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
)