[Genex-cvs-commit] genex-server/DB/scripts fix-array-mas5.pl,1.1,1.2

[<jas...@us...>]

Update of /cvsroot/genex/genex-server/DB/scripts
In directory sc8-pr-cvs1:/tmp/cvs-serv19032

Modified Files:
	fix-array-mas5.pl 
Log Message:
* DB/scripts/fix-array-mas5.pl (Repository): 
Added the ability to handle short MAS5 files



Index: fix-array-mas5.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/DB/scripts/fix-array-mas5.pl,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** fix-array-mas5.pl	17 Dec 2002 19:55:54 -0000	1.1
--- fix-array-mas5.pl	7 Apr 2003 19:07:31 -0000	1.2
***************
*** 7,10 ****
--- 7,11 ----
  my $rc = GetOptions(\%OPTIONS,
  		    'infile=s',
+ 		    'short',
  		    'design=s',
  		    'help',
***************
*** 18,21 ****
--- 19,23 ----
  
    optional flags:
+     --short           : MAS5 short files
      --help            : print this message
  EOU
***************
*** 38,41 ****
--- 40,44 ----
  print DESIGN "# id\tname\n";
  
+ # These are the long MAS5 files
  
  # 0) Line Num
***************
*** 78,96 ****
  # 37) Sort Score
  
  # all we need are:
  
! # 0) Line Num
! # 2) Probe Set Name
  
  my @INDICES = qw(0 2);
  
  my $in_data;
- my $data_start_regexp = qr/^Expression\s+Analysis/o;
  my $reading_data;
! my $reading_data_regexp = qr/^\tAnalysis/;
  my @spots;
  my $count = 0;
  my %REPS;
  my %IDS;
  while (<IN>) {
    # see if we've found the Data section already
--- 81,120 ----
  # 37) Sort Score
  
+ # the short files are
+ 
+ # 0) Probe Set Name
+ # 1) Signal
+ # 2) Detection
+ # 3) Detection p-value
+ # 4) Descriptions
+ 
  # all we need are:
  
! # Line Num
! # Probe Set Name
! 
! # the long files have all we need, for the short files we need to
! # create the line number
! 
  
  my @INDICES = qw(0 2);
+ my $data_start_regexp = qr/^Expression\s+Analysis/o;
+ my $reading_data_regexp = qr/^\tAnalysis/;
  
  my $in_data;
  my $reading_data;
! 
! if (exists $OPTIONS{short}) {
!   @INDICES = qw(0 0);
!   $data_start_regexp = qr/^\s+/;
!   $reading_data = 1;
! }
! 
  my @spots;
  my $count = 0;
  my %REPS;
  my %IDS;
+ 
+ 
  while (<IN>) {
    # see if we've found the Data section already
***************
*** 109,115 ****
  
    # check if this is the header line of the Data section
!   if (/$reading_data_regexp/) {
!     $reading_data = 1;
!     next;
    }
  
--- 133,141 ----
  
    # check if this is the header line of the Data section
!   unless (exists $OPTIONS{short}) {
!     if (/$reading_data_regexp/) {
!       $reading_data = 1;
!       next;
!     }
    }
  
***************
*** 117,122 ****
--- 143,152 ----
    last if /^End/;
  
+   $count++;
    my @data = split /\t/;
    my ($num,$name) = @data[@INDICES];
+ 
+   # we create the line number for short files
+   $num = $count if exists $OPTIONS{short};
  
    # commence error checking