INNER CODE UNIT · Python
range_corrector
hillerlab/TOGA · CESAR_wrapper.py:578
def range_corrector(g_range):
"""Swap start and end if start > end."""
chrom, start_end = g_range.split(":")
start_end_split = start_end.split("-")
start, end = int(start_end_split[0]), int(start_end_split[1])
if start < end:
return g_range
else:
return f"{chrom}:{end}-{start}"
def chain_cut(chain_str, gene_range, gene_flank, extra_flank=0):
"""Call chain_cut binary.
Project reference gene coordinates to query through a chain.
Also add flanks if shift is > 0.
"""
# need to get genomic region for the gene