#!/opt/mambaforge/envs/bioconda/conda-bld/bx-python_1733805827733/_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 MAF file. Reads an AXT file from standard
input and writes a MAF file to standard out;  some statistics are written to
standard error.

axt_to_maf primary:lengths_file secondary:lengths_file < axt_file > maf_file
  --silent: prevents stats report

  Lengths files provide the length of each chromosome (maf format needs this
  information but axt file does not contain it).  The format is a series of
  lines of the form:

    <chromosome name> <length>

  The chromosome field in each axt block must match some <chromosome name> in
  the lengths file.
"""

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

import copy
import sys

import bx.align.axt
import bx.align.maf


def usage(s=None):
    message = __doc__
    if s is None:
        sys.exit(message)
    else:
        sys.exit(f"{s}\n{message}")


def main():
    global debug

    ##########
    # parse the command line
    ##########

    primary = None
    secondary = None
    silent = False

    # pick off options

    args = sys.argv[1:]
    while len(args) > 0:
        arg = args.pop(0)
        val = None
        fields = arg.split("=", 1)
        if len(fields) == 2:
            arg = fields[0]
            val = fields[1]
            if val == "":
                usage(f"missing a value in {arg}=")

        if (arg == "--silent") and (val is None):
            silent = True
        elif (primary is None) and (val is None):
            primary = arg
        elif (secondary is None) and (val is None):
            secondary = arg
        else:
            usage(f"unknown argument: {arg}")

    if primary is None:
        usage("missing primary species")

    if secondary is None:
        usage("missing secondary species")

    fields = primary.split(":")
    if len(fields) != 2:
        usage("bad primary species (must be species:lengths_file")
    primary = fields[0]
    primaryLengths = fields[1]

    fields = secondary.split(":")
    if len(fields) != 2:
        usage("bad secondary species (must be species:lengths_file")
    secondary = fields[0]
    secondaryLengths = fields[1]

    ##########
    # read the lengths
    ##########

    speciesToLengths = {}
    speciesToLengths[primary] = read_lengths(primaryLengths)
    speciesToLengths[secondary] = read_lengths(secondaryLengths)

    ##########
    # read the alignments
    ##########

    out = bx.align.maf.Writer(sys.stdout)

    axtsRead = 0
    axtsWritten = 0
    for axtBlock in bx.align.axt.Reader(
        sys.stdin, species_to_lengths=speciesToLengths, species1=primary, species2=secondary
    ):
        axtsRead += 1

        p = axtBlock.get_component_by_src_start(primary)
        if p is None:
            continue
        s = axtBlock.get_component_by_src_start(secondary)
        if s is None:
            continue

        mafBlock = bx.align.Alignment(axtBlock.score, axtBlock.attributes)
        mafBlock.add_component(clone_component(p))
        mafBlock.add_component(clone_component(s))

        out.write(mafBlock)
        axtsWritten += 1

    if not silent:
        sys.stderr.write("%d blocks read, %d written\n" % (axtsRead, axtsWritten))


def clone_component(c):
    return bx.align.Component(c.src, c.start, c.size, c.strand, c.src_size, copy.copy(c.text))


def read_lengths(fileName):
    chromToLength = {}

    f = open(fileName)

    for lineNumber, line in enumerate(f):
        line = line.strip()
        if line == "":
            continue
        if line.startswith("#"):
            continue

        fields = line.split()
        if len(fields) != 2:
            raise ValueError("bad lengths line (%s:%d): %s" % (fileName, lineNumber, line))

        chrom = fields[0]
        try:
            length = int(fields[1])
        except ValueError:
            raise ValueError("bad lengths line (%s:%d): %s" % (fileName, lineNumber, line))

        if chrom in chromToLength:
            raise ValueError("%s appears more than once (%s:%d): %s" % (chrom, fileName, lineNumber, line))

        chromToLength[chrom] = length

    f.close()

    return chromToLength


if __name__ == "__main__":
    main()
