#!/opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720643686971/_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 LAV file. Reads an AXT file from standard
input and writes a LAV file to standard out; some statistics are written to
standard error.

usage: %prog primary_spec secondary_spec [--silent] < axt_file > lav_file

Each spec is of the form seq_file[:species_name]:lengths_file.

- seq_file should be a format string for the file names for the individual
  sequences, with %s to be replaced by the alignment's src field.  For
  example, "hg18/%s.nib" would prescribe files named "hg18/chr1.nib",
  "hg18/chr2.nib", etc.

- species_name is optional.  If present, it is prepended to the alignment's
  src field.

- Lengths files provide the length of each chromosome (lav 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 sys

import bx.align.axt
import bx.align.lav


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


def main():
    global debug

    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("missing a value in %s=" % 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("unknown argument: %s" % arg)

    if primary is None:
        usage("missing primary file name and length")

    if secondary is None:
        usage("missing secondary file name and length")

    try:
        (primaryFile, primary, primaryLengths) = parse_spec(primary)
    except Exception:
        usage("bad primary spec (must be seq_file[:species_name]:lengths_file")

    try:
        (secondaryFile, secondary, secondaryLengths) = parse_spec(secondary)
    except Exception:
        usage("bad secondary spec (must be seq_file[:species_name]:lengths_file")

    # read the lengths

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

    # read the alignments

    out = bx.align.lav.Writer(sys.stdout, attributes={"name_format_1": primaryFile, "name_format_2": secondaryFile})

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

    out.close()

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


def parse_spec(spec):  # returns (seq_file,species_name,lengths_file)
    fields = spec.split(":")
    if len(fields) == 2:
        return (fields[0], "", fields[1])
    elif len(fields) == 3:
        return (fields[0], fields[1], fields[2])
    else:
        raise ValueError


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()
