# HG changeset patch
# User devteam
# Date 1390832739 18000
# Node ID 5a7b5751617b652be1541191fe0943d37c371bfc

Imported from capsule None

diff -r 000000000000 -r 5a7b5751617b fastq_masker_by_quality.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fastq_masker_by_quality.py	Mon Jan 27 09:25:39 2014 -0500
@@ -0,0 +1,83 @@
+#Dan Blankenberg
+import string
+from optparse import OptionParser
+from galaxy_utils.sequence.fastq import fastqReader, fastqWriter
+
+
+def get_score_comparer( operator ):
+    if operator == 'gt':
+        return compare_gt
+    elif operator == 'ge':
+        return compare_ge
+    elif operator == 'eq':
+        return compare_eq
+    elif operator == 'lt':
+        return compare_lt
+    elif operator == 'le':
+        return compare_le
+    elif operator == 'ne':
+        return compare_ne
+    raise 'Invalid operator provided: %s' % operator
+
+def compare_gt( quality_score, threshold_value ):
+    return quality_score > threshold_value
+
+def compare_ge( quality_score, threshold_value ):
+    return quality_score >= threshold_value
+
+def compare_eq( quality_score, threshold_value ):
+    return quality_score == threshold_value
+
+def compare_ne( quality_score, threshold_value ):
+    return quality_score != threshold_value
+
+def compare_lt( quality_score, threshold_value ):
+    return quality_score < threshold_value
+
+def compare_le( quality_score, threshold_value ):
+    return quality_score <= threshold_value
+
+class BaseReplacer( object ):
+    def __init__( self, replace_character ):
+        self.replace_character = replace_character
+    def __call__( self, base_character ):
+        return self.replace_character
+
+def main():
+    usage = "usage: %prog [options] input_file output_file"
+    parser = OptionParser( usage=usage )
+    parser.add_option( '-f', '--format', dest='format', type='choice', default='sanger', choices=( 'sanger', 'solexa', 'illumina' ), help='FASTQ variant type' )
+    parser.add_option( '-m', '--mask_character', dest='mask_character', default='N', help='Mask Character to use' )
+    parser.add_option( '-c', '--score_comparison', type="choice", dest='score_comparison', default='le', choices=('gt','ge','eq','lt', 'le', 'ne' ), help='Mask base when score is' )
+    parser.add_option( '-s', '--quality_score', type="float", dest='quality_score', default='0', help='Quality Score' )
+    parser.add_option( "-l", "--lowercase", action="store_true", dest="lowercase", default=False, help="Use lowercase masking")
+    ( options, args ) = parser.parse_args()
+    
+    if len ( args ) != 2:
+        parser.error( "Need to specify an input file and an output file" )
+    
+    score_comparer = get_score_comparer( options.score_comparison )
+    
+    if options.lowercase:
+        base_masker = string.lower
+    else:
+        base_masker = BaseReplacer( options.mask_character )
+    
+    out = fastqWriter( open( args[1], 'wb' ), format = options.format )
+    
+    num_reads = None
+    num_reads_excluded = 0
+    for num_reads, fastq_read in enumerate( fastqReader( open( args[0] ), format = options.format ) ):
+        sequence_list = list( fastq_read.sequence )
+        for i, quality_score in enumerate( fastq_read.get_decimal_quality_scores() ):
+            if score_comparer( quality_score, options.quality_score ):
+                sequence_list[ i ] = base_masker( sequence_list[ i ] )
+        fastq_read.sequence = "".join( sequence_list )
+        out.write( fastq_read )
+    
+    if num_reads is not None:
+        print "Processed %i %s reads." % ( num_reads + 1, options.format )
+    else:
+        print "No valid FASTQ reads were provided."
+
+if __name__ == "__main__": main()
diff -r 000000000000 -r 5a7b5751617b fastq_masker_by_quality.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fastq_masker_by_quality.xml	Mon Jan 27 09:25:39 2014 -0500
@@ -0,0 +1,63 @@
+<tool id="fastq_masker_by_quality" name="FASTQ Masker" version="1.0.0">
+  <description>by quality score</description>
+  <requirements>
+    <requirement type="package" version="1.0.0">galaxy_sequence_utils</requirement>
+  </requirements>
+  <command interpreter="python">fastq_masker_by_quality.py '$input_file' '$output_file' -f '${input_file.extension[len( 'fastq' ):]}' -s '${quality_score}' -c '${score_comparison}'
+      #if $mask_type.value == 'lowercase'
+      --lowercase
+      #else
+      -m '${mask_type}'
+      #end if
+  </command>
+  <inputs>
+    <param name="input_file" type="data" format="fastqsanger" label="File to mask" />
+    <param name="mask_type" type="select" label="Mask input with">
+      <option value="N">N's</option>
+      <option value="lowercase">Lowercase</option>
+    </param>
+    <param name="score_comparison" type="select" label="When score is">
+      <option value="le" selected="True">Less than or equal</option>
+      <option value="lt">Less than</option>
+      <option value="eq">Equal to</option>
+      <option value="ne">Not Equal to</option>
+      <option value="ge">Greater than</option>
+      <option value="gt">Greater than or equal</option>
+    </param>
+    <param name="quality_score" type="integer" value="0" label="Quality score"/>
+  </inputs>
+  <outputs>
+    <data name="output_file" format="fastqsanger" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
+      <param name="mask_type" value="N" />
+      <param name="score_comparison" value="le" />
+      <param name="quality_score" value="20" />
+      <output name="output_file" file="sanger_full_range_masked_N.fastqsanger" />
+    </test>
+    <test>
+      <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
+      <param name="mask_type" value="lowercase" />
+      <param name="score_comparison" value="le" />
+      <param name="quality_score" value="20" />
+      <output name="output_file" file="sanger_full_range_masked_lowercase.fastqsanger" />
+    </test>
+  </tests>
+  <help>
+**What it does**
+
+This tool allows masking base characters in FASTQ format files dependent upon user specified quality score value and comparison method.
+
+This tool is not available for use on color space (csSanger) formats.
+
+------
+
+**Citation**
+
+If you use this tool, please cite `Blankenberg D, Gordon A, Von Kuster G, Coraor N, Taylor J, Nekrutenko A; Galaxy Team. Manipulation of FASTQ data with Galaxy. Bioinformatics. 2010 Jul 15;26(14):1783-5. &lt;http://www.ncbi.nlm.nih.gov/pubmed/20562416&gt;`_
+
+
+  </help>
+</tool>
diff -r 000000000000 -r 5a7b5751617b test-data/sanger_full_range_masked_N.fastqsanger
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sanger_full_range_masked_N.fastqsanger	Mon Jan 27 09:25:39 2014 -0500
@@ -0,0 +1,8 @@
+@FAKE0001 Original version has PHRED scores from 0 to 93 inclusive (in that order)
+NNNNNNNNNNNNNNNNNNNNNCGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTAC
++
+!"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
+@FAKE0002 Original version has PHRED scores from 93 to 0 inclusive (in that order)
+CATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCNNNNNNNNNNNNNNNNNNNNN
++
+~}|{zyxwvutsrqponmlkjihgfedcba`_^]\[ZYXWVUTSRQPONMLKJIHGFEDCBA@?>=<;:9876543210/.-,+*)('&%$#"!
diff -r 000000000000 -r 5a7b5751617b test-data/sanger_full_range_masked_lowercase.fastqsanger
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sanger_full_range_masked_lowercase.fastqsanger	Mon Jan 27 09:25:39 2014 -0500
@@ -0,0 +1,8 @@
+@FAKE0001 Original version has PHRED scores from 0 to 93 inclusive (in that order)
+acgtacgtacgtacgtacgtaCGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTAC
++
+!"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
+@FAKE0002 Original version has PHRED scores from 93 to 0 inclusive (in that order)
+CATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCatgcatgcatgcatgcatgca
++
+~}|{zyxwvutsrqponmlkjihgfedcba`_^]\[ZYXWVUTSRQPONMLKJIHGFEDCBA@?>=<;:9876543210/.-,+*)('&%$#"!
diff -r 000000000000 -r 5a7b5751617b test-data/sanger_full_range_original_sanger.fastqsanger
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sanger_full_range_original_sanger.fastqsanger	Mon Jan 27 09:25:39 2014 -0500
@@ -0,0 +1,8 @@
+@FAKE0001 Original version has PHRED scores from 0 to 93 inclusive (in that order)
+ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTAC
++
+!"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
+@FAKE0002 Original version has PHRED scores from 93 to 0 inclusive (in that order)
+CATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA
++
+~}|{zyxwvutsrqponmlkjihgfedcba`_^]\[ZYXWVUTSRQPONMLKJIHGFEDCBA@?>=<;:9876543210/.-,+*)('&%$#"!
diff -r 000000000000 -r 5a7b5751617b tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Mon Jan 27 09:25:39 2014 -0500
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+  <package name="galaxy_sequence_utils" version="1.0.0">
+      <repository changeset_revision="0643676ad5f7" name="package_galaxy_utils_1_0" owner="devteam" prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>