#!/usr/bin/env python

import logging, sys, optparse, string
from collections import defaultdict
from os.path import join, basename, dirname, isfile

# ==== functions =====
    
def parseArgs():
    " setup logging, parse command line arguments and options. -h shows auto-generated help page "
    parser = optparse.OptionParser("""usage: %prog [options] inFile tagName replaceFile outFile - mass-rename trackDb tags given a file with oldVal<tab>newVal
            
    Examples:
        %prog trackDb.orig.txt track replace.tsv trackDb.txt
        %prog trackDb.orig.txt shortLabel replace.tsv trackDb.txt
    """)

    parser.add_option("-d", "--debug", dest="debug", action="store_true", help="show debug messages")
    parser.add_option("", "--newMeta", dest="newMeta", action="store", help="keep the old name as metadata tag with this name")
    parser.add_option("", "--suffList", dest="suffList", action="store", help="comma-sep list of suffixes. These are ignored when comparing values. Many tracks need suffixes for the various track types, e.g. peaks and coverage. A typical value could be 'pk,cov'")
    #parser.add_option("-f", "--file", dest="file", action="store", help="run on file") 
    #parser.add_option("", "--test", dest="test", action="store_true", help="do something") 
    (options, args) = parser.parse_args()

    if args==[]:
        parser.print_help()
        exit(1)

    if options.debug:
        logging.basicConfig(level=logging.DEBUG)
        logging.getLogger().setLevel(logging.DEBUG)
    else:
        logging.basicConfig(level=logging.INFO)
        logging.getLogger().setLevel(logging.INFO)

    return args, options

def parseRepl(fname):
    d = {}
    for line in open(fname):
        key, val = line.rstrip("\n").split("\t")
        assert(key not in d) # error: duplicate keys in replace file
        d[key] = val
    return d

# ----------- main --------------
def main():
    args, options = parseArgs()

    inFn, onlyTag, replFn, outFn = args
    newMeta = options.newMeta

    suffList = []
    if options.suffList:
        suffList = options.suffList.split(",")

    replDict = parseRepl(replFn)
    

    ofh = open(outFn, "w")
    for line in open(inFn):
        if line=="\n":
            ofh.write(line)
            continue

        tag, val = string.split(line.strip(), " ",maxsplit=1)
        if tag!=onlyTag:
            ofh.write(line)
            continue

        origVal = val
        for suf in suffList:
            val = val.replace(suf, "")
        val = val.strip()

        if val not in replDict:
            logging.info("value '%s' (original: '%s') was not replaced, line passed though" % (val, origVal))
            ofh.write(line)
            continue

        spcCount = len(line) - len(line.lstrip(" "))
        suffix = origVal.replace(val, "")
        suffix = suffix.replace("Cov", "Cv")
        suffix = suffix.replace("Junc", "Sp")
        newLine = "%s%s %s%s" % (" "*spcCount, tag, replDict[val], suffix)
        ofh.write(newLine+"\n")
        if newMeta:
            ofh.write("%smetadata %s=%s\n" % (" "*spcCount, newMeta, val.replace(" ", "_")))

    ofh.close()
    print("Wrote "+ofh.name)



main()