#!/usr/bin/env python

"""
Adds Manually created builds and chrom info to Galaxy's info tables

Usage:
python add_manual_builds.py input_file builds.txt chrom_length_dir
"""

import sys,os

def add_manual_builds(input_file, build_file, chr_dir):
    #determine existing builds, so as to not overwrite
    existing_builds = []
    for line in open(build_file):
        try:
            if line.startswith("#"): continue
            existing_builds.append(line.replace("\n","").replace("\r","").split("\t")[0])
        except:
            continue
    build_file_out = open(build_file,'a')
    for line in open(input_file):
        try:
            fields = line.replace("\n","").replace("\r","").split("\t")
            build = fields.pop(0)
            if build in existing_builds: continue # if build exists, leave alone
            name = fields.pop(0)
            try: # get chrom lens if included in file, otherwise still add build
                chrs = fields.pop(0).split(",")
            except:
                chrs = []
            print>>build_file_out, build+"\t"+name+" ("+build+")"
            if chrs: # create len file if provided chrom lens
                chr_len_out=open( os.path.join(chr_dir,build+".len"),'w')
                for chr in chrs:
                    print>>chr_len_out, chr.replace("=","\t")
                chr_len_out.close()
        except:
            continue
    build_file_out.close()

if __name__ == "__main__":
    if len(sys.argv) < 4:
        print "USAGE: python add_manual_builds.py input_file builds.txt chrom_length_dir"
        sys.exit(1)
    input_file = sys.argv[1]
    build_file = sys.argv[2]
    chr_dir = sys.argv[3]
    add_manual_builds(input_file,build_file,chr_dir)