#!/opt/mambaforge/envs/bioconda/conda-bld/bx-python_1724774845760/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/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.

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

usage: %prog < maf > column_counts
"""

import sys

import bx.align.maf

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]):
        try:
            counts[col] += 1
        except Exception:
            counts[col] = 1

counts = sorted((value, key) for key, value in counts.items())
counts.reverse()

for count, col in counts:
    print("".join(col), count)
