def parsingCLIP(args): """Parse the CLIP (BG) BAM files.""" GeneAnnotation = gffutils.FeatureDB(args.db_file, keep_order=True) LoadReads.load_data( bam_files=args.clip_libs, genome_dir=args.genome_dir, gene_annotation=GeneAnnotation, out_file=args.out_file, Collapse=args.collapsed, mask_flank_variants=args.mask_flank_variants, max_mm=args.max_mm, ign_out_rds=args.ign_out_rds, rev_strand=args.rev_strand, CLIP_exp=True, min_coverage=int(args.min_coverage), min_peak=int(args.min_peak) ) Sequences = LoadReads.get_data_handle(args.out_file, write=True) if args.mask_miRNA: print('Removing miRNA-coverage') ParsingPositions.mask_miRNA_positions(Sequences, GeneAnnotation) if args.mask_ovrlp: print('Masking overlapping positions') ParsingPositions.mask_overlapping_positions(Sequences, GeneAnnotation)
def parsingBG(args): """Parse the background (BG) BAM files.""" GeneAnnotation = gffutils.FeatureDB(args.db_file, keep_order=True) LoadReads.load_data( bam_files=args.bg_libs, genome_dir=args.genome_dir, gene_annotation=GeneAnnotation, out_file=args.out_file, Collapse=args.collapsed, OnlyCoverage=args.only_coverage, mask_flank_variants=args.mask_flank_variants, max_mm=args.max_mm, ign_out_rds=args.ign_out_rds, rev_strand=args.rev_strand )