/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__()