diff fastq_groomer_parallel.py @ 2:cac848910bd8

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fastq_groomer_parallel.py	Fri Sep 14 03:17:38 2012 -0400
@@ -0,0 +1,164 @@
+# Kenneth Sabir
+# Garvan Institute
+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()