INNER CODE UNIT · Python
expansion
BirolLab/straglr · straglr_compare.py:203
expansion = round(np.median(list(expanded_alleles)) - np.median(control_alleles_list), 1)
expanded_loci[locus] = [list(expanded_alleles), control_alleles, pvals, ','.join(map(str, list(supports))), expansion]
return expanded_loci
def olap_gtf(bed, gtf_file):
gtf = BedTool(gtf_file)
skipped_types = ('retained_intron', 'nonsense_mediated_decay', 'processed_transcript')
olaps = defaultdict(list)
assigned = {}
for cols in bed.intersect(gtf, wao=True, f=1.0):
locus = tuple(cols[:3])
if cols[3] == '.':
assigned[locus] = None
continue