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Source code for galaxy.visualization.data_providers.cigar
""" Functions for working with SAM/BAM CIGAR representation. """ import operator[docs]def get_ref_based_read_seq_and_cigar(read_seq, read_start, ref_seq, ref_seq_start, cigar): """ Returns a ( new_read_seq, new_cigar ) that can be used with reference sequence to reconstruct the read. The new read sequence includes only bases that cannot be recovered from the reference: mismatches and insertions (soft clipped bases are not included). The new cigar replaces Ms with =s and Xs because the M operation can denote a sequence match or mismatch. """ if not ref_seq: return read_seq, cigar # Set up position for reference, read. ref_seq_pos = read_start - ref_seq_start read_pos = 0 # Create new read sequence, cigar. new_read_seq = "" new_cigar = "" cigar_ops = "MIDNSHP=X" for op_tuple in cigar: op, op_len = op_tuple # Op is index into string 'MIDNSHP=X' if op == 0: # Match # Transform Ms to =s and Xs using reference. new_op = "" total_count = 0 while total_count < op_len and ref_seq_pos < len(ref_seq): match, count = _match_mismatch_counter(read_seq, read_pos, ref_seq, ref_seq_pos) # Use min because count cannot exceed remainder of operation. count = min(count, op_len - total_count) if match: new_op = "=" else: new_op = "X" # Include mismatched bases in new read sequence. new_read_seq += read_seq[read_pos : read_pos + count] new_cigar += "%i%s" % (count, new_op) total_count += count read_pos += count ref_seq_pos += count # If end of read falls outside of ref_seq data, leave as M. if total_count < op_len: new_cigar += "%iM" % (op_len - total_count) elif op == 1: # Insertion new_cigar += "%i%s" % (op_len, cigar_ops[op]) # Include insertion bases in new read sequence. new_read_seq += read_seq[read_pos : read_pos + op_len] read_pos += op_len elif op in [2, 3, 6]: # Deletion, Skip, or Padding ref_seq_pos += op_len new_cigar += "%i%s" % (op_len, cigar_ops[op]) elif op == 4: # Soft clipping read_pos += op_len new_cigar += "%i%s" % (op_len, cigar_ops[op]) elif op == 5: # Hard clipping new_cigar += "%i%s" % (op_len, cigar_ops[op]) elif op in [7, 8]: # Match or mismatch if op == 8: # Include mismatched bases in new read sequence. new_read_seq += read_seq[read_pos : read_pos + op_len] read_pos += op_len ref_seq_pos += op_len new_cigar += "%i%s" % (op_len, cigar_ops[op]) return (new_read_seq, new_cigar)def _match_mismatch_counter(s1, p1, s2, p2): """ Count consecutive matches/mismatches between strings s1 and s2 starting at p1 and p2, respectively. """ # Do initial comparison to determine whether to count matches or # mismatches. if s1[p1] == s2[p2]: cmp_fn = operator.eq match = True else: cmp_fn = operator.ne match = False # Increment counts to move to next characters. count = 1 p1 += 1 p2 += 1 # Count matches/mismatches. while p1 < len(s1) and p2 < len(s2) and cmp_fn(s1[p1], s2[p2]): count += 1 p1 += 1 p2 += 1 return match, count