#! /usr/bin/env python
# Convert a file of JASPAR matrices to Clover's input format.
# Martin C. Frith, 2012.
# This file is in the Public Domain.

import fileinput, optparse

def fastaInput(lines):
    head = ""
    for line in lines:
        line = line.rstrip()
        if line.startswith(">"):
            if head: yield head, body
            head = line
            body = []
        else:
            body.append(line)
    if head: yield head, body

usage = """%prog matrix_only.txt > converted_jaspar_matrices

This program reads matrices in a format used by the JASPAR database,
and writes them in a format that can be used by Clover.  The JASPAR
format looks something like this:

>MA0001.1 AGL3
A  [ 0  3 79 40 66 48 65 11 65  0 ]
C  [94 75  4  3  1  2  5  2  3  3 ]
G  [ 1  0  3  4  1  0  5  3 28 88 ]
T  [ 2 19 11 50 29 47 22 81  1  6 ]"""

op = optparse.OptionParser(usage=usage)
(opts, args) = op.parse_args()
if not args: op.error("please specify an input file")

for head, body in fastaInput(fileinput.input(args)):
    matrix = []
    for line in body:
        line = "".join(i for i in line if i not in "[]")
        w = line.split()
        numbers = w[1:]
        matrix.append(numbers)
    matrix = zip(*matrix)
    print head
    for i in matrix:
        print "\t".join(i)