#!/opt/conda/conda-bld/bx-python_1720643340496/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/bin/python

"""
For every column that occurs in a multiple alignment print the column
and the number of times it occurs (one column/count per line, tab
separated), sorted by count descending.

This version allows special handling of the 'wildcard' symbol in alignments.

Note: all blocks must have exactly the same number of species.

usage: %prog [options] < maf > column_counts
    -w, --wildcard: include wildcards
    -m, --maxwildcards=N: only allow N missing species
"""

import sys

import bx.align.maf
from bx.cookbook import (
    cross_lists,
    doc_optparse,
)

counts = {}

nspecies = None

for block in bx.align.maf.Reader(sys.stdin):
    # Ensure all blocks have the same number of rows
    if nspecies:
        assert len(block.components) == nspecies
    else:
        nspecies = len(block.components)
    # Increment count for each column
    for col in zip(*[iter(comp.text.upper()) for comp in block.components]):
        col = "".join(col)
        try:
            counts[col] += 1
        except Exception:
            counts[col] = 1

options, args = doc_optparse.parse(__doc__)

wildcard = False
if options.wildcard:
    wildcard = True
    max_wildcard = nspecies - 1
if options.maxwildcards:
    wildcard = True
    max_wildcard = int(options.maxwildcards)

nucs = "ACGT-"
if wildcard:
    nucs += "*"

for col in cross_lists(*([nucs] * nspecies)):
    col = "".join(col)
    if wildcard and col.count("*") > max_wildcard:
        continue
    if col.count("-") == nspecies:
        continue
    print(col, counts.get(col, 0))
