[Nelsonlab-cmts] dev-boconnor/project_logic_analysis/lib/perl/Nelson/Pipe/Container/Job ReadVGLOutput.pm,1.7,1.8 ScoreSamplesViaVGL.pm,1.5,1.6

[<boc...@su...>]

Update of /cvsroot/dev-boconnor/project_logic_analysis/lib/perl/Nelson/Pipe/Container/Job
In directory sumo.genetics.ucla.edu:/tmp/cvs-serv7391/lib/perl/Nelson/Pipe/Container/Job

Modified Files:
	ReadVGLOutput.pm ScoreSamplesViaVGL.pm 
Log Message:
Updates


Index: ScoreSamplesViaVGL.pm
===================================================================
RCS file: /cvsroot/dev-boconnor/project_logic_analysis/lib/perl/Nelson/Pipe/Container/Job/ScoreSamplesViaVGL.pm,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** ScoreSamplesViaVGL.pm	22 Feb 2006 09:14:59 -0000	1.5
--- ScoreSamplesViaVGL.pm	23 Feb 2006 22:11:59 -0000	1.6
***************
*** 67,71 ****
     # now loop through each profile cutoff and score each file
     foreach my $profile_count_cutoff (@profile_count_cutoffs) {
!      open SUMMARY, ">".$self->{output_summary_file}."_profile_count_$profile_count_cutoff.txt" or die;
       if ($profile_count_cutoff ne 'all') {
         # read the profiles to test with here
--- 67,71 ----
     # now loop through each profile cutoff and score each file
     foreach my $profile_count_cutoff (@profile_count_cutoffs) {
!      open SUMMARY, ">".$self->{output_summary_file}."_profile_count_$profile_count_cutoff.txt" or die "Can't open ".$self->{output_summary_file}."_profile_count_$profile_count_cutoff.txt for writing\n";
       if ($profile_count_cutoff ne 'all') {
         # read the profiles to test with here
***************
*** 124,128 ****
        if (!defined ($sample_mean )) { die "Sample Mean not defined for $file $probe\n"; }
        
!       if (defined($sample_mean) && abs($sample_mean/$score_mean) >= 2) {
          #print " Yes this is positive for $hc\n";
          $class->{$subdir}{$profile_count_cutoff}{$file}{scores}{$hc}{raw_score} += 1;
--- 124,132 ----
        if (!defined ($sample_mean )) { die "Sample Mean not defined for $file $probe\n"; }
        
!       # BUG: I think the next line of code was incorrect!!
!       # FIXME: this actually performs worse so I think I need to keep track of which VG are actually lower expression
!       # then the others
!       #if (defined($sample_mean) && abs($sample_mean/$score_mean) >= 2) {
!       if (defined($sample_mean) && (($sample_mean/$score_mean) >= 2 || ($sample_mean/$score_mean) <= 0.5 )) {
          #print " Yes this is positive for $hc\n";
          $class->{$subdir}{$profile_count_cutoff}{$file}{scores}{$hc}{raw_score} += 1;

Index: ReadVGLOutput.pm
===================================================================
RCS file: /cvsroot/dev-boconnor/project_logic_analysis/lib/perl/Nelson/Pipe/Container/Job/ReadVGLOutput.pm,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** ReadVGLOutput.pm	22 Feb 2006 09:14:59 -0000	1.7
--- ReadVGLOutput.pm	23 Feb 2006 22:11:58 -0000	1.8
***************
*** 61,65 ****
      $results->{frequency}{$subdir} = {};
      $results->{comparison_to_reference}{$subdir} = {};
- 
      # FIXME
      my @files = glob("$profile_output_dir/$subdir/file_list_*.txt_results");
--- 61,64 ----
***************
*** 68,72 ****
        my $curr_output;
        if ($parser_type eq '2_phenotypes') { $curr_output = $self->_parse_2_pheno_vgl_output("$file/$input_file_name", $col_offset, $base_col, $pheno_str_1, $pheno_str_2); }
!       else { $curr_output = $self->_parse_vgl_output("$file/$input_file_name", $col_offset); }
        # this is used to store a count/lines for all profiles encountered in this particular subdir
        $self->_add_to_all_profiles($curr_output, $results->{all_profiles}{$subdir});
--- 67,75 ----
        my $curr_output;
        if ($parser_type eq '2_phenotypes') { $curr_output = $self->_parse_2_pheno_vgl_output("$file/$input_file_name", $col_offset, $base_col, $pheno_str_1, $pheno_str_2); }
!       else { 
! 	$curr_output = $self->_parse_vgl_output("$file/$input_file_name", $col_offset); 
!         #print "HERE!!!!".Dumper $curr_output;
!         #die;
!       }
        # this is used to store a count/lines for all profiles encountered in this particular subdir
        $self->_add_to_all_profiles($curr_output, $results->{all_profiles}{$subdir});