# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1389991853 21600
# Node ID 856033fb26e83c5ad65f457b09544f8048608f32
# Parent  fe0327a3ba814a0e1440b3a97addb24c120dcb26
Add case insensitive option

diff -r fe0327a3ba81 -r 856033fb26e8 find_in_reference.py
--- a/find_in_reference.py	Sat Jan 04 09:03:57 2014 -0500
+++ b/find_in_reference.py	Fri Jan 17 14:50:53 2014 -0600
@@ -40,6 +40,7 @@
   parser.add_option( '-f', '--filtered', dest='filtered', help='The output file for input lines not in the output')
   parser.add_option('-c','--input_column', dest='input_column', default=None, help='The column for the value in the input file. (first column = 1, default to last column)')
   parser.add_option('-C','--reference_column', dest='reference_column', default=None, help='The column for the value in the reference file. (first column = 1, default to last column)')
+  parser.add_option( '-I', '--case_insensitive', dest='ignore_case', action="store_true", default=False, help='case insensitive' )
   parser.add_option( '-k', '--keep', dest='keep', action="store_true", default=False, help='' )
   parser.add_option( '-d', '--debug', dest='debug', action='store_true', default=False, help='Turn on wrapper debugging to stdout'  )
   (options, args) = parser.parse_args()
@@ -89,11 +90,15 @@
     try:
       found = False
       search_string = line.split('\t')[incol].rstrip('\r\n')
+      if options.ignore_case:
+        search_string = search_string.upper()
       if options.debug: 
         print >> sys.stderr, "search: %s" % (search_string)
       refFile = open(options.reference,'r')
       for tn,fline in enumerate(refFile):
         target_string = fline.split('\t')[refcol]
+        if options.ignore_case:
+          target_string = target_string.upper()
         if options.debug: 
           print >> sys.stderr, "in: %s %s %s" % (search_string,search_string in target_string,target_string)
         if search_string in target_string:
diff -r fe0327a3ba81 -r 856033fb26e8 find_in_reference.xml
--- a/find_in_reference.xml	Sat Jan 04 09:03:57 2014 -0500
+++ b/find_in_reference.xml	Fri Jan 17 14:50:53 2014 -0600
@@ -7,6 +7,7 @@
     --input_column $column.input_column
     --reference_column $column.reference_column
   #end if
+  $case_insensitive
   #if 'novel' in $outputs.__str__ or not 'found' in $outputs.__str__:
     --output "$novel"
   #end if
@@ -16,9 +17,9 @@
   </command>
   <inputs>
     <param name="input" type="data" format="tabular" label="Input file to be filtered" 
-           help="e.g. tophat junctions.bed run without GTF option or no-novel-junctions"/> 
+           help="e.g. a peptide fasta converted to tabular"/> 
     <param name="reference" type="data" format="tabular" label="reference file to search" 
-           help="e.g. tophat junctions.bed run with GTF option and no-novel-junctions"/> 
+           help="e.g. a protein fasta converted to tabular"/> 
     <conditional name="column">
       <param name="set" type="select" label="select columns to compare">
         <option value="no" selected="true">Use last column of input and reference</option>
@@ -32,6 +33,7 @@
            help=""/>
       </when>
     </conditional>
+    <param name="case_insensitive" type="boolean" truevalue="--case_insensitive" falsevalue="" checked="false" label="Ignore case when comparing"/>
     <param name="outputs" type="select" multiple="true" display="checkboxes" label="Choose outputs">
       <option value="novel" selected="true">lines with no match in reference</option>
       <option value="found">lines with match in reference</option>
@@ -58,11 +60,34 @@
   <help>
 **Find in Reference**
 
-Filters lines of a tabular input file by checking if the selected input column 
+Filters lines of a tabular input file by checking if the selected input column value
 is a substring of the selected column of any line in the reference file.  
 
 This can be used to check if peptides sequences are present in a set of reference proteins,  
 as a means of filtering out uninteresting peptide sequences.
 
+For Example with::
+
+  Input
+    >pep1	LIL
+    >pep2	WTF
+    >pep3	ISK
+
+  Reference
+    >prot1	RLET
+    >prot2	LLIL
+    >prot3	LAPSE
+    >prot3	RISKY
+
+  The outputs
+
+  Not found in reference
+    >pep2	WTF
+
+  Found in reference
+    >pep1	LIL
+    >pep3	ISK
+
+
   </help>
 </tool>