#!/usr/bin/env python
from __future__ import print_function

import sys

from bx.bbi.bigwig_file import BigWigFile


def die(message):
    print(message, file=sys.stderr)
    sys.exit(1)


def open_or_die(filename, mode='r', message=None):
    if message is None:
        message = 'Error opening %s' % filename
    try:
        fh = open(filename, mode)
    except IOError as err:
        die('%s: %s' % (message, err.strerror))
    return fh


class LocationFile(object):
    def __init__(self, filename, comment_chars=None, delimiter='\t', key_column=0):
        self.filename = filename
        if comment_chars is None:
            self.comment_chars = ('#')
        else:
            self.comment_chars = tuple(comment_chars)
        self.delimiter = delimiter
        self.key_column = key_column
        self._map = {}
        self._populate_map()

    def _populate_map(self):
        try:
            with open(self.filename) as fh:
                line_number = 0
                for line in fh:
                    line_number += 1
                    line = line.rstrip('\r\n')
                    if not line.startswith(self.comment_chars):
                        elems = line.split(self.delimiter)
                        if len(elems) <= self.key_column:
                            die('Location file %s line %d: less than %d columns' % (self.filename, line_number, self.key_column + 1))
                        else:
                            key = elems.pop(self.key_column)
                            if key in self._map:
                                if self._map[key] != elems:
                                    die('Location file %s line %d: duplicate key "%s"' % (self.filename, line_number, key))
                            else:
                                self._map[key] = elems
        except IOError as err:
            die('Error opening location file %s: %s' % (self.filename, err.strerror))

    def get_values(self, key):
        if key in self._map:
            rval = self._map[key]
            if len(rval) == 1:
                return rval[0]
            else:
                return rval
        else:
            die('key "%s" not found in location file %s' % (key, self.filename))


def main():
    input_filename, output_filename, loc_filename, loc_key, chrom_col, start_col = sys.argv[1:]

    # open input, output, and bigwig files
    location_file = LocationFile(loc_filename)
    bigwig_filename = location_file.get_values(loc_key)
    bwfh = open_or_die(bigwig_filename, message='Error opening BigWig file %s' % bigwig_filename)
    bw = BigWigFile(file=bwfh)
    ifh = open_or_die(input_filename, message='Error opening input file %s' % input_filename)
    ofh = open_or_die(output_filename, mode='w', message='Error opening output file %s' % output_filename)

    # make column numbers 0-based
    chrom_col = int(chrom_col) - 1
    start_col = int(start_col) - 1
    min_cols = max(chrom_col, start_col)

    # add score column to imput file
    line_number = 0
    for line in ifh:
        line_number += 1
        line = line.rstrip('\r\n')
        elems = line.split('\t')
        if len(elems) > min_cols:
            chrom = elems[chrom_col].strip()
            # base-0 position in chrom
            start = int(elems[start_col])
            score_list = bw.get(chrom, start, start + 1)
            score_list_len = len(score_list)
            if score_list_len == 1:
                beg, end, score = score_list[0]
                score_val = '%1.3f' % score
            elif score_list_len == 0:
                score_val = 'NA'
            else:
                die('%s line %d: chrom=%s, start=%d, score_list_len = %d' % (input_filename, line_number, chrom, start, score_list_len))
            print('\t'.join([line, score_val]), file=ofh)
        else:
            print(line, file=ofh)

    bwfh.close()
    ifh.close()
    ofh.close()


if __name__ == "__main__":
    main()