# HG changeset patch
# User kevyin
# Date 1347599896 14400
# Node ID 18a08d476d5e3e3bfae3d94987347e8a22ee9d5d

First upload 0.3.0

diff -r 000000000000 -r 18a08d476d5e README
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README	Fri Sep 14 01:18:16 2012 -0400
@@ -0,0 +1,32 @@
+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.
+
+##################################################
+Installation:
+#================================================#
+
+Set the number of threads to use edit fastq_groomer_parallel.xml:
+Modify the last argument in the <command> tag, Default is 2
+
+
+Tested on -r e6444e7a1685
+This currently depends on the following galaxy_utils python library which should come with the default galaxy install
+
+More info:
+    from galaxy_utils.sequence.fastq import fastqReader, fastqVerboseErrorReader, fastqAggregator, fastqWriter
+##################################################
diff -r 000000000000 -r 18a08d476d5e fastq_groomer_parallel.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fastq_groomer_parallel.py	Fri Sep 14 01:18:16 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()
diff -r 000000000000 -r 18a08d476d5e fastq_groomer_parallel.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fastq_groomer_parallel.xml	Fri Sep 14 01:18:16 2012 -0400
@@ -0,0 +1,71 @@
+<tool id="fastq_groomer_parallel" name="FASTQ Parallel Groomer" version="0.3.0">
+  <description>Parallel Implementation of FASTQ Groomer</description>
+  <command interpreter="python">fastq_groomer_parallel.py '$input_file' '$input_type' '$output_file'
+#if str( $options_type['options_type_selector'] ) == 'basic':
+#if str( $input_type ) == 'cssanger':
+'cssanger'
+#else:
+'sanger'
+#end if
+'ascii' 'summarize_input'
+#else:
+'${options_type.output_type}' '${options_type.force_quality_encoding}' '${options_type.summarize_input}'
+#end if
+'2'
+</command>
+  <inputs>
+    <param name="input_file" type="data" format="fastq" label="File to groom" />
+    <param name="input_type" type="select" label="Input FASTQ quality scores type">
+      <option value="solexa">Solexa</option>
+      <option value="illumina">Illumina 1.3-1.7</option>
+      <option value="sanger" selected="True">Sanger</option>
+      <option value="cssanger">Color Space Sanger</option>
+    </param>
+    <conditional name="options_type">
+    <param name="options_type_selector" type="select" label="Advanced Options">
+      <option value="basic" selected="True">Hide Advanced Options</option>
+      <option value="advanced">Show Advanced Options</option>
+    </param>
+    <when value="basic">
+      <!-- no options -->
+    </when>
+    <when value="advanced">
+      <param name="output_type" type="select" label="Output FASTQ quality scores type" help="Galaxy tools are designed to work with the Sanger Quality score format.">
+        <option value="solexa">Solexa</option>
+        <option value="illumina">Illumina 1.3+</option>
+        <option value="sanger" selected="True">Sanger (recommended)</option>
+        <option value="cssanger">Color Space Sanger</option>
+      </param>
+      <param name="force_quality_encoding" type="select" label="Force Quality Score encoding">
+        <option value="None">Use Source Encoding</option>
+        <option value="ascii" selected="True">ASCII</option>
+        <option value="decimal">Decimal</option>
+      </param>
+      <param name="summarize_input" type="select" label="Summarize input data">
+        <option value="summarize_input" selected="True">Summarize Input</option>
+        <option value="dont_summarize_input">Do not Summarize Input (faster)</option>
+      </param>
+    </when>
+  </conditional>
+  </inputs>
+  <outputs>
+    <data name="output_file" format="fastqsanger">
+      <change_format>
+        <when input="input_type" value="cssanger" format="fastqcssanger" />
+        <when input="options_type.output_type" value="solexa" format="fastqsolexa" />
+        <when input="options_type.output_type" value="illumina" format="fastqillumina" />
+        <when input="options_type.output_type" value="sanger" format="fastqsanger" />
+        <when input="options_type.output_type" value="cssanger" format="fastqcssanger" />
+      </change_format>
+    </data>
+  </outputs>
+  <tests>
+    <!-- These tests include test files adapted from supplemental material in Cock PJ, Fields CJ, Goto N, Heuer ML, Rice PM. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res. 2009 Dec 16. -->
+    <!-- Unfortunately, cannot test for expected failures -->
+  </tests>
+  <help>
+**What it does**
+
+This is a parallel implementation of FASTQ Groomer. It utilizes multiple CPUs thus runs much faster than the original implementation.
+  </help>
+</tool>