#!/usr/bin/env python
# Guruprasad Ananda
"""
Converts coordinates from one build/assembly to another using liftOver binary and mapping files downloaded from UCSC.
"""

import os
import re
import subprocess
import sys
import tempfile
from typing import Union


def stop_err(msg):
    sys.stderr.write(msg)
    sys.exit()


def safe_bed_file(infile):
    """Make a BED file with track and browser lines ready for liftOver.

    liftOver will fail with track or browser lines. We can make it happy
    by converting these to comments. See:

    https://lists.soe.ucsc.edu/pipermail/genome/2007-May/013561.html
    """
    fix_pat = re.compile("^(track|browser)")
    with tempfile.NamedTemporaryFile(mode="w", delete=False) as out_handle, open(infile, "r") as in_handle:
        for line in in_handle:
            if fix_pat.match(line):
                line = "#" + line
            out_handle.write(line)
    return out_handle.name


if len(sys.argv) < 9:
    stop_err(
        "USAGE: prog input out_file1 out_file2 input_dbkey output_dbkey infile_type minMatch multiple <minChainT> <minChainQ> <minSizeQ>"
    )

infile = sys.argv[1]
outfile1 = sys.argv[2]
outfile2 = sys.argv[3]
in_dbkey = sys.argv[4]
mapfilepath = sys.argv[5]
infile_type = sys.argv[6]
gff_option = ""
if infile_type == "gff":
    gff_option = "-gff "
minMatch: Union[str, float] = sys.argv[7]
multiple = int(sys.argv[8])
multiple_option = ""
if multiple:
    minChainT = sys.argv[9]
    minChainQ = sys.argv[10]
    minSizeQ = sys.argv[11]
    multiple_option = " -multiple -minChainT=%s -minChainQ=%s -minSizeQ=%s " % (minChainT, minChainQ, minSizeQ)

try:
    assert float(minMatch)
except Exception:
    minMatch = 0.1
# ensure dbkey is set
if in_dbkey == "?":
    stop_err("Input dataset genome build unspecified, click the pencil icon in the history item to specify it.")

if not os.path.isfile(mapfilepath):
    stop_err("%s mapping is not currently available." % (mapfilepath.split("/")[-1].split(".")[0]))

safe_infile = safe_bed_file(infile)
cmd_line = (
    "liftOver "
    + gff_option
    + "-minMatch="
    + str(minMatch)
    + multiple_option
    + " "
    + safe_infile
    + " "
    + mapfilepath
    + " "
    + outfile1
    + " "
    + outfile2
    + "  > /dev/null"
)

try:
    # have to nest try-except in try-finally to handle 2.4
    try:
        proc = subprocess.Popen(args=cmd_line, shell=True, stderr=subprocess.PIPE)
        stderr = proc.communicate()[1]
        if proc.returncode != 0:
            raise Exception(stderr)
    except Exception as e:
        raise Exception("Exception caught attempting conversion: " + str(e))
finally:
    os.remove(safe_infile)