1 new changeset in galaxy-central:

http://bitbucket.org/galaxy/galaxy-central/changeset/3dce98e473f1/ changeset: r5143:3dce98e473f1 user: guru date: 2011-02-28 20:04:53 summary: Fixed functional test for 'compute q values' tool - q-value is rounded to 6 significant digits, which shouldn't differ between different runs of the tool. Also, fixed a bug in microsatellite birth/death tool - cases where microsatellite boundaries aren't defined are skipped. affected #: 4 files (317 bytes)

--- a/test-data/q_values.tabular Mon Feb 28 12:16:28 2011 -0500 +++ b/test-data/q_values.tabular Mon Feb 28 14:04:53 2011 -0500 @@ -1,4 +1,4 @@ -pi0: 0.243863648325601 +pi0: 0.243864

FDR level: 0.05

--- a/tools/regVariation/compute_q_values.pl Mon Feb 28 12:16:28 2011 -0500 +++ b/tools/regVariation/compute_q_values.pl Mon Feb 28 14:04:53 2011 -0500 @@ -11,6 +11,8 @@ use strict; use warnings; use IO::Handle; +use File::Temp qw/ tempfile tempdir /; +my $tdir = tempdir( CLEANUP => 0 );

# check to make sure having correct input and output files my $usage = "usage: compute_q_values.pl [TABULAR.in] [lambda] [pi0_method] [fdr_level] [robust] [TABULAR.out] [PDF.out] \n"; @@ -44,7 +46,8 @@ my $r_script;

# R script to implement the calcualtion of q-values based on multiple simultaneous tests p-values -# construct an R script file and save it in the same directory where the perl file is located +# construct an R script file and save it in a temp directory +chdir $tdir; $r_script = "q_values_computation.r";

open(Rcmd,">", $r_script) or die "Cannot open $r_script \n\n"; @@ -76,6 +79,7 @@ dev.off(); #save the q-values in the output file $q_valuesOutputFile + qobj$pi0 <- signif(qobj$pi0,digits=6) qwrite(qobj, filename="$q_valuesOutputFile");

#options(show.error.messages = TRUE);

--- a/tools/regVariation/compute_q_values.xml Mon Feb 28 12:16:28 2011 -0500 +++ b/tools/regVariation/compute_q_values.xml Mon Feb 28 14:04:53 2011 -0500 @@ -1,4 +1,4 @@ -<tool id="compute_q_values" name="Compute q-values" version="1.0.0"> +<tool id="compute_q_values" name="Compute q-values" version="1.0.1"><description>based on multiple simultaneous tests p-values</description><command interpreter="perl">

--- a/tools/regVariation/microsatellite_birthdeath.pl Mon Feb 28 12:16:28 2011 -0500 +++ b/tools/regVariation/microsatellite_birthdeath.pl Mon Feb 28 14:04:53 2011 -0500 @@ -643,7 +643,11 @@ my %microsatstarts=(); #1 WITHIN EACH ALIGNMENT, IF THERE EXISTS A MICROSATELLITE #2 THIS HASH CONTAINS THE START SITE OF THE MICROSATELLITE #3 WIHIN THE ALIGNMENT - + next if !defined $extreme_start; + next if !defined $extreme_end; + next if $extreme_start > length($sequences{$tags[0]}); + next if $extreme_start < 0; + next if $extreme_end > length($sequences{$tags[0]}); for my $i (0 ... $#tags){ #1 NOW THAT WE HAVE GATHERED INFORMATION REGARDING #2 SEQUENCE ALIGNMENT AND MICROSATELLITE COORDINATES @@ -3977,3 +3981,4 @@ foreach my $line (@_) {print "$line\n";} print "::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::<\n"; } +

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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