[Bioperl-guts-l] [15652] bioperl-live/trunk/t/Microarray/Tools/ReseqChip.t: bug fixes

[Marian Thieme]

Revision: 15652
Author:   thm09830
Date:     2009-04-17 13:23:16 -0400 (Fri, 17 Apr 2009)

Log Message:
-----------
bug fixes

Modified Paths:
--------------
    bioperl-live/trunk/t/Microarray/Tools/ReseqChip.t

Modified: bioperl-live/trunk/t/Microarray/Tools/ReseqChip.t
===================================================================
--- bioperl-live/trunk/t/Microarray/Tools/ReseqChip.t	2009-04-17 15:20:04 UTC (rev 15651)
+++ bioperl-live/trunk/t/Microarray/Tools/ReseqChip.t	2009-04-17 17:23:16 UTC (rev 15652)
@@ -31,14 +31,11 @@
   while (<PARAMSFILE>) {
     if (/$ploidy/) {
       if (/$mut_type/) {
-
         $test=1;
         @params = split(' ', $_);
         @p_array=split('_', $params[0]);
         $cur_ncall=$params[1];
-#        print("Jo da wernma hier: ".$_." Crit: $ncall_threshold, $old_ncall, $cur_ncall\n");
-        if ($ncall_threshold<$cur_ncall and $ncall_threshold>=$old_ncall) {
-
+        if (($ncall_threshold<$cur_ncall and $ncall_threshold>=$old_ncall)) {
           last;
         }
         $old_ncall=$cur_ncall;
@@ -46,6 +43,7 @@
     }
   }
   close(ROCFILE);
+  #print("the ncalllevel: $cur_ncall\n");
   ok($test, 'read_params');
 
   if ($mut_type eq 'Subdel') {
@@ -131,10 +129,16 @@
 
 
 ##data specific options have to set by parsing parameter file
+
 ##subdel
-read_params($Parameter_file, \%options_hash, 4.5, 'Hap', 'Subdel');
+my $subdel_ncalls=4.5;  #specify value between 0 and 16.9 for Hap
+                        # and 0 and 55.6 for Dip model, respectively
+read_params($Parameter_file, \%options_hash, $subdel_ncalls, 'Hap', 'Subdel');
+
 ##insertions
-read_params($Parameter_file, \%options_hash, 5.4, 'Hap', 'Ins');
+my $ins_ncalls=5.4; #specify value between 0 and 20.9
+                    # and 0.1 and 54.9
+read_params($Parameter_file, \%options_hash, $ins_ncalls, 'Hap', 'Ins');
 #for my $pos (sort{$a<=>$b}keys %options_hash) {
 #  print "$pos :".$options_hash{$pos}."\n";
 #}
@@ -161,9 +165,6 @@
     ##alternative basecalls
     $locseq_alt=$myReseqChip->insert_gaps2frag($seq_alt);
     $options_hash{alternative_sequence_hash}->{$locseq_alt->id}=$locseq_alt;
-    #my $start=$options_hash{alternative_sequence_hash}->{$locseq_alt->id}->start;
-    #my $end=$options_hash{alternative_sequence_hash}->{$locseq_alt->id}->end;
-    #print($options_hash{alternative_sequence_hash}->{$locseq_alt->id}->subseq(1, 12)."\n")
     
   } else {
     if ($aln->length>0) {
@@ -175,7 +176,8 @@
     $aln = new Bio::SimpleAlign();
     $locseq=$myReseqChip->insert_gaps2reference_sequence($seq);
     $aln->add_seq($locseq);
-    ##alternative basecalls
+
+    ##alternative primary basecalls for insertions
     $locseq_alt=$myReseqChip->insert_gaps2reference_sequence($seq_alt);
     $options_hash{alternative_sequence_hash}->{$locseq_alt->id}=$locseq_alt;
     
@@ -189,4 +191,4 @@
 $workbook->close();
 ##test if xls file has expected size
 #print((-s $xls_filename)."xlsfile size\n");
-ok((-s $xls_filename)==1144832, 'write_alignment2xls');
\ No newline at end of file
+ok((-s $xls_filename)==1144832, 'write_alignment2xls');