root/galaxy-central/scripts/microbes/get_builds_lengths.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']
            
        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__()