#!/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']

            print "ORG\t%s\t%s\t%s\t%s\t%s\t%s\tUCSC" % ( build, org['name'], org['kingdom'], org['group'], org['chromosomes'], org['info url'] )

        else:

            print "ORG\t%s\t%s\t%s\t%s\t%s\t%s\tNone" % ( build, org['name'], org['kingdom'], org['group'], org['chromosomes'], org['info url'] )

        

        for chr in org['chrs']:

            chr = org['chrs'][chr]

            print "CHR\t%s\t%s\t%s\t%s\t%s\t%s\t%s" % ( build, chr['chromosome'], chr['name'], chr['length'], chr['gi'], chr['gb'], "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val="+chr['refseq'] )

            for feature in ['CDS','tRNA','rRNA']:

                print "DATA\t%s_%s_%s\t%s\t%s\t%s\t%s\t%s" % ( build, chr['chromosome'], feature, build, chr['chromosome'], feature, "bed", os.path.join( org['base_dir'], "%s.%s.bed" % ( chr['chromosome'], feature ) ) )

            #FASTA

            print "DATA\t%s_%s_%s\t%s\t%s\t%s\t%s\t%s" % ( build, chr['chromosome'], "seq", build, chr['chromosome'], "sequence", "fasta", os.path.join( org['base_dir'], "%s.fna" % chr['chromosome'] ) )

            #GeneMark

            if os.path.exists( os.path.join( org['base_dir'], "%s.GeneMark.bed" % chr['chromosome'] ) ):

                print "DATA\t%s_%s_%s\t%s\t%s\t%s\t%s\t%s" % ( build, chr['chromosome'], "GeneMark", build, chr['chromosome'], "GeneMark", "bed", os.path.join( org['base_dir'], "%s.GeneMark.bed" % chr['chromosome'] ) )

            #GenMarkHMM

            if os.path.exists( os.path.join( org['base_dir'], "%s.GeneMarkHMM.bed" % chr['chromosome'] ) ):

                print "DATA\t%s_%s_%s\t%s\t%s\t%s\t%s\t%s" % ( build, chr['chromosome'], "GeneMarkHMM", build, chr['chromosome'], "GeneMarkHMM", "bed", os.path.join( org['base_dir'], "%s.GeneMarkHMM.bed" % chr['chromosome'] ) )

            #Glimmer3

            if os.path.exists( os.path.join( org['base_dir'], "%s.Glimmer3.bed" % chr['chromosome'] ) ):

                print "DATA\t%s_%s_%s\t%s\t%s\t%s\t%s\t%s" % ( build, chr['chromosome'], "Glimmer3", build, chr['chromosome'], "Glimmer3", "bed", os.path.join( org['base_dir'], "%s.Glimmer3.bed" % chr['chromosome'] ) )

     

if __name__ == "__main__": __main__()