#!/usr/bin/env python

#Dan Blankenberg



import sys, os



assert sys.version_info[:2] >= ( 2, 4 )



def __main__():

    base_dir = os.path.join( os.getcwd(), "bacteria" )

    try:

        base_dir = sys.argv[1]

    except:

        pass

        #print "using default base_dir:", base_dir



    organisms = {}

    for result in os.walk(base_dir):

        this_base_dir,sub_dirs,files = result

        for file in files:

            if file[-5:] == ".info":

                dict = {}

                info_file = open(os.path.join(this_base_dir,file),'r')

                info = info_file.readlines()

                info_file.close()

                for line in info:

                    fields = line.replace("\n","").split("=")

                    dict[fields[0]]="=".join(fields[1:])

                if 'genome project id' in dict.keys():

                    name = dict['genome project id']

                    if 'build' in dict.keys():

                        name = dict['build']

                    if name not in organisms.keys():

                        organisms[name] = {'chrs':{},'base_dir':this_base_dir}

                    for key in dict.keys():

                        organisms[name][key]=dict[key]

                else:

                    if dict['organism'] not in organisms.keys():

                        organisms[dict['organism']] = {'chrs':{},'base_dir':this_base_dir}

                    organisms[dict['organism']]['chrs'][dict['chromosome']]=dict

    for org in organisms:

        org = organisms[org]

        #if no gpi, then must be a ncbi chr which corresponds to a UCSC org, w/o matching UCSC designation

        try:

            build = org['genome project id']

        except: continue

        

        if 'build' in org:

            build = org['build']

            

        chrs=[]

        for chrom in org['chrs']:

            chrom = org['chrs'][chrom]

            chrs.append( "%s=%s" % ( chrom['chromosome'], chrom['length'] ) )

        print "%s\t%s\t%s" % ( build, org['name'], ",".join( chrs ) )

     

if __name__ == "__main__": __main__()