#!/usr/bin/env python
"""
Adapted from bx/scripts/axt_to_concat_fasta.py
"""

from __future__ import print_function

import sys

import bx.align.axt


def usage(s=None):
    message = """
axt_to_fasta species1 species2 < axt_file > fasta_file
"""
    if s is None:
        sys.exit(message)
    else:
        sys.exit("%s\n%s" % (s, message))


def main():
    # check the command line
    species1 = sys.argv[1]
    species2 = sys.argv[2]

    # convert the alignment blocks

    reader = bx.align.axt.Reader(sys.stdin, support_ids=True, species1=species1, species2=species2)
    sp1text = []
    sp2text = []
    for a in reader:
        sp1text.append(a.components[0].text)
        sp2text.append(a.components[1].text)
    sp1seq = "".join(sp1text)
    sp2seq = "".join(sp2text)
    print_component_as_fasta(sp1seq, species1)
    print_component_as_fasta(sp2seq, species2)


# TODO: this should be moved to a bx.align.fasta module
def print_component_as_fasta(text, src):
    header = ">" + src
    print(header)
    print(text)


if __name__ == "__main__":
    main()
