Changeset 665

Timestamp:

Apr 17, 2008, 12:46:13 AM (15 years ago)

Author:

Jari Häkkinen

Message:

Added support for using configurable columns. Useful if BASE extra values are used for intensity and background SD.

Location:

plugins/base1/se.lu.thep.wenni/trunk

Files:

• INSTALL (modified) (4 diffs)
• README (modified) (3 diffs)
• base/base1/base_plugin_script/plugin_WeNNI.base.in (modified) (1 diff)
• base/base1/base_plugin_script/wenni.pl (modified) (9 diffs)

plugins/base1/se.lu.thep.wenni/trunk/INSTALL

@@ -5 +5 @@
 Copyright (C) 2005, 2006 Jari Häkkinen, Peter Johansson
 Copyright (C) 2007 Peter Johansson
+Copyright (C) 2008 Jari Häkkinen
 
 This file is part of WeNNI,
@@ -34 +35 @@
 stand-alone. The base2 mode is default and the mode you should use if
 you plan on running WeNNI as plugin to BASE2. The base1 mode is the
-old (classic) mode similar WeNNI 0.6 (or earlier). This is the mode
+old (classic) mode similar to WeNNI 0.6 (or earlier). This is the mode
 you should use if you plan on using WeNNI as a plugin to BASE1. The
 stand-alone mode is intended for you who want to use the WeNNI
@@ -68 +69 @@
 installed in `<DIR>/se/lu/thep/wenni/`. Default `DIR` is set to
 `path/to/base/www/plugins/`. You may use `with-gsl=DIR` to provide
-•information on GSL location. The option `enable-debug` turns on debug
+information on GSL location. The option `enable-debug` turns on debug
 options on the compilation of binary `nni` (e.g. enables assertions).
 
@@ -246 +247 @@
    above. If you prefer to make the change in the file you should
    manipulate the line looking like
+
          'execName        thep.lu.se/jari/wenni/wenni.pl'
 
+   If you want use other than the default fields for intensity1,
+   intensity2, BCh1SD, and BCh2SD, you need to indicate this in the
+   WeNNIParams section of the plug-in definition file. Change the 5th
+   column of parameters 4 through 7 appropriately, i.e., if the
+   standard deviation is defined in another column than the default
+   change lines 6 and 7:
+
+      6 h BCh1SD    30  _xc_BCh1SD    0
+      7 h BCh2SD    30  _xc_BCh2SD    0
+
 
 viii) Now you should go to the README file.

plugins/base1/se.lu.thep.wenni/trunk/README

@@ -5 +5 @@
 Copyright (C) 2005, 2006 Jari Häkkinen, Peter Johansson
 Copyright (C) 2007 Peter Johansson
+Copyright (C) 2008 Jari Häkkinen
 
 This file is part of WeNNI,
@@ -26 +27 @@
 ----------------------------------------------------------------------
 
-This directory contains the 0.7 release of WeNNI.
+This directory contains the future 0.7 release of WeNNI.
 
 Send comments, suggestion, complaints, or questions about this
@@ -293 +294 @@
    Command syntax:
 
-      wenni.pl --option value < basefile_in.data > basefile_out.dat
+      wenni.pl --option value < basefile_in.data > basefile_out.data
 
    wenni.pl will read options from basefile_in.data, but the settings

plugins/base1/se.lu.thep.wenni/trunk/base/base1/base_plugin_script/plugin_WeNNI.base.in

@@ -22 +22 @@
 2 f beta  Beta  30  0.6   0
 3 i neighbours  Neighbours  30  4   0
+4 h intensity1    30  intensity1    0
+5 h intensity2    30  intensity2    0
+6 h BCh1SD    30  BCh1SD    0
+7 h BCh2SD    30  BCh2SD    0
 

plugins/base1/se.lu.thep.wenni/trunk/base/base1/base_plugin_script/wenni.pl

@@ -29 +29 @@
 sub basefile_options($$);
 sub BaseFileConverter($);
-sub cleanup($);
+sub cleanup($$);
 sub cmdline_options($);
 sub nni($);
-sub NNIFileConverter($$);
+sub NNIFileConverter($);
 sub result($$);
 
@@ -49 +49 @@
 # determine beta and number of neighbours. Presedence order is (low to
 # high priority): default value, basefile value, command line value.
-my %option=( beta => 0.6, datatype => "derived",
-             neighbours => 4, nodelete => 0 );
+my %option=(
+    beta => 0.6,
+    datatype => "derived",
+    intensity1 => "intensity1",
+    intensity2 => "intensity2",
+    neighbours => 4,
+    nodelete => 0,
+    BCh1SD => "BCh1SD",
+    BCh2SD => "BCh2SD"
+    );
 basefile_options(\%option,$basefile);
 foreach my $key (keys %cmdline_option) {
@@ -59 +67 @@
 }
 
-BaseFileConverter($option{'datatype'});
-NNIFileConverter($option{'beta'},$option{'datatype'});
+BaseFileConverter(\%option);
+NNIFileConverter(\%option);
 nni($option{'neighbours'});
-result($basefile,$option{'datatype'});
+result($basefile,\%option);
 if (!$option{'nodelete'}) {
-    cleanup($basefile);
+    cleanup($basefile,\%option);
 }
 
@@ -92 +100 @@
 
 sub BaseFileConverter($) {
-    my $datatype=$_[0];
+    my $option=$_[0];
     my $command="$FindBin::Bin/BaseFileConverter";
     $command.=" BASEfile.data";
     $command.=" wenni_";
-    if ($datatype eq "derived") {
-      $command.=" -assayFields intensity1";
-      $command.=" -assayFields intensity2";
+    if ($option{"datatype"} eq "derived") {
+      $command.=" -assayFields $$option{intensity1}";
+      $command.=" -assayFields $$option{intensity2}";
     }
     else {
@@ -106 +114 @@
       $command.=" -assayFields BCh2Mean";
     }
-    $command.=" -assayFields BCh1SD";
-    $command.=" -assayFields BCh2SD";
+    $command.=" -assayFields $$option{BCh1SD}";
+    $command.=" -assayFields $$option{BCh2SD}";
     return system("$command");
 }
 
-sub cleanup($) {
+sub cleanup($$) {
     my $basefile=$_[0];
+    my $option=$_[1];
     unlink($basefile);
     unlink("wenni_BCh1Mean.data");
-    unlink("wenni_BCh1SD.data");
+    unlink("wenni_$$option{BCh1SD}.data");
     unlink("wenni_BCh2Mean.data");
-    unlink("wenni_BCh2SD.data");
+    unlink("wenni_$$option{BCh2SD}.data");
     unlink("wenni_FCh1Mean.data");
     unlink("wenni_FCh2Mean.data");
     unlink("wenni_imputed.data");
-    unlink("wenni_intensity1.data");
-    unlink("wenni_intensity2.data");
+    unlink("wenni_$$option{intensity1}.data");
+    unlink("wenni_$$option{intensity2}.data");
     unlink("wenni_logratio.data");
     unlink("wenni_weight.data");
@@ -187 +196 @@
 }
 
-sub NNIFileConverter($$) {
-    my $beta=$_[0];
-    my $datatype=$_[1];
+sub NNIFileConverter($) {
+    my $option=$_[0];
     my $command="$FindBin::Bin/NNIFileConverter";
-    $command.=" -beta $beta";
-    if ($datatype eq "derived") {
-      $command.=" -fg1 wenni_intensity1.data";
-      $command.=" -fg2 wenni_intensity2.data";
+    $command.=" -beta $$option{'beta'}";
+    if ($$option{'datatype'} eq "derived") {
+      $command.=" -fg1 wenni_$$option{intensity1}.data";
+      $command.=" -fg2 wenni_$$option{intensity2}.data";
       $command.=" -datatype derived";
     }
@@ -204 +212 @@
         $command.=" -datatype raw";
     }
-    $command.=" -bgstd1 wenni_BCh1SD.data";
-    $command.=" -bgstd2 wenni_BCh2SD.data";
+    $command.=" -bgstd1 wenni_$$option{BCh1SD}.data";
+    $command.=" -bgstd2 wenni_$$option{BCh2SD}.data";
     $command.=" -logratio wenni_logratio.data";
     $command.=" -weight wenni_weight.data";
@@ -213 +221 @@
 sub result($$) {
     my $basefile=$_[0];
-    my $datatype=$_[1];
+    my $option=$_[1];
+    my $datatype=$$option{'datatype'};
     print "BASEfile\n";
     print "section\tspots\n";
@@ -255 +264 @@
     }
     else {
-        open(F1FILE,"<wenni_intensity1.data");
-        open(F2FILE,"<wenni_intensity2.data");
+        open(F1FILE,"<wenni_$$option{intensity1}.data");
+        open(F2FILE,"<wenni_$$option{intensity2}.data");
     }
     while (<IMPUTEFILE>) {