Describe alignment

describe_align.py

sbjct_aln = "C-GGLK-GAPFLAC"
query_aln = "CHG--KTGASFLQC"

gap = "-"

sbjct_idx = -1
query_idx = -1
for sbjct_resn, query_resn in zip(sbjct_aln, query_aln):

    # Check for gaps
    sbjct_gap = bool(sbjct_resn == gap)
    query_gap = bool(query_resn == gap)

    if not query_gap:
        # Always increment count
        query_idx += 1

    if not sbjct_gap:
        # Always increment count
        sbjct_idx += 1

        if query_gap:
            end_clause = "not aligned"
        else:
            # Adding to change from 0 to 1 based indexing
            end_clause = "aligned to position %s in query" % query_idx + 1
        # Adding to change from 0 to 1 based indexing
        print("Position %s in subject is %s" % (sbjct_idx + 1, end_clause))