[Genabel-commits] r1055 - in pkg/ProbABEL: src tests

[noreply at r-forge.r-project.org]

Author: lckarssen
Date: 2012-12-13 18:12:18 +0100 (Thu, 13 Dec 2012)
New Revision: 1055

Modified:
   pkg/ProbABEL/src/probabel.pl
   pkg/ProbABEL/tests/check_probabel.pl_chunk.sh
Log:
ProbABEL: Fixed bug #2436, probabel.pl doesn't overwrite output file.


Modified: pkg/ProbABEL/src/probabel.pl
===================================================================
--- pkg/ProbABEL/src/probabel.pl	2012-12-13 17:10:39 UTC (rev 1054)
+++ pkg/ProbABEL/src/probabel.pl	2012-12-13 17:12:18 UTC (rev 1055)
@@ -201,6 +201,7 @@
 my $mlinfo_arg;
 my $mldose_arg;
 my $legend_arg;
+my $outfile_arg;
 
 # Separate command for the sex chromosomes.
 if ($chr eq "X" || $chr eq "Y") {
@@ -225,6 +226,18 @@
     exit;
 }
 
+# Clean up any existing output files
+if($model_option_num==2)
+{
+    system "rm ${outfile_prefix}${_2df_file_postfix} 2>/dev/null";
+    system "rm ${outfile_prefix}${_add_file_postfix} 2>/dev/null";
+    system "rm ${outfile_prefix}${_domin_file_postfix} 2>/dev/null";
+    system "rm ${outfile_prefix}${_recess_file_postfix} 2>/dev/null";
+    system "rm ${outfile_prefix}${_over_domin_file_postfix} 2>/dev/null";
+} else {
+    system "rm ${outfile_prefix}${_add_file_postfix} 2>/dev/null";
+}
+
 # Commands for the autosomes
 for($chr=$startchr; $chr<=$endchr; $chr++) {
 
@@ -262,34 +275,42 @@
         $legend_arg =~ s/$chr_replacement/$chr/g;
         $legend_arg =~ s/$chunk_replacement/$chunk/g;
 
-        my $command = "$prog -p $phename.PHE --ngpreds $model_option_num -i $mlinfo_arg -d $mldose_arg -m $legend_arg --chrom $chr -o $outfile_prefix.chunk$chunk.chr$chr $head $keys";
+        $outfile_arg = "$outfile_prefix.chunk${chunk}.chr${chr}";
+
+        my $command = "$prog -p $phename.PHE --ngpreds $model_option_num ";
+        $command = $command . "-i $mlinfo_arg -d $mldose_arg -m $legend_arg";
+        $command = $command . " --chrom $chr";
+        $command = $command . " -o $outfile_arg ";
+        $command = $command . "$head $keys";
         print "$command \n";
         system $command;
 
+        # Combine the output data for all chunks of this chromosome
         if($model_option_num==2)
         {
-            `cat $outfile_prefix.chunk${chunk}.chr${chr}$_2df_file_postfix >> ${outfile_prefix}.${chr}${_2df_file_postfix}`;
-            `rm $outfile_prefix.chunk${chunk}.chr${chr}$_2df_file_postfix`;
+            `cat $outfile_arg$_2df_file_postfix >> ${outfile_prefix}.${chr}${_2df_file_postfix}`;
+            `rm $outfile_arg$_2df_file_postfix`;
 
-            `cat $outfile_prefix.chunk${chunk}.chr${chr}$_add_file_postfix >> ${outfile_prefix}.${chr}${_add_file_postfix}`;
-            `rm $outfile_prefix.chunk${chunk}.chr${chr}$_add_file_postfix`;
+            `cat $outfile_arg$_add_file_postfix >> ${outfile_prefix}.${chr}${_add_file_postfix}`;
+            `rm $outfile_arg$_add_file_postfix`;
 
-            `cat $outfile_prefix.chunk${chunk}.chr${chr}$_domin_file_postfix >> ${outfile_prefix}.${chr}${_domin_file_postfix}`;
-            `rm $outfile_prefix.chunk${chunk}.chr${chr}$_domin_file_postfix`;
+            `cat $outfile_arg$_domin_file_postfix >> ${outfile_prefix}.${chr}${_domin_file_postfix}`;
+            `rm $outfile_arg$_domin_file_postfix`;
 
-            `cat $outfile_prefix.chunk${chunk}.chr${chr}$_recess_file_postfix >> ${outfile_prefix}.${chr}${_recess_file_postfix}`;
-            `rm $outfile_prefix.chunk${chunk}.chr${chr}$_recess_file_postfix`;
+            `cat $outfile_arg$_recess_file_postfix >> ${outfile_prefix}.${chr}${_recess_file_postfix}`;
+            `rm $outfile_arg$_recess_file_postfix`;
 
-            `cat $outfile_prefix.chunk${chunk}.chr${chr}$_over_domin_file_postfix >> ${outfile_prefix}.${chr}${_over_domin_file_postfix}`;
-            `rm $outfile_prefix.chunk${chunk}.chr${chr}$_over_domin_file_postfix`;
+            `cat $outfile_arg$_over_domin_file_postfix >> ${outfile_prefix}.${chr}${_over_domin_file_postfix}`;
+            `rm $outfile_arg$_over_domin_file_postfix`;
         } else {
-            `cat $outfile_prefix.chunk${chunk}.chr${chr}$_add_file_postfix >> $outfile_prefix.${chr}${_add_file_postfix}`;
-            print "cat $outfile_prefix.chunk${chunk}.chr${chr}$_add_file_postfix >> $outfile_prefix.chr${chr}${_add_file_postfix}\n";
-            `rm $outfile_prefix.chunk${chunk}.chr${chr}$_add_file_postfix`;
-            print "rm $outfile_prefix.chunk${chunk}.chr${chr}$_add_file_postfix\n";
+            `cat $outfile_arg$_add_file_postfix >> $outfile_prefix.${chr}${_add_file_postfix}`;
+            print "cat $outfile_arg$_add_file_postfix >> $outfile_prefix.chr${chr}${_add_file_postfix}\n";
+            `rm $outfile_arg$_add_file_postfix`;
+            print "rm $outfile_arg$_add_file_postfix\n";
         }
     }
 
+    # Combine the output data for all chromosomes into one file
     if($model_option_num==2)
     {
         `cat $outfile_prefix.${chr}$_2df_file_postfix >> ${outfile_prefix}${_2df_file_postfix}`;
@@ -307,8 +328,8 @@
         `cat $outfile_prefix.${chr}$_over_domin_file_postfix >> ${outfile_prefix}${_over_domin_file_postfix}`;
         `rm $outfile_prefix.${chr}$_over_domin_file_postfix`;
     } else {
-        `cat $outfile_prefix.${chr}$_add_file_postfix >> $outfile_prefix${_add_file_postfix}`;
-        print "cat $outfile_prefix.${chr}$_add_file_postfix >> $outfile_prefix${_add_file_postfix}\n";
+        `cat $outfile_prefix.${chr}$_add_file_postfix >> ${outfile_prefix}${_add_file_postfix}`;
+        print "cat $outfile_prefix.${chr}$_add_file_postfix >> ${outfile_prefix}${_add_file_postfix}\n";
         `rm $outfile_prefix.${chr}$_add_file_postfix`;
         print "rm $outfile_prefix.${chr}$_add_file_postfix\n";
     }

Modified: pkg/ProbABEL/tests/check_probabel.pl_chunk.sh
===================================================================
--- pkg/ProbABEL/tests/check_probabel.pl_chunk.sh	2012-12-13 17:10:39 UTC (rev 1054)
+++ pkg/ProbABEL/tests/check_probabel.pl_chunk.sh	2012-12-13 17:12:18 UTC (rev 1055)
@@ -106,7 +106,7 @@
 {
     # Run an analysis on dosage data
     outfile="height_add.out.txt"
-    rm -f $outfile
+
     echo "Checking output using dosages $WithOrWithout chunks..."
     ./probabel.pl 1 2 linear $1 --additive height
     echo -n "  Verifying $outfile: "
@@ -122,10 +122,6 @@
     height_ngp2_over_domin.out.txt height_ngp2_domin.out.txt
     height_ngp2_add.out.txt"
 
-    for file in $outfilelist; do
-        rm -f $file
-    done
-
     echo "Checking output using probabilities $WithOrWithout chunks..."
     ./probabel.pl 1 2 linear $1 --allmodels height -o _ngp2
     for file in $outfilelist; do