[Nelsonlab-cmts] dev-boconnor/project_logic_analysis/lib/perl/Nelson/Pipe/Container/Job CreateProfiles.pm,1.14,1.15 SifFileParser.pm,1.8,1.9

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

Update of /cvsroot/dev-boconnor/project_logic_analysis/lib/perl/Nelson/Pipe/Container/Job
In directory sumo.genetics.ucla.edu:/tmp/cvs-serv31102/lib/perl/Nelson/Pipe/Container/Job

Modified Files:
	CreateProfiles.pm SifFileParser.pm 
Log Message:
Changes to libs


Index: SifFileParser.pm
===================================================================
RCS file: /cvsroot/dev-boconnor/project_logic_analysis/lib/perl/Nelson/Pipe/Container/Job/SifFileParser.pm,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** SifFileParser.pm	16 Feb 2006 00:31:19 -0000	1.8
--- SifFileParser.pm	17 Feb 2006 00:09:22 -0000	1.9
***************
*** 167,187 ****
            my $grade = $tokens[4];
  
!           # ER status (ER+=mutant; ER-=wt)
!           my $er_wt = 1;
!           if ($tokens[5] eq 'ER+') { $er_wt = 0; }
  
            # PgR status (PgR+=mutant; PgR-=wt)
!           my $pgr_wt = 1;
!           if ($tokens[6] eq 'PgR+') { $pgr_wt = 0; }
  
            # Lymph node status 
!           my $lymph_pos = 1;
!           if ($tokens[9] eq 'LN-') { $lymph_pos = 0; }
  
            $self->{files}{$filename}{p53_wt} = $p53_wt;
            $self->{files}{$filename}{dlda_mt} = $dlda_mt;
            $self->{files}{$filename}{grade} = $grade;
!           $self->{files}{$filename}{er_wt} = $er_wt;
!           $self->{files}{$filename}{pgr_wt} = $pgr_wt;
            $self->{files}{$filename}{lymph_pos} = $lymph_pos;
        }
--- 167,187 ----
            my $grade = $tokens[4];
  
!           # ER status
!           my $er_pos = 0;
!           if ($tokens[5] eq 'ER+') { $er_pos = 1; }
  
            # PgR status (PgR+=mutant; PgR-=wt)
!           my $pgr_pos = 0;
!           if ($tokens[6] eq 'PgR+') { $pgr_pos = 1; }
  
            # Lymph node status 
!           my $lymph_pos = 0;
!           if ($tokens[9] eq 'LN+') { $lymph_pos = 1; }
  
            $self->{files}{$filename}{p53_wt} = $p53_wt;
            $self->{files}{$filename}{dlda_mt} = $dlda_mt;
            $self->{files}{$filename}{grade} = $grade;
!           $self->{files}{$filename}{er_pos} = $er_pos;
!           $self->{files}{$filename}{pgr_pos} = $pgr_pos;
            $self->{files}{$filename}{lymph_pos} = $lymph_pos;
        }

Index: CreateProfiles.pm
===================================================================
RCS file: /cvsroot/dev-boconnor/project_logic_analysis/lib/perl/Nelson/Pipe/Container/Job/CreateProfiles.pm,v
retrieving revision 1.14
retrieving revision 1.15
diff -C2 -d -r1.14 -r1.15
*** CreateProfiles.pm	16 Feb 2006 20:44:14 -0000	1.14
--- CreateProfiles.pm	17 Feb 2006 00:09:22 -0000	1.15
***************
*** 245,248 ****
--- 245,253 ----
      $results->{samples}{annotations}{grade_3}{$filename} = 1;
      $results->{samples}{annotations}{grade_4}{$filename} = 0;
+   } elsif ($sif_hash->{'files'}{$old_filename}{grade} =~ /G\?/) {
+     $results->{samples}{annotations}{grade_1}{$filename} = 0;
+     $results->{samples}{annotations}{grade_2}{$filename} = 0;
+     $results->{samples}{annotations}{grade_3}{$filename} = 0;
+     $results->{samples}{annotations}{grade_4}{$filename} = 0;
    }
  
***************
*** 256,275 ****
    }
  
!   # er_wt
!   if ($sif_hash->{'files'}{$old_filename}{er_wt} =~ /1/) {
!     $results->{samples}{annotations}{er_wt}{$filename} = 1;
!     $results->{samples}{annotations}{er_mt}{$filename} = 0;
!   } elsif ($sif_hash->{'files'}{$old_filename}{er_wt} =~ /0/) {
!     $results->{samples}{annotations}{er_wt}{$filename} = 0;
!     $results->{samples}{annotations}{er_mt}{$filename} = 1;
    }
  
!   # pgr_wt
!   if ($sif_hash->{'files'}{$old_filename}{pgr_wt} =~ /1/) {
!     $results->{samples}{annotations}{pgr_wt}{$filename} = 1;
!     $results->{samples}{annotations}{pgr_mt}{$filename} = 0;
!   } elsif ($sif_hash->{'files'}{$old_filename}{pgr_wt} =~ /0/) {
!     $results->{samples}{annotations}{pgr_wt}{$filename} = 0;
!     $results->{samples}{annotations}{pgr_mt}{$filename} = 1;
    }
  
--- 261,280 ----
    }
  
!   # er_pos
!   if ($sif_hash->{'files'}{$old_filename}{er_pos} =~ /1/) {
!     $results->{samples}{annotations}{er_pos}{$filename} = 1;
!     $results->{samples}{annotations}{er_neg}{$filename} = 0;
!   } elsif ($sif_hash->{'files'}{$old_filename}{er_pos} =~ /0/) {
!     $results->{samples}{annotations}{er_pos}{$filename} = 0;
!     $results->{samples}{annotations}{er_neg}{$filename} = 1;
    }
  
!   # pgr_pos
!   if ($sif_hash->{'files'}{$old_filename}{pgr_pos} =~ /1/) {
!     $results->{samples}{annotations}{pgr_pos}{$filename} = 1;
!     $results->{samples}{annotations}{pgr_neg}{$filename} = 0;
!   } elsif ($sif_hash->{'files'}{$old_filename}{pgr_pos} =~ /0/) {
!     $results->{samples}{annotations}{pgr_pos}{$filename} = 0;
!     $results->{samples}{annotations}{pgr_neg}{$filename} = 1;
    }