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From: <boc...@su...> - 2006-02-23 22:12:11
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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}); |