#!/opt/mambaforge/envs/bioconda/conda-bld/bx-python_1733806329480/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/bin/python
"""
Application to convert AXT file to FASTA file. Reads an AXT file from standard
input and writes a FASTA file to standard out.

usage: %prog < axt_file > fasta_file
"""

__author__ = "Bob Harris (rsharris@bx.psu.edu)"

import sys

import bx.align.axt


def usage(s=None):
    message = """
axt_to_fasta < axt_file > fasta_file
"""
    if s is None:
        sys.exit(message)
    else:
        sys.exit(f"{s}\n{message}")


def main():
    # check the command line

    if len(sys.argv) > 1:
        usage("give me no arguments")

    # convert the alignment blocks

    reader = bx.align.axt.Reader(sys.stdin, support_ids=True, species1="", species2="")

    for a in reader:
        if "id" in a.attributes:
            id = a.attributes["id"]
        else:
            id = None
        print_component_as_fasta(a.components[0], id)
        print_component_as_fasta(a.components[1], id)
        print()


# $$$ this should be moved to a bx.align.fasta module


def print_component_as_fasta(c, id=None):
    header = f">{c.src}_{c.start}_{c.start + c.size}"
    if id is not None:
        header += " " + id
    print(header)
    print(c.text)


if __name__ == "__main__":
    main()
