source: plugins/base1/se.lu.onk.cgh_dataDumper/cgh_dataDumper.pl @ 720

Last change on this file since 720 was 720, checked in by Jari Häkkinen, 15 years ago

Importing CGH Data Dumper
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1#!/usr/bin/perl
2
3# $Id: cgh_dataDumper.pl 720 2008-06-11 14:05:18Z jari $
4
5# Document name: cgh_dataDumper.pl
6# cgh_dataDumper.pl version 2.0
7#
8#
9# Copyright (C) 2004 Johan Staaf
10
11# cgh_dataDumper.pl is free software; you can redistribute it and/or
12# modify it under the terms of the GNU General Public License
13# as published by the Free Software Foundation; either version 2
14# of the License, or (at your option) any later version.
15
16# This program is distributed in the hope that it will be useful,
17# but WITHOUT ANY WARRANTY; without even the implied warranty of
18# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
19# GNU General Public License for more details.
20
21# You should have received a copy of the GNU General Public License
22# along with this program; if not, write to the Free Software
23# Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
24
25# johan.staaf@onk.lu.se
26# Johan Staaf, Dept Oncology, Lund University, S-221 85 Lund, Sweden
27
28use strict;
29use FindBin ();
30
31# VER 1.0 of cgh_dataDumper.pl
32
33
34######## BASE file requirements #########
35# The BASEfile format should be normal.
36# expect per row:
37# [reporterId]  [geneSymbol]  [chromosome]  [cytoBand]  [startPosition] [endPosition] [assayData = M]
38
39
40############################################
41############# MAIN  PROGRAM    #############
42############################################
43
44
45### Main Variables ###
46my (@final);
47my (%param_hash,%base_hash,%bacToGene);
48my @annoStat;
49#################
50
51## Read the file and extract BASE column data #######
52
53$/="%"; #Gives every section as one lump
54my $i=0;
55
56while(<>){
57  $i++;
58  chomp;
59  if($i==1){ #Parameters
60   
61    $_ =~ /filename\t(.+)\n/;
62    $param_hash{'filename'}=$1;
63    $_ =~ /sort\t(\w+)\n/;
64    $param_hash{'sort'}=$1;
65    $_ =~ /exportMode\t(\w+)\n/;
66    $param_hash{'exportMode'}=$1;
67    $_ =~ /annotationType\t(.+)\n/;
68    $param_hash{'annotationType'}=$1;
69   
70    $_ =~ /annoForStat\t(.+)\n/;  #in format |ER Status|p_brca_family_status|etc..|
71    $param_hash{'annoForStat'}=$1;
72    my @tmp=split(/\|/,$param_hash{'annoForStat'}); #holding the annotations to get stats for!
73    foreach my $line (@tmp){
74      if($line ne ""){
75        push(@annoStat,$line);
76      }
77    }
78  }elsif($i==2){ #section assays info
79    $_=~ /count\t(\d*)/;
80    $base_hash{'NumberOfAssays'}=$1;
81    $_=~ /columns\t(.*)/;
82    $base_hash{'AssayColumns'}=$1;
83    $_=~ /annotationColumns\t(.*)/;
84    $base_hash{'AnnotationColumns'}=$1;
85  }elsif($i==3){ #assay info + section spots
86    $_=~ /columns\t(.*)\tassayData/;
87    $base_hash{'Columns'}=$1;
88    $_=~ /channels\t(.*)/;
89    $base_hash{'channels'}=$1;
90    $_=~/assayFields\t(.*)/;
91    $base_hash{'assayFields'}=$1;
92    (my $text,my $dump)=split("\n\n",$_);
93    $text=~ s/^\n//;
94    $base_hash{'Assays'}=$text;
95    last; #Dont read in the large bulk of data now!
96  }
97}
98#### OBSERVE, all base headers now printed to STDOUT!
99
100
101
102## Do export of data points, global boolean
103my $doExport="TRUE";
104
105
106#### Locate the assay field columns for each annotation group to extract data from
107my @assays = split("\n",$base_hash{'Assays'}); 
108my @assaynames = ();
109foreach my $line (@assays) {
110  my @tmp=split("\t",$line);
111  push(@assaynames,$tmp[1]); #keep only the assay name in the order sent to the plugin
112}
113
114if($param_hash{'exportMode'} eq "sampleName_annotation"){
115  my @sampleannotations;
116
117  ### Assign an assay to an annotation type and save in @control vector
118  my @base_annotations=split("\t",$base_hash{'AnnotationColumns'});
119  my $annotation_index= -1;  #tracks which column index to use to get the annotation values
120  for (my $i=0;$i<@base_annotations;$i++){
121    if($param_hash{'annotationType'} eq $base_annotations[$i]){ #found the right annotation!
122      $annotation_index=$i;   
123      last;
124    }
125  }
126  for (my $i=0;$i<@assays;$i++) {
127    my @tmp=split("\t",$assays[$i]);
128    if($annotation_index > -1){ # a real annotation index found
129      if($tmp[$annotation_index+2] eq ""){ #[assaynbr] [assayname] then annotations, thats why +2
130        $sampleannotations[$i]="NONE"; #Na for annotation for this assay!
131      }else{
132        $sampleannotations[$i]=$tmp[$annotation_index+2]; #a real annotation
133      }
134    }else{
135      #basically this means no annotation analysis from start, use Na instead in control file
136      $sampleannotations[$i]="NONE"; #Na for annotation for this assay!
137     
138    }
139  }
140 
141  ### print the binding of @assaynames, @sampleannotations
142  open(myfile,">SampleNames_and_selectedAnnotation.txt");
143  for (my $i=0;$i<@assaynames;$i++) {
144    print myfile "$assaynames[$i]\t$sampleannotations[$i]\n";
145  }
146  close(myfile);
147  $doExport="FALSE";
148}elsif($param_hash{'exportMode'} eq "sampleName"){
149 
150  ### print @assaynames
151  open(myfile,">SampleNames.txt");
152  for (my $i=0;$i<@assaynames;$i++) {
153    print myfile "$assaynames[$i]\n";
154  }
155  close(myfile);
156  $doExport="FALSE";
157}elsif(($param_hash{'exportMode'} eq "annotationStatistics") && ($param_hash{'annoForStat'} ne "NULL") ){
158  my @base_annotations=split("\t",$base_hash{'AnnotationColumns'}); #all possible base annotations for this sample
159 
160  ### Fixing the issue with blanks ( :( )
161  my $annos=$base_hash{'Assays'};
162  $annos =~s/\t\t/\tNA\t/g;
163  $annos =~s/\t\n/\tNA\n/g;
164  $annos =~s/\t\t/\tNA\t/g;
165  my @annos=split("\n",$annos); #a row is a sample with its annotations
166 
167  #print "$base_hash{'Assays'}";
168  #print "\n#####\n";
169  #print "nbr assay $base_hash{'AnnotationColumns'}\n";
170  #print "$annos";
171 
172  ### Find the subset of annotations to get statistics for
173  my @annotation_index;  #tracks which column index to use to get the annotation values
174  for (my $i=0;$i<@base_annotations;$i++){
175    foreach my $anno (@annoStat){
176      if(($anno eq $base_annotations[$i]) && ($anno ne "")){ #found the right annotation!
177        push(@annotation_index,$i);
178        last;
179      }
180    }
181  }
182 
183  # @annoStat and @annotation_index are now matched!
184  my %annoStat; #key = selected annotation type, value = the column of values for that type,
185      # separated with tab.
186  my %annoUnique; #key = selected annotation type, value = unique annotation values for that type
187  for(my $i=0;$i<@annoStat;$i++){
188    #foreach selected annotation extract its column
189    my @tempCol;
190    foreach my $line (@annos) {
191      my @tmp=split("\t",$line);
192      shift(@tmp); #removing assay id
193      shift(@tmp); #removing assay name
194      # only the annotations are left!
195      push(@tempCol,$tmp[$annotation_index[$i]]);
196    }
197    $annoStat{$annoStat[$i]}=join("\t",@tempCol);
198    my %saw;
199    @saw{@tempCol}=();
200    $annoUnique{$annoStat[$i]}=join("\t",keys(%saw));
201  }
202  open(myfile,">AnnotationStatistics.txt");
203  foreach my $annotype (keys(%annoUnique)){
204    #count how many instances of each unique annotation value there is for this annotation type
205    my @uniqueV=split("\t",$annoUnique{$annotype});
206    my @values=split("\t",$annoStat{$annotype});
207    my %saw;
208    print myfile "$annotype\tNbrAssays\n";
209    foreach my $uniqueValue (@uniqueV){
210      my $r=scalar(grep(/$uniqueValue/,@values));
211      print myfile "$uniqueValue\t$r\n";
212    }
213    print myfile "\n";
214  }
215  close(myfile);
216  $doExport="FALSE";
217}elsif($param_hash{'exportMode'} eq "annotationAll"){
218  #create an annotation file for all annotations
219 
220  my @base_annotations=split("\t",$base_hash{'AnnotationColumns'}); #all possible base annotations for this sample
221 
222  ### Fixing the issue with blanks ( :( )
223  my $annos=$base_hash{'Assays'};
224  $annos =~s/\t\t/\tNA\t/g;
225  $annos =~s/\t\n/\tNA\n/g;
226  $annos =~s/\t\t/\tNA\t/g;
227  my @annos=split("\n",$annos); #a row is a sample with its annotations
228   
229  open(myfile,">AnnotationAllFile.txt");
230  print myfile "Assay\t$base_hash{'AnnotationColumns'}\n";
231  foreach my $line (@annos){
232    my @tmp=split("\t",$line);
233    shift(@tmp); #remove the BASE assay id nummer
234    $line=join("\t",@tmp);
235    print myfile "$line\n";
236  }
237  close(myfile);
238  $doExport="FALSE";
239}elsif(($param_hash{'exportMode'} eq "annotationSelected") && ($param_hash{'annoForStat'} ne "NULL")){
240  #create an annotation file based on only selected annotations
241
242  my @base_annotations=split("\t",$base_hash{'AnnotationColumns'}); #all possible base annotations for this sample
243 
244  ### Fixing the issue with blanks ( :( )
245  my $annos=$base_hash{'Assays'};
246  $annos =~s/\t\t/\tNA\t/g;
247  $annos =~s/\t\n/\tNA\n/g;
248  $annos =~s/\t\t/\tNA\t/g;
249  my @annos=split("\n",$annos); #a row is a sample with its annotations
250 
251   
252  ### Find the subset of annotations to get statistics for
253  my @annotation_index;  #tracks which column index to use to get the annotation values
254  my @matched_annoStat;
255 
256  foreach my $anno (@annoStat){
257    if($anno =~/~/){
258      # pattern matching!! Get all annotations that match the specified pattern
259      # e.g. ~Her130 = all Her130 annotations
260      $anno=~ /~(.+)/;
261      my $pattern=$1;
262      for(my $i=0;$i<@base_annotations;$i++){
263        if($base_annotations[$i]=~/$pattern/){
264          push(@matched_annoStat,$base_annotations[$i]);
265          push(@annotation_index,$i);
266        }
267      }
268    }else{
269      for (my $i=0;$i<@base_annotations;$i++){
270        if(($anno eq $base_annotations[$i]) && ($anno ne "")){ #found the right annotation!
271          push(@matched_annoStat,$anno);
272          push(@annotation_index,$i);
273          last;
274        }
275      }
276    }
277  }
278  # @annoStat and @annotation_index are now matched!
279 
280  my $annoHeader=join("\t","Assay",@matched_annoStat);
281  open(myfile,">AnnotationSelectedFile.txt");
282  print myfile "$annoHeader\n";
283  foreach my $line (@annos){
284    my @tmp=split("\t",$line);
285    my $printline=$tmp[1]; #assay name
286    for(my $i=0;$i<@matched_annoStat;$i++){
287      #print "$annotation_index[$i] $tmp[$annotation_index[$i]+2]\n";
288      $printline=join("\t",$printline,$tmp[$annotation_index[$i]+2]);
289    }
290    print myfile "$printline\n";
291  }
292  close(myfile);
293  $doExport="FALSE";
294}elsif(($param_hash{'exportMode'} eq "annotationDisplaySelected") && ($param_hash{'annoForStat'} ne "NULL")){
295  #create an annotation display file based on only selected annotations
296
297  my @base_annotations=split("\t",$base_hash{'AnnotationColumns'}); #all possible base annotations for this sample
298 
299  ### Fixing the issue with blanks ( :( )
300  my $annos=$base_hash{'Assays'};
301  $annos =~s/\t\t/\tNA\t/g;
302  $annos =~s/\t\n/\tNA\n/g;
303  $annos =~s/\t\t/\tNA\t/g;
304  my @annos=split("\n",$annos); #a row is a sample with its annotations
305 
306 
307  ### Find the subset of annotations to get statistics for
308  my @annotation_index;  #tracks which column index to use to get the annotation values
309  my @matched_annoStat;
310 
311  foreach my $anno (@annoStat){
312    if($anno =~/~/){
313      # pattern matching!! Get all annotations that match the specified pattern
314      # e.g. ~Her130 = all Her130 annotations
315      $anno=~ /~(.+)/;
316      my $pattern=$1;
317      for(my $i=0;$i<@base_annotations;$i++){
318        if($base_annotations[$i]=~/$pattern/){
319          push(@matched_annoStat,$base_annotations[$i]);
320          push(@annotation_index,$i);
321        }
322      }
323    }else{
324      for (my $i=0;$i<@base_annotations;$i++){
325        if(($anno eq $base_annotations[$i]) && ($anno ne "")){ #found the right annotation!
326          push(@matched_annoStat,$anno);
327          push(@annotation_index,$i);
328          last;
329        }
330      }
331    }
332  }
333  # @annoStat and @annotation_index are now matched! 
334  # i.e matched_annoStat contains all annotation types to extract data from,
335  # and annotation_index contains which columns to use respectively.
336 
337  # go through each matched_annoStat entry, find the unique annotation values (k)
338  # and for each unique value, create a column with value 1 for match on the unique value
339  #for a given sample, 0 for no match. Iterate this over all matched annotation types.
340  # blank samples have the value NA in @annos. They retain NA in the export, however NA is not
341  # allowed as a column type!
342 
343  my @annotationDisplayMatrix; #N rows = N samples
344  my @annotationDisplayHeader;
345  push(@annotationDisplayHeader,"AssayName");
346 
347  #Initiate the Display matrix with sample names
348  for(my $j=0;$j<@annos;$j++){
349    my @tmp=split("\t",$annos[$j]);
350    push(@annotationDisplayMatrix,$tmp[1]); #initiate with sample name!
351  } 
352 
353  for(my $i=0;$i<@matched_annoStat;$i++){
354    my %uniqueValues;
355    my @uniqueValueColumns;
356   
357    #find unique annotation values
358    for(my $j=0;$j<@annos;$j++){
359      my @tmp=split("\t",$annos[$j]);
360      if(($tmp[$annotation_index[$i]+2] eq "NA") || ($tmp[$annotation_index[$i]+2] eq "")){
361        #not allowed as a unique entry
362      }else{
363        $uniqueValues{$tmp[$annotation_index[$i]+2]}="";
364      }
365    }
366    my @uniqueValueColumn=sort(keys(%uniqueValues));
367   
368   
369    #foreach of the unique annotation values, make a column, 1 for present, 0 for absent
370    # for each sample
371    foreach my $uniqueValue (@uniqueValueColumn){
372      #my $ttt<-$uniqueValue;
373      #$ttt =~s/\s/\_/g;
374      push(@annotationDisplayHeader,$uniqueValue); #push to the header
375      for(my $j=0;$j<@annos;$j++){
376        #for each sample
377        my @tmp=split("\t",$annos[$j]);
378       
379        if($tmp[$annotation_index[$i]+2] eq $uniqueValue){
380          # push in a 1
381          $annotationDisplayMatrix[$j]=$annotationDisplayMatrix[$j]."\t".1;
382        }else{
383          #push in a 0
384          $annotationDisplayMatrix[$j]=$annotationDisplayMatrix[$j]."\t".0;
385        }
386      }
387    }
388  }
389 
390  my $annoHeader= join("\t",@annotationDisplayHeader);
391 
392  open(myfile,">AnnotationDisplaySelectedFile.txt");
393  print myfile "$annoHeader\n";
394  foreach my $row (@annotationDisplayMatrix){
395    print myfile "$row\n";
396   
397  }
398  close(myfile);
399  $doExport="FALSE";
400}#end annotationDisplay
401
402
403if($doExport eq "TRUE"){
404  #### Determine how many common columns to add to get to assaydata
405  my @cc = split("\t",$base_hash{'Columns'});
406
407  #### Make header and calculate nbr of data columns in total
408  my $header=join("\t",@cc,@assaynames);
409  my $nbrCols=scalar(@cc)+scalar(@assaynames);
410
411   
412  ####### Parse the spot data one row at a time #######
413  # each row looks like:
414  # [reporterId]  [geneSymbol]  [chromosome]  [cytoBand]  [startPosition] [endPosition] [assayData = M]
415  my $chromosomeIndex=2;
416  my $geneIndex=1;
417  my $repIdIndex=0;
418  my $endPositionIndex=5;
419  my @highlightToWrite=();
420  my @toSort=(); #vector for holding data to sort in format as above
421
422  $/="\n"; #reset
423  my $found = "FALSE";
424
425
426  ## Create a file with the assay names for the stac_format.R script. Also modify the header for stac output
427  ## so that the header is sample1 .. sampleN instead of real assay names (column conflict in R for weird assay names
428  if($param_hash{'exportMode'} eq "stac"){
429    $header=join("\t",@cc);
430    my $index=0;
431    open(myoutfile,">assays.txt");
432    foreach my $line (@assaynames){
433      $index++;
434      print myoutfile "$line\n";
435      $header=$header."\t"."sample".$index;
436    }
437    close(myoutfile);
438  }
439
440  if(($param_hash{'exportMode'} eq "standard_lite") || ($param_hash{'exportMode'} eq "singleLite")){
441    #lite format is reporterId,chromosome,startPosition,endPosition
442    $header=join("\t","reporterId","chromosome","startPosition","endPosition",@assaynames);
443  }
444
445  my $file="basematrix.txt";
446  if($param_hash{'filename'} ne "NULL"){
447    $file=$param_hash{'filename'};
448  }
449
450  ## open file for printing of data values
451  if($param_hash{'exportMode'} ne "singleLite"){
452    open (myoutfile,">$file");
453  }
454 
455  if(($param_hash{'exportMode'} ne "agilent") || ($param_hash{'exportMode'} ne "bed") || ($param_hash{'exportMode'} ne "singleLite") ){
456    #print defined header if not Agilent mode, or BED or single lite
457    print myoutfile "$header\n";
458  }
459
460  while(<>){
461    chomp;
462    if($_ =~ /section spots/){  #found the spot section
463      $found="TRUE";
464      next; #skip to next line ?
465    }
466    if(($_ !~/columns/) || ($_ !~/channels  2/) || ($_ !~ /assayFields/) || ($_ !~/assays/) || ($_ !~/%/) && ($found eq "TRUE") ){
467      # now reading real data line
468      if ($_ eq ""){
469        # do nada
470      }else{
471        # [reporterId]  [geneSymbol]  [chromosome]  [cytoBand]  [startPosition] [endPosition] [assayData = M]
472        my @temp = split("\t",$_); #split each line
473        if( ($temp[$endPositionIndex]>0) && ($temp[$chromosomeIndex]=~ /\w/) && ($temp[$chromosomeIndex]>0)  ){ #reporterId must have a bp end and a chromosome not = ""
474          foreach my $row (@temp){ #replace empty string with NaN ..
475            if($row eq ""){
476              $row = "NaN";
477            }
478          }
479          if(scalar(@temp)<$nbrCols){ # To cope with dropped tabs..
480            while(scalar(@temp)<$nbrCols){
481              push(@temp,"NaN");
482            }
483          }
484          my $line; 
485          if(($param_hash{'exportMode'} eq "standard_lite") || ($param_hash{'exportMode'} eq "singleLite")){
486            splice(@temp, 1, 1);
487            #new format of temp
488            # [reporterId]  [chromosome]  [cytoBand]  [startPosition] [endPosition] [assayData = M]
489            splice(@temp, 2, 1);
490            #new format of temp
491            # [reporterId]  [chromosome]  [startPosition] [endPosition] [assayData = M]
492            $line = join("\t",@temp);
493          }elsif($param_hash{'exportMode'} eq "bed"){
494            #format: chr start stop reporterId
495            my $bed_chrom="chr".$temp[$chromosomeIndex];
496            if($temp[$chromosomeIndex] eq "23"){
497              $bed_chrom="chrX";
498            }
499            if($temp[$chromosomeIndex] eq "24"){
500              $bed_chrom="chrY";         
501            }
502            $line = join("\t",$bed_chrom,$temp[4],$temp[$endPositionIndex],$temp[$repIdIndex]);
503          }else{
504            $line = join("\t",@temp);
505          }
506         
507          if(($param_hash{'sort'} eq "TRUE") || ($param_hash{'exportMode'} eq "singleLite") || ($param_hash{'exportMode'} eq "agilent") || ($param_hash{'exportMode'} eq "stac") ){
508            push(@toSort,$line);
509          }else{
510            print myoutfile "$line\n";
511          }
512        }
513      }
514    }# end of if ( !~/columns etc..
515  } #end of while(<>)
516 
517  if($param_hash{'exportMode'} eq "stac"){
518    #to format the data correctly and easiest, use a small R script, stac_format.R
519    open(myfile,"<$FindBin::Bin/stac_format.R");
520    open (myoutfile, ">stac_formatCommands.R");
521    while(<myfile>){
522      chomp;
523      print myoutfile "$_\n";
524    }
525    close (myfile);
526    close (myoutfile);
527   
528    my $success = system("R --no-save < stac_formatCommands.R > r-debug.txt");
529 
530    #catch the output
531 
532  }
533
534  ## Sort data and print it if selected
535  if(($param_hash{'sort'} eq "TRUE") || ($param_hash{'exportMode'} eq "agilent") || ($param_hash{'exportMode'} eq "singleLite")){
536    #sort on chromosome and then on startPosition
537    if($param_hash{'sort'} eq "TRUE"){
538      if(($param_hash{'exportMode'} eq "standard_lite") || ($param_hash{'exportMode'} eq "singleLite")){
539        # [reporterId]  [chromosome]  [startPosition] [endPosition] [assayData = M]
540        @toSort =
541            map  $_->[0] =>
542            sort { $a->[1] <=> $b->[1] 
543                 ||
544                   $a->[2] <=> $b->[2] }
545            map  [ $_, (split /\t/)[1], (split /\t/)[2] ]
546            #map [ $_, (split /\t/)[1,2] ]
547              => @toSort;           
548      }elsif($param_hash{'exportMode'} eq "bed"){
549        #format: [chromosome] [startPosition] [stopPosition] [reporterId]
550        @toSort =
551            map  $_->[0] =>
552            sort { $a->[1] <=> $b->[1] 
553                   ||
554                   $a->[2] <=> $b->[2] }
555            map  [ $_, (split /\t/)[0], (split /\t/)[1] ]
556              => @toSort;           
557      }else{
558        #standard format
559        # [reporterId]  [geneSymbol]  [chromosome]  [cytoBand]  [startPosition] [endPosition] [assayData = M]
560   
561        @toSort =
562            map  $_->[0] =>
563            sort { $a->[1] <=> $b->[1] ||
564                   $a->[2] <=> $b->[2] }
565            map  [ $_, (split /\t/)[2], (split /\t/)[4] ]
566              => @toSort;
567      }
568    }#end if to sort data
569    if($param_hash{'exportMode'} eq "singleLite"){
570      # split the matrix into separate files...
571      # [reporterId]  [chromosome]  [startPosition] [endPosition] [assayData = M]
572     
573      #split header
574      my @tmpHeader=split("\t",$header);
575      my $commonHeader=join("\t",shift(@tmpHeader),shift(@tmpHeader),shift(@tmpHeader),shift(@tmpHeader));
576      my $ccN=4;
577      for(my $i=0;$i<@tmpHeader;$i++){
578        #foreach assay create individual files, through iteration.. VERY SLOW!
579        my $fileN=$tmpHeader[$i]."_".$file;
580        open(mySingleFileHandle,">$fileN");
581        print mySingleFileHandle "$commonHeader\t$tmpHeader[$i]\n";
582        for(my $j=0;$j<@toSort;$j++){ 
583          my @ttt= split("\t",$toSort[$j]);
584          my $lineN=join("\t",$ttt[0],$ttt[1],$ttt[2],$ttt[3],$ttt[$i+$ccN]);
585          print mySingleFileHandle "$lineN\n";
586        }
587        close(mySingleFileHandle);
588      } 
589    }elsif($param_hash{'exportMode'} eq "agilent"){
590      #create the agilent format and print
591      my $headerA=join("\t","FeatureNum","Chr","Start","Stop","SystematicName","Gene Name","Description",@assaynames);
592      my $featureNum=0;
593      print myoutfile "AMADID 1234567\n"; #check if to use random number?
594      print myoutfile "$headerA\n";
595   
596      # Format of toSort:
597      # [reporterId]  [geneSymbol]  [chromosome]  [cytoBand]  [startPosition] [endPosition] [assayData = M]
598      foreach my $line (@toSort){
599        $featureNum++;
600        my @tmp=split("\t",$line);
601        if($tmp[2] eq "23"){
602          $tmp[2]="X";
603        }elsif($tmp[2] eq "24"){
604          $tmp[2]="Y";
605        }
606        #my $agilentLine=join("\t",$featureNum,$tmp[2],$tmp[4],$tmp[5],$tmp[0],$tmp[1],""); #if it works with bundled gene symbols..
607        my $agilentLine=join("\t",$featureNum,$tmp[2],$tmp[4],$tmp[5],$tmp[0],"","");
608     
609        splice(@tmp,0,6); #only log2data left
610        $agilentLine=join("\t",$agilentLine,@tmp);
611        print myoutfile "$agilentLine\n";
612      }
613    }else{
614      #just print!
615      foreach my $line (@toSort){
616        print myoutfile "$line\n";
617      }
618    }
619  }
620  if($param_hash{'exportMode'} ne "singleLite"){
621    close(myoutfile);
622  }
623}#end doExport
624
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