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There was still some inconsistency in the ordering of the output targ…

…et and

background TFBS hit and rate columns. Fixed so that all follow the order:
Target Hits, Target Rate, Background Hits, Background Rate
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1 parent 31c7ecf commit dc293dcaabe436a7f0bfa4ce85fb44b6c8dc9796 @darenillas darenillas committed Jun 21, 2012
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6 lib/OPOSSUM/Include/SeqACSAInclude.pm
@@ -172,7 +172,7 @@ sub write_results_text
#
my $text .= "TF Name\t";
$text .= "JASPAR_ID\t";
- $text .= "Class\tFamily\tTax Group\tIC\tGC Content\tTarget seq hits\tTarget seq non-hits\tBackground seq hits\tBackground seq non-hits\tTarget TFBS hits\tBackground TFBS hits\tTarget TFBS nucleotide rate\tBackground TFBS nucleotide rate\tZ-score\tFisher score\n";
+ $text .= "Class\tFamily\tTax Group\tIC\tGC Content\tTarget seq hits\tTarget seq non-hits\tBackground seq hits\tBackground seq non-hits\tTarget TFBS hits\tTarget TFBS nucleotide rate\tBackground TFBS hits\tBackground TFBS nucleotide rate\tZ-score\tFisher score\n";
foreach my $result (@$results)
{
@@ -190,7 +190,7 @@ sub write_results_text
$text .= $tf->name() . "\t";
$text .= $tf->ID() . "\t" if $tf_db;
$text .= sprintf
- "%s\t%s\t%s\t%s\t%.3f\t%d\t%d\t%d\t%d\t%d\t%d\t%s\t%s\t%s\t%s\n",
+ "%s\t%s\t%s\t%s\t%.3f\t%d\t%d\t%d\t%d\t%d\t%s\t%d\t%s\t%s\t%s\n",
$tf->class() || 'NA',
$tf->tag('family') || 'NA',
$tf->tag('tax_group') || 'NA',
@@ -201,9 +201,9 @@ sub write_results_text
$result->bg_gene_hits() || 0,
$result->bg_gene_no_hits() || 0,
$result->t_tfbs_hits() || 0,
- $result->bg_tfbs_hits() || 0,
defined $result->t_tfbs_rate()
? sprintf("%.3f", $result->t_tfbs_rate()) : 'NA',
+ $result->bg_tfbs_hits() || 0,
defined $result->bg_tfbs_rate()
? sprintf("%.3f", $result->bg_tfbs_rate()) : 'NA',
defined $result->zscore()
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10 lib/OPOSSUM/Include/SeqSSAInclude.pm
@@ -263,7 +263,7 @@ sub write_results_text
my $gc_content = sprintf("%.3f", $tf->tag('gc_content'));
$text .= sprintf
- "%s\t%s\t%s\t%s\t%s\t%s\t%s\t%d\t%d\t%d\t%d\t%d\t%d\t%s\t%s\t%s\t%s\t%s\n",
+ "%s\t%s\t%s\t%s\t%s\t%s\t%s\t%d\t%d\t%d\t%d\t%d\t%s\t%d\t%s\t%s\t%s\t%s\n",
$tf->name(),
$tf->ID(),
$tf->class() || 'NA',
@@ -276,9 +276,9 @@ sub write_results_text
$result->bg_gene_hits() || 0,
$result->bg_gene_no_hits() || 0,
$result->t_tfbs_hits() || 0,
- $result->bg_tfbs_hits() || 0,
defined $result->t_tfbs_rate()
? sprintf("%.3f", $result->t_tfbs_rate()) : 'NA',
+ $result->bg_tfbs_hits() || 0,
defined $result->bg_tfbs_rate()
? sprintf("%.3f", $result->bg_tfbs_rate()) : 'NA',
defined $result->zscore()
@@ -289,7 +289,7 @@ sub write_results_text
? sprintf("%.3f", $result->ks_p_value()) : 'NA';
}
} else {
- $text = "TF Name\tClass\tFamily\tTax Group\tIC\tTarget seq hits\tTarget seq non-hits\tBackground seq hits\tBackground seq non-hits\tTarget TFBS hits\tBackground TFBS hits\tTarget TFBS nucleotide rate\tBackground TFBS nucleotide rate\tZ-score\tFisher score\tPeakDist p-value\n";
+ $text = "TF Name\tClass\tFamily\tTax Group\tIC\tTarget seq hits\tTarget seq non-hits\tBackground seq hits\tBackground seq non-hits\tTarget TFBS hits\tTarget TFBS nucleotide rate\tBackground TFBS hits\tBackground TFBS nucleotide rate\tZ-score\tFisher score\tPeakDist p-value\n";
foreach my $result (@$results) {
my $tf = $tf_set->get_tf($result->id());
@@ -302,7 +302,7 @@ sub write_results_text
}
$text .= sprintf
- "%s\t%s\t%s\t%s\t%s\t%d\t%d\t%d\t%d\t%d\t%d\t%s\t%s\t%s\t%s\t%s\n",
+ "%s\t%s\t%s\t%s\t%s\t%d\t%d\t%d\t%d\t%d\t%s\t%d\t%s\t%s\t%s\t%s\n",
$tf->name(),
$tf->class() || 'NA',
$tf->tag('family') || 'NA',
@@ -313,9 +313,9 @@ sub write_results_text
$result->bg_gene_hits() || 0,
$result->bg_gene_no_hits() || 0,
$result->t_tfbs_hits() || 0,
- $result->bg_tfbs_hits() || 0,
defined $result->t_tfbs_rate()
? sprintf("%.3f", $result->t_tfbs_rate()) : 'NA',
+ $result->bg_tfbs_hits() || 0,
defined $result->bg_tfbs_rate()
? sprintf("%.3f", $result->bg_tfbs_rate()) : 'NA',
defined $result->zscore()
View
16 lib/OPOSSUM/Include/SeqTCAInclude.pm
@@ -256,17 +256,17 @@ sub write_results_text
return unless $results && $results->[0];
- my $text = "TFBS Cluster ID\tClass\tFamily\t";
- $text .= "Target seq hits\tTarget seq non-hits\t";
- $text .= "Background seq hits\tBackground seq non-hits\t";
- $text .= "Target cluster hits\tBackground cluster hits\t";
- $text .= "Target cluster nucleotide rate\tBackground cluster nucleotide rate\t";
- $text .= "Z-score\tFisher score\tKS score\n";
+ my $text = "TFBS Cluster ID\tClass\tFamily";
+ $text .= "\tTarget seq hits\tTarget seq non-hits";
+ $text .= "\tBackground seq hits\tBackground seq non-hits";
+ $text .= "\tTarget cluster hits\tTarget cluster nucleotide rate";
+ $text .= "\tBackground cluster hits\tBackground cluster nucleotide rate";
+ $text .= "\tZ-score\tFisher score\tKS score\n";
foreach my $result (@$results) {
my $cl = $tf_cluster_set->get_tf_cluster($result->id());
- $text .= sprintf "%s\t%s\t%s\t%d\t%d\t%d\t%d\t%d\t%d\t%s\t%s\t%s\t%s\t%s\n",
+ $text .= sprintf "%s\t%s\t%s\t%d\t%d\t%d\t%d\t%d\t%s\t%d\t%s\t%s\t%s\t%s\n",
'c' . $cl->id(),
$cl->class() || 'NA',
$cl->family() || 'NA',
@@ -275,9 +275,9 @@ sub write_results_text
$result->bg_gene_hits() || 0,
$result->bg_gene_no_hits() || 0,
$result->t_cluster_hits() || 0,
- $result->bg_cluster_hits() || 0,
defined $result->t_cluster_rate()
? sprintf("%.3f", $result->t_cluster_rate()) : 'NA',
+ $result->bg_cluster_hits() || 0,
defined $result->bg_cluster_rate()
? sprintf("%.3f", $result->bg_cluster_rate()) : 'NA',
defined $result->zscore()
View
6 scripts/opossum_seq_actca.pl
@@ -176,7 +176,7 @@ =head1 AUTHOR
use warnings;
-use lib '/apps/oPOSSUM3/lib';
+use lib '/devel/oPOSSUM3/lib';
use Getopt::Long;
use Pod::Usage;
@@ -694,7 +694,7 @@ sub write_results_text
my $tfcl = $tf_cluster_set->get_tf_cluster($result->id());
printf FH
- "%s\t%s\t%s\t%d\t%d\t%d\t%d\t%d\t%d\t%s\t%s\t%s\t%s\n",
+ "%s\t%s\t%s\t%d\t%d\t%d\t%d\t%d\t%s\t%d\t%s\t%s\t%s\n",
$tfcl->name(),
$tfcl->class() || 'N/A',
$tfcl->family() || 'N/A',
@@ -703,9 +703,9 @@ sub write_results_text
$result->bg_gene_hits() || 0,
$result->bg_gene_no_hits() || 0,
$result->t_cluster_hits() || 0,
- $result->bg_cluster_hits() || 0,
defined $result->t_cluster_rate()
? sprintf("%.3f", $result->t_cluster_rate()) : 'N/A',
+ $result->bg_cluster_hits() || 0,
defined $result->bg_cluster_rate()
? sprintf("%.3f", $result->bg_cluster_rate()) : 'N/A',
defined $result->zscore()

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