INNER CODE UNIT · Python
start
hillerlab/TOGA · CESAR_wrapper.py:419
start = min_pos - SS_SIZE if min_pos not in gene_borders else min_pos
end = max_pos + SS_SIZE if max_pos not in gene_borders else max_pos
# get exon 10 bp flanks:
left_brd_ = min_pos - EXON_SEQ_FLANK if min_pos - EXON_SEQ_FLANK > 0 else 0
left_flank_coord = (left_brd_, min_pos)
right_flank_coord = (max_pos, max_pos + EXON_SEQ_FLANK)
left_flank = chrom_seq[left_flank_coord[0]: left_flank_coord[1]].upper()
right_flank = chrom_seq[right_flank_coord[0]: right_flank_coord[1]].upper()
# correct for strand:
left_flank = left_flank if bed_data["strand"] else revert(left_flank)
right_flank = right_flank if bed_data["strand"] else revert(right_flank)
if not bed_data["strand"]:
left_flank, right_flank = right_flank, left_flank
# placeholder in case we coudld not extract flanks
left_flank = left_flank if len(left_flank) > 0 else "X"
right_flank = right_flank if len(right_flank) > 0 else "X"
exon_seq_raw = chrom_seq[start:end].upper()