,
self._args.table_best, self._args.decrease_intergenic,
self._args.decrease_utr, self._args.fuzzy_intergenic,
self._args.fuzzy_utr, self._args.cutoff_nr_hit,
self._args.sORF, self._args.best_with_all_sRNAhit,
self._args.best_without_sORF_candidate,
self._args.overlap_percent_CDS,
self._args.terminator_folder,
self._args.terminator_fuzzy_in_CDS,
self._args.terminator_fuzzy_out_CDS,
self._args.best_with_terminator,
self._args.ignore_hypothetical_protein, self._args.TSS_source,
self._args.min_utr_coverage, self._args.promoter_table,
self._args.best_with_promoter,
self._args.ranking_time_promoter, self._args.promoter_name)
srna = sRNADetection(args_srna)
srna.run_srna_detection(args_srna)