#!/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



    orgs = organisms.keys()

    for org in orgs:

        if 'name' not in organisms[org]:del organisms[org]



    orgs = organisms.keys()

    #need to sort by name

    swap_test = False

    for i in range(0, len(orgs) - 1):

        for j in range(0, len(orgs) - i - 1):

            if organisms[orgs[j]]['name'] >  organisms[orgs[j + 1]]['name']:

                orgs[j], orgs[j + 1] = orgs[j + 1], orgs[j]

            swap_test = True

        if swap_test == False:

            break









    print "||'''Organism'''||'''Kingdom'''||'''Group'''||'''Links to UCSC Archaea Browser'''||"





    for org in orgs:

        org = organisms[org]

        at_ucsc = False

        #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']

            at_ucsc = True

            

        out_str = "||"+org['name']+"||"+org['kingdom']+"||"+org['group']+"||"

        if at_ucsc:

            out_str = out_str + "Yes"

        out_str = out_str + "||"

        print out_str



if __name__ == "__main__": __main__()