root/galaxy-central/scripts/microbes/create_bacteria_loc_file.py

#!/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__()