root/galaxy-central/scripts/microbes/create_nib_seq_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:
        print "using default base_dir:", base_dir

    loc_out = os.path.join( base_dir, "seq.loc" )
    try:
        loc_out = os.path.join( base_dir, sys.argv[2] )
    except:
        print "using default seq.loc:", loc_out



    organisms = {}

    loc_out = open( loc_out, 'wb' )

    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]
        try:
            build = org['genome project id']
        except: continue
        if 'build' in org:
            build = org['build']
        
        seq_path = os.path.join( org['base_dir'], "seq" )
        
        #create seq dir, if exists go to next org
        ##TODO: add better checking, i.e. for updating
        try:
            os.mkdir( seq_path )
        except:
            print "Skipping", build
            #continue
        
        loc_out.write( "seq %s %s\n" % ( build, seq_path ) )
        
        #print org info
        
        for chr in org['chrs']:
            chr = org['chrs'][chr]
            
            fasta_file = os.path.join( org['base_dir'], "%s.fna" % chr['chromosome'] )
            nib_out_file = os.path.join( seq_path, "%s.nib "% chr['chromosome'] )
            #create nibs using faToNib binary
            #TODO: when bx supports writing nib, use it here instead
            command = "faToNib %s %s" % ( fasta_file, nib_out_file )
            os.system( command )
    
    loc_out.close()
    
    

if __name__ == "__main__": __main__()