comparison fastq_groomer_parallel.py @ 4:28a0718eb9e7

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4:28a0718eb9e7

# Kenneth Sabir
# Garvan Institute

# Copyright (c) 2012, Kenneth Sabir
# All rights reserved.
# 
# Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
# 
#         Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
#             Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
#                 Neither the name of the Garvan Institute nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
# 
#                 THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

import sys
import time
import os
import math
import subprocess
import string
import shutil
import pickle
import io
from multiprocessing import Process
from galaxy_utils.sequence.fastq import fastqReader, fastqVerboseErrorReader, fastqAggregator, fastqWriter

  

def main():
    split_program = "split"
    cat_program = "cat"
    input_filename =  sys.argv[1]
    output_filename = sys.argv[3]
    number_of_processes = 1;
    if (len(sys.argv) > 7):
        number_of_processes = int(sys.argv[7])
    file_prefix = "temp_groomer_part_"
    
    t1 = time.time()
    old_path = os.getcwd()

    lines_per_process,number_of_lines = calculate_lines_per_process(input_filename, number_of_processes)                 
    temp_dir_name = move_to_temp_dir()
    sequences = number_of_lines/4;
    args = [split_program, "-l"+str(lines_per_process), input_filename, file_prefix]
#    print "The args are: " , args
    subprocess.call(args)
#    print "Finished"
    file_count = 0;
    keep_checking = True
    processes = []
    output_filenames = []
    while keep_checking: 
        
        # only need to support 26x26 different processes, so do it brute force (ie not in a loop) for 2 chars.
        lastchar = string.letters[file_count % len(string.letters)] 
        firstchar = string.letters[(file_count / len(string.letters)) % len(string.letters)] 
        temp_input_filename = "%s%c%c" % (file_prefix, firstchar, lastchar)
        
 #       print 'looking for ' + temp_input_filename
        if os.path.exists(temp_input_filename):
#            print 'found ' + temp_input_filename
            temp_output_filename = temp_input_filename + "_output"
            output_filenames.append(temp_output_filename)
            p = Process(target=partition, args=([temp_input_filename, temp_output_filename, file_count]))
            p.start()
            processes.append(p)
            file_count = file_count + 1
        else:
            break
    for p in processes :
        p.join()
    cat_params = [cat_program]
    cat_params.extend(output_filenames)
    with open(output_filename, 'w') as catOutputFile:
        subprocess.call(cat_params, stdout=catOutputFile)
    summarize_input = sys.argv[6] == 'summarize_input'
    input_type = sys.argv[2]
    output_type = sys.argv[4]
    print "Groomed %i %s reads into %s reads." % ( sequences, input_type, output_type )

    aggregators = []
    if summarize_input:
        for temp_output_filename in output_filenames :
            with open(temp_output_filename + "_summary", 'r') as summaryLogFile:
                temp_aggregator = pickle.load(summaryLogFile)
                aggregators.append(temp_aggregator)

        print_aggregators(aggregators)
    os.chdir(old_path)
    shutil.rmtree(temp_dir_name)
    time2 = time.time()
    print 'Groomer took: %0.3f ms using %d processes' % (((time2 - t1)*1000.0), number_of_processes)

def calculate_lines_per_process(input_filename, number_of_processes):
    wc_program = "wc"
    p = subprocess.Popen([wc_program, "-l", input_filename], stdout=subprocess.PIPE)
    out, err = p.communicate()
    number_of_lines = int(string.split(string.lstrip(out), ' ', 1)[0])
    exact_lines_per_process = number_of_lines * 1.0 / number_of_processes
    lines_per_process = int(math.ceil((exact_lines_per_process / 4.0))) * 4
    return lines_per_process,number_of_lines

def move_to_temp_dir():
    dirExists = False;
    dir_name = None
    
    while not dirExists:
        dir_name = "temp_groomer_part_" + str(time.time())
        if not os.path.exists(dir_name):
            os.makedirs(dir_name)
            break;
    os.chdir(dir_name)
    return dir_name

def print_aggregators(aggregators):
    total_ascii_range = [None, None]
    total_decimal_range = [None, None]
    total_valid_formats = set()
    for aggregator in aggregators:
#        print "This aggregators valid formats are: " + str(aggregator.get_valid_formats())
        total_valid_formats = total_valid_formats.union(set(aggregator.get_valid_formats()))
        ascii_range = aggregator.get_ascii_range()
        decimal_range =  aggregator.get_decimal_range()
        
        if total_ascii_range[0] is None:
            total_ascii_range[0] = ascii_range[0]
        else:
            total_ascii_range[0] = min (total_ascii_range[0], ascii_range[0]) 

        # max of None and a value is the value
        total_ascii_range[1] = max (total_ascii_range[1], ascii_range[1]) 
        if total_decimal_range[0] is None:
            total_decimal_range[0] = decimal_range[0]
        else:
            total_decimal_range[0] = min (total_decimal_range[0], decimal_range[0]) 
        # max of None and a value is the value
        total_decimal_range[1] = max (total_decimal_range[1], decimal_range[1]) 
    print "total_valid_formats= " + str(total_valid_formats)
    print "Based upon quality and sequence, the input data is valid for: %s" % ( ", ".join( total_valid_formats )  or "None" )
    print "Input ASCII range: %s(%i) - %s(%i)" % ( repr( total_ascii_range[0] ), ord( total_ascii_range[0] ), repr( total_ascii_range[1] ), ord( total_ascii_range[1] ) ) #print using repr, since \x00 (null) causes info truncation in galaxy when printed
    print "Input decimal range: %i - %i" % ( total_decimal_range[0], total_decimal_range[1] )        
                

def partition(input_filename, temp_output_filename, fileCount):
#    print 'Starting Thread: ' + str(fileCount)
#    input_filename = sys.argv[1]
    input_type = sys.argv[2]
    output_type = sys.argv[4]
    force_quality_encoding = sys.argv[5]
    summarize_input = sys.argv[6] == 'summarize_input'
    if force_quality_encoding == 'None':
        force_quality_encoding = None
    aggregator = fastqAggregator()
    temp_process_file = fastqWriter( open( temp_output_filename, 'wb'), format = output_type, force_quality_encoding = force_quality_encoding )
    read_count = None
    if summarize_input:
        reader = fastqVerboseErrorReader
    else:
        reader = fastqReader
    for read_count, fastq_read in enumerate( reader( open(input_filename, 'rb'), format = input_type, apply_galaxy_conventions = True ) ):
        if summarize_input:
            aggregator.consume_read( fastq_read )
        temp_process_file.write( fastq_read )
#        print "Just wrote (%d): " % read_count + str(fastq_read)
    temp_process_file.close()
    if read_count is not None:
        if input_type != output_type and 'solexa' in [ input_type, output_type ]:
            print "Converted between Solexa and PHRED scores."
        if summarize_input:
            with open(temp_output_filename + "_summary", 'w') as summaryLogFile :
                pickle.dump(aggregator, summaryLogFile)
    else:
        print "No valid FASTQ reads were provided."

if __name__ == "__main__": main()