--- a/find_in_reference.py	Thu Nov 13 14:09:50 2014 -0600
+++ b/find_in_reference.py	Thu May 12 19:30:54 2022 +0000
@@ -1,168 +1,177 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
+
+
+import os.path
+import sys
+import optparse
+
+
 """
 #
 #------------------------------------------------------------------------------
-#                         University of Minnesota
-#         Copyright 2013, Regents of the University of Minnesota
+#                                                 University of Minnesota
+#                 Copyright 2013, Regents of the University of Minnesota
 #------------------------------------------------------------------------------
 # Author:
 #
-#  James E Johnson
+#    James E Johnson
 #
 #------------------------------------------------------------------------------
 """
 
 """
-Takes 2 tabular files as input:  
-  1. The file to be filtered 
-  2. The reference file 
+Takes 2 tabular files as input:
+    1. The file to be filtered
+    2. The reference file
 
-The string value of selected column of the input file is searched for 
+The string value of selected column of the input file is searched for
 in the string values of the selected column of the reference file.
 
-The intended purpose is to filter a peptide fasta file in tabular format 
+The intended purpose is to filter a peptide fasta file in tabular format
 by whether those peptide sequences are found in a reference fasta file.
 
 """
-import sys,re,os.path
-import tempfile
-import optparse
-from optparse import OptionParser
-import logging
 
 
 def __main__():
-  #Parse Command Line
-  parser = optparse.OptionParser()
-  parser.add_option( '-i', '--input', dest='input', help='The input file to filter. (Otherwise read from stdin)' )
-  parser.add_option( '-r', '--reference', dest='reference', help='The reference file to filter against' )
-  parser.add_option( '-o', '--output', dest='output', help='The output file for input lines filtered by reference')
-  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( '-R', '--reverse_find', dest='reverse_find', action="store_true", default=False, help='find the reference string in the input string' )
-  parser.add_option( '-B', '--test_reverse', dest='test_reverse', action="store_true", default=False, help='Also search for reversed input string in reference' )
-  parser.add_option( '-D', '--test_dna_reverse_complement', dest='test_reverse_comp', action="store_true", default=False, help='Also search for the DNA reverse complement of input string' )
-  parser.add_option( '-k', '--keep', dest='keep', action="store_true", default=False, help='' )
-  parser.add_option( '-a', '--annotation_columns', dest='annotation_columns', default=None, help='If string is found, add these columns from reference' )
-  parser.add_option( '-s', '--annotation_separator', dest='annotation_separator', default=';', help='separator character between annotations from different lines' )
-  parser.add_option( '-S', '--annotation_col_sep', dest='annotation_col_sep', default=',', help='separator character between annotation column from the same line' )
-  parser.add_option( '-d', '--debug', dest='debug', action='store_true', default=False, help='Turn on wrapper debugging to stdout'  )
-  (options, args) = parser.parse_args()
+    # Parse Command Line
+    parser = optparse.OptionParser()
+    parser.add_option('-i', '--input', dest='input', help='The input file to filter. (Otherwise read from stdin)')
+    parser.add_option('-r', '--reference', dest='reference', help='The reference file to filter against')
+    parser.add_option('-o', '--output', dest='output', help='The output file for input lines filtered by reference')
+    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', type="int", 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', type="int", 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('-R', '--reverse_find', dest='reverse_find', action="store_true", default=False, help='find the reference string in the input string')
+    parser.add_option('-B', '--test_reverse', dest='test_reverse', action="store_true", default=False, help='Also search for reversed input string in reference')
+    parser.add_option('-D', '--test_dna_reverse_complement', dest='test_reverse_comp', action="store_true", default=False, help='Also search for the DNA reverse complement of input string')
+    parser.add_option('-k', '--keep', dest='keep', action="store_true", default=False, help='')
+    parser.add_option('-a', '--annotation_columns', dest='annotation_columns', default=None, help='If string is found, add these columns from reference')
+    parser.add_option('-s', '--annotation_separator', dest='annotation_separator', default=';', help='separator character between annotations from different lines')
+    parser.add_option('-S', '--annotation_col_sep', dest='annotation_col_sep', default=', ', help='separator character between annotation column from the same line')
+    parser.add_option('-d', '--debug', dest='debug', action='store_true', default=False, help='Turn on wrapper debugging to stdout')
+    (options, args) = parser.parse_args()
 
-  revcompl = lambda x: ''.join([{'A':'T','C':'G','G':'C','T':'A','a':'t','c':'g','g':'c','t':'a','N':'N','n':'n'}[B] for B in x][::-1])
-  def test_rcomplement(seq, target):
-    if options.test_reverse_comp:
-      try:
-        comp = revcompl(seq)
-        return comp in target
-      except:
-        pass
-    return False
+    # revcompl = lambda x: ''.join([{'A': 'T', 'C': 'G', 'G': 'C', 'T': 'A', 'a': 't', 'c': 'g', 'g': 'c', 't': 'a', 'N': 'N', 'n': 'n'}[B] for B in x][: : -1])
+
+    COMP = {'A': 'T', 'C': 'G', 'G': 'C', 'T': 'A', 'a': 't', 'c': 'g', 'g': 'c', 't': 'a', 'N': 'N', 'n': 'n'}
+
+    def revcompl(seq):
+        return ''.join([COMP[B] for B in seq][::-1])
+
+    def test_rcomplement(seq, target):
+        if options.test_reverse_comp:
+            try:
+                comp = revcompl(seq)
+                return comp in target
+            except Exception:
+                pass
+        return False
+
+    def test_reverse(seq, target):
+        return options.test_reverse and seq and seq[::-1] in target
 
-  def test_reverse(seq,target):
-    return options.test_reverse and seq and seq[::-1] in target
-  
-  # Input files
-  if options.input != None:
-    try:
-      inputPath = os.path.abspath(options.input)
-      inputFile = open(inputPath, 'r')
-    except Exception, e:
-      print >> sys.stderr, "failed: %s" % e
-      exit(2)
-  else:
-    inputFile = sys.stdin
-  # Reference
-  if options.reference == None:
-      print >> sys.stderr, "failed: reference file is required" 
-      exit(2)
-  # Output files
-  outFile = None
-  filteredFile = None
-  if options.filtered == None and options.output == None:
-    #write to stdout
-    outFile = sys.stdout
-  else:
-    if options.output != None:
-      try:
-        outPath = os.path.abspath(options.output)
-        outFile = open(outPath, 'w')
-      except Exception, e:
-        print >> sys.stderr, "failed: %s" % e
-        exit(3)
-    if options.filtered != None:
-      try:
-        filteredPath = os.path.abspath(options.filtered)
-        filteredFile = open(filteredPath, 'w')
-      except Exception, e:
-        print >> sys.stderr, "failed: %s" % e
-        exit(3)
-  incol = -1
-  if options.input_column and options.input_column > 0:
-    incol = int(options.input_column)-1
-  refcol = -1
-  if options.reference_column and options.reference_column > 0:
-    refcol = int(options.reference_column)-1
-  if options.annotation_columns:
-    annotate = True
-    annotation_columns = [int(x) - 1 for x in options.annotation_columns.split(',')]
-  else:
-    annotate = False
-  refFile = None
-  num_found = 0
-  num_novel = 0
-  for ln,line in enumerate(inputFile):
-    annotations = []
-    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):
-        fields = fline.split('\t')
-        target_string = fields[refcol].rstrip('\r\n')
-        if options.ignore_case:
-          target_string = target_string.upper()
-        search = search_string if not options.reverse_find else target_string
-        target = target_string if not options.reverse_find else search_string
-        if options.debug: 
-          print >> sys.stderr, "in: %s %s %s" % (search,search in target,target)
-        if search in target or test_reverse(search,target) or test_rcomplement(search,target):
-          found = True
-          if annotate:
-            annotation = options.annotation_col_sep.join([fields[i] for i in annotation_columns])
-            annotations.append(annotation)  
-          else:
-            break
-      if found:
-        num_found += 1
-        if annotate:
-          line = '%s\t%s\n' % (line.rstrip('\r\n'),options.annotation_separator.join(annotations))
-        if options.keep == True:
-          if outFile:
-            outFile.write(line)
-        else:
-          if filteredFile:
-            filteredFile.write(line)
-      else:
-        num_novel += 1
-        if options.keep == True:
-          if filteredFile:
-            filteredFile.write(line)
-        else:
-          if outFile:
-            outFile.write(line)
-    except Exception, e:
-      print >> sys.stderr, "failed: Error reading %s - %s" % (options.reference,e)
-    finally:
-      if refFile:
-        refFile.close()
-  print >> sys.stdout, "found: %d novel: %d" % (num_found,num_novel)
+    # Input files
+    if options.input is not None:
+        try:
+            inputPath = os.path.abspath(options.input)
+            inputFile = open(inputPath, 'r')
+        except Exception as e:
+            print("failed: %s" % e, file=sys.stderr)
+            exit(2)
+    else:
+        inputFile = sys.stdin
+    # Reference
+    if options.reference is None:
+        print("failed: reference file is required", file=sys.stderr)
+        exit(2)
+    # Output files
+    outFile = None
+    filteredFile = None
+    if options.filtered is None and options.output is None:
+        # write to stdout
+        outFile = sys.stdout
+    else:
+        if options.output is not None:
+            try:
+                outPath = os.path.abspath(options.output)
+                outFile = open(outPath, 'w')
+            except Exception as e:
+                print("failed: %s" % e, file=sys.stderr)
+                exit(3)
+        if options.filtered is not None:
+            try:
+                filteredPath = os.path.abspath(options.filtered)
+                filteredFile = open(filteredPath, 'w')
+            except Exception as e:
+                print("failed: %s" % e, file=sys.stderr)
+                exit(3)
+    incol = -1
+    if options.input_column and options.input_column > 0:
+        incol = int(options.input_column)-1
+    refcol = -1
+    if options.reference_column and options.reference_column > 0:
+        refcol = int(options.reference_column)-1
+    if options.annotation_columns:
+        annotate = True
+        annotation_columns = [int(x) - 1 for x in options.annotation_columns.split(', ')]
+    else:
+        annotate = False
+    refFile = None
+    num_found = 0
+    num_novel = 0
+    for ln, line in enumerate(inputFile):
+        annotations = []
+        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("search: %s" % (search_string), file=sys.stderr)
+            refFile = open(options.reference, 'r')
+            for tn, fline in enumerate(refFile):
+                fields = fline.split('\t')
+                target_string = fields[refcol].rstrip('\r\n')
+                if options.ignore_case:
+                    target_string = target_string.upper()
+                search = search_string if not options.reverse_find else target_string
+                target = target_string if not options.reverse_find else search_string
+                if options.debug:
+                    print("in: %s %s %s" % (search, search in target, target), file=sys.stderr)
+                if search in target or test_reverse(search, target) or test_rcomplement(search, target):
+                    found = True
+                    if annotate:
+                        annotation = options.annotation_col_sep.join([fields[i] for i in annotation_columns])
+                        annotations.append(annotation)
+                    else:
+                        break
+            if found:
+                num_found += 1
+                if annotate:
+                    line = '%s\t%s\n' % (line.rstrip('\r\n'), options.annotation_separator.join(annotations))
+                if options.keep is True:
+                    if outFile:
+                        outFile.write(line)
+                else:
+                    if filteredFile:
+                        filteredFile.write(line)
+            else:
+                num_novel += 1
+                if options.keep is True:
+                    if filteredFile:
+                        filteredFile.write(line)
+                else:
+                    if outFile:
+                        outFile.write(line)
+        except Exception as e:
+            print("failed: Error reading %s - %s" % (options.reference, e), file=sys.stderr)
+        finally:
+            if refFile:
+                refFile.close()
+    print("found: %d novel: %d" % (num_found, num_novel), file=sys.stdout)
 
-if __name__ == "__main__" : __main__()
 
+if __name__ == "__main__":
+    __main__()

--- a/find_in_reference.xml	Thu Nov 13 14:09:50 2014 -0600
+++ b/find_in_reference.xml	Thu May 12 19:30:54 2022 +0000
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="find_in_reference" name="find in reference" version="0.0.3">
+<tool id="find_in_reference" name="find in reference" version="0.1.0">
   <description>filter peptides that are present in proteins</description>
   <command interpreter="python">find_in_reference.py  --input "$input" 
   --reference "$reference" 
@@ -106,6 +106,11 @@
     <test>
       <param name="input" value="human_proteins.tabular" ftype="tabular" dbkey="hg19"/>
       <param name="reference" value="human_peptides.tabular" ftype="tabular" dbkey="hg19"/>
+      <conditional name="column">
+          <param name="set" value="yes"/>
+          <param name="input_column" value="2"/>
+          <param name="reference_column" value="2"/>
+      </conditional>
       <param name="reverse_find" value="True"/>
       <param name="outputs" value="found"/>
       <output name="found" file="found_proteins.tabular"/>