Example #1
0
def build_kmer_distribution(datafile, kmer_patterns, sampling_proportion, num_processes, builddir, reverse_complement, pattern_window_length, input_driver_config):

    if os.path.exists(get_save_filename(datafile, builddir)):
        print("build_kmer_distribution- skipping %s as already done"%datafile)
        distob = Distribution.load(get_save_filename(datafile, builddir))
        distob.summary()
        
    else:
        filetype = get_file_type(datafile)
        distob = Distribution([datafile], num_processes)
        distob.interval_locator_parameters = (None,)
        distob.interval_locator_funcs = (bin_discrete_value,)
        distob.assignments_files = ("kmer_binning.txt",)
        distob.file_to_stream_func = seq_from_sequence_file
        distob.file_to_stream_func_xargs = [filetype,sampling_proportion]
        distob.weight_value_provider_func = kmer_count_from_sequence
        distob.weight_value_provider_func_xargs = [reverse_complement, pattern_window_length, 1] + kmer_patterns        
        
        if filetype == ".cnt":
            print "DEBUG setting methods for count file"
            distob.file_to_stream_func = tag_count_from_tag_count_file
            distob.file_to_stream_func_xargs = [input_driver_config,sampling_proportion]
            distob.weight_value_provider_func = kmer_count_from_tag_count
            
        #distdata = build(distob, use="singlethread")
        distdata = build(distob, proc_pool_size=num_processes)
        distob.save(get_save_filename(datafile, builddir))
            
        print "Distribution %s has %d points distributed over %d intervals, stored in %d parts"%(get_save_filename(datafile, builddir), distob.point_weight, len(distdata), len(distob.part_dict))

    return get_save_filename(datafile, builddir)
def build_tax_distribution(datafile):
    distob = Distribution([datafile], 1)
    distob.file_to_stream_func = my_top_hit_provider
    #distob.DEBUG = True
    distob.file_to_stream_func_xargs = [0,7,6] # i.e. pick out first field, then kingdom, comnames
    distob.interval_locator_funcs = [bin_discrete_value, bin_discrete_value]
    distdata = build(distob,"singlethread")
    distob.save("%s.pickle"%datafile)
    return distdata