"""
Copyright [2009-2017] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
     http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
"""

# ---------------------------------IMPORTS-------------------------------------

import os
import sys
import subprocess
import logging


# -----------------------------------------------------------------------------

def wiki_redirects_parser(redirects):
    """
    Parses wiki redirects and reports rfam accessions and changes to WK tags
    Returns a dictionary with changes per family accession

    redirects: redirects.txt file from wiki
    """

    wk_edits = {}
    fp = open(redirects, 'r')

    rfam_lines = [x.strip() for x in fp if x.find('Rfam') != -1]
    fp.close()

    c = '"'
    for line in rfam_lines:
        rfam_acc = line[len(line) - 7:len(line)]
        positions = [pos for pos, char in enumerate(line) if char == c]
        old_str = line[positions[0] + 1:positions[1]]
        new_str = line[positions[2] + 1:positions[3]]
        wk_edits[rfam_acc] = (old_str, new_str)