[Bioperl-guts-l] [15323] bioperl-run/trunk/t: * finish up bioperl-run conversion
Christopher John Fields
cjfields at dev.open-bio.org
Sat Jan 10 11:21:47 EST 2009
Revision: 15323
Author: cjfields
Date: 2009-01-10 11:21:46 -0500 (Sat, 10 Jan 2009)
Log Message:
-----------
* finish up bioperl-run conversion
* will need to add a Bio::Root::Test test_cleanup method for unlinking some files
Modified Paths:
--------------
bioperl-run/trunk/t/Clustalw.t
bioperl-run/trunk/t/Coil.t
bioperl-run/trunk/t/DrawGram.t
bioperl-run/trunk/t/DrawTree.t
bioperl-run/trunk/t/EMBOSS.t
bioperl-run/trunk/t/Genemark.hmm.prokaryotic.t
bioperl-run/trunk/t/Genewise.t
bioperl-run/trunk/t/Genscan.t
bioperl-run/trunk/t/Gerp.t
bioperl-run/trunk/t/Glimmer2.t
bioperl-run/trunk/t/Glimmer3.t
bioperl-run/trunk/t/Gumby.t
bioperl-run/trunk/t/Hmmer.t
bioperl-run/trunk/t/Hyphy.t
bioperl-run/trunk/t/Kalign.t
bioperl-run/trunk/t/LVB.t
bioperl-run/trunk/t/MAFFT.t
bioperl-run/trunk/t/MCS.t
bioperl-run/trunk/t/Match.t
bioperl-run/trunk/t/Mdust.t
bioperl-run/trunk/t/Meme.t
bioperl-run/trunk/t/Molphy.t
bioperl-run/trunk/t/Muscle.t
bioperl-run/trunk/t/Neighbor.t
bioperl-run/trunk/t/Njtree.t
bioperl-run/trunk/t/PAML.t
bioperl-run/trunk/t/Pal2Nal.t
bioperl-run/trunk/t/PhastCons.t
bioperl-run/trunk/t/Phrap.t
bioperl-run/trunk/t/Phyml.t
bioperl-run/trunk/t/Pise.t
bioperl-run/trunk/t/Primate.t
bioperl-run/trunk/t/Primer3.t
bioperl-run/trunk/t/Prints.t
bioperl-run/trunk/t/Probalign.t
bioperl-run/trunk/t/Probcons.t
bioperl-run/trunk/t/Profile.t
bioperl-run/trunk/t/Promoterwise.t
bioperl-run/trunk/t/ProtDist.t
bioperl-run/trunk/t/ProtPars.t
bioperl-run/trunk/t/Pseudowise.t
bioperl-run/trunk/t/QuickTree.t
bioperl-run/trunk/t/RepeatMasker.t
bioperl-run/trunk/t/SLR.t
bioperl-run/trunk/t/Seg.t
bioperl-run/trunk/t/Semphy.t
bioperl-run/trunk/t/SeqBoot.t
bioperl-run/trunk/t/Signalp.t
bioperl-run/trunk/t/Sim4.t
bioperl-run/trunk/t/Simprot.t
bioperl-run/trunk/t/StandAloneFasta.t
bioperl-run/trunk/t/TCoffee.t
bioperl-run/trunk/t/TigrAssembler.t
bioperl-run/trunk/t/Tmhmm.t
bioperl-run/trunk/t/TribeMCL.t
bioperl-run/trunk/t/Vista.t
bioperl-run/trunk/t/tRNAscanSE.t
Modified: bioperl-run/trunk/t/Clustalw.t
===================================================================
--- bioperl-run/trunk/t/Clustalw.t 2009-01-10 00:15:32 UTC (rev 15322)
+++ bioperl-run/trunk/t/Clustalw.t 2009-01-10 16:21:46 UTC (rev 15323)
@@ -18,11 +18,11 @@
# setup input files etc
-my $inputfilename = File::Spec->catfile("t","data","cysprot.fa");
+my $inputfilename = test_input_file("cysprot.fa");
ok( -e $inputfilename, 'Found input file' );
-my $profile1 = File::Spec->catfile('t','data','cysprot1a.msf');
+my $profile1 = test_input_file('cysprot1a.msf');
ok( -e $profile1, 'Found profile1 file' );
-my $profile2 = File::Spec->catfile('t','data','cysprot1b.msf');
+my $profile2 = test_input_file('cysprot1b.msf');
ok( -e $profile2, 'Found profile2 file' );
# setup global objects that are to be used in more than one test
@@ -53,17 +53,14 @@
# remove last bit
$ver =~ s{^(\d+\.\d+)\.\d+}{$1};
- my $skip;
-
# clustalw2 isn't supported yet.
if ($ver < 1.8) {
diag("ClustalW version $ver not supported");
- $skip++;
+ skip("ClustalW version $ver not supported", 16);
} if ($ver >= 2.0) {
- diag("ClustalW version $ver not supported yet.");
- $skip++
+ diag("Warning: ClustalW version $ver not supported yet.");
+ skip("ClustalW version $ver not supported yet", 16);
}
- skip("ClustalW version $ver not supported yet", 16) if $skip;
ok( $ver, "Supported program version $ver" );
@@ -142,7 +139,7 @@
$aln = $factory->profile_align($aln1,$aln2);
is($aln->get_seq_by_pos(2)->get_nse, 'CATH_HUMAN/1-335', 'Got correct sequence by position');
- $str2 = Bio::SeqIO->new(-file=> Bio::Root::IO->catfile("t","data","cysprot1b.fa"));
+ $str2 = Bio::SeqIO->new(-file=> test_input_file("cysprot1b.fa"));
my $seq = $str2->next_seq();
$aln = $factory->profile_align($aln1,$seq);
is($aln->get_seq_by_pos(2)->get_nse, 'CATH_HUMAN/1-335', 'Got correct sequence by position');
Modified: bioperl-run/trunk/t/Coil.t
===================================================================
--- bioperl-run/trunk/t/Coil.t 2009-01-10 00:15:32 UTC (rev 15322)
+++ bioperl-run/trunk/t/Coil.t 2009-01-10 16:21:46 UTC (rev 15323)
@@ -19,7 +19,7 @@
-tests => 4);
ok $factory->isa('Bio::Tools::Run::Coil');
- my $prot_file= Bio::Root::IO->catfile("t","data","coil_protein_input");
+ my $prot_file= test_input_file("coil_protein_input");
my $seq1 = Bio::Seq->new();
my $seqstream = Bio::SeqIO->new(-file => $prot_file, -fmt => 'Fasta');
Modified: bioperl-run/trunk/t/DrawGram.t
===================================================================
--- bioperl-run/trunk/t/DrawGram.t 2009-01-10 00:15:32 UTC (rev 15322)
+++ bioperl-run/trunk/t/DrawGram.t 2009-01-10 16:21:46 UTC (rev 15323)
@@ -3,9 +3,7 @@
## $Id$
use strict;
-use vars qw($DEBUG);
-$DEBUG = $ENV{'BIOPERLDEBUG'} || 0;
BEGIN {
use lib '.';
use Bio::Root::Test;
@@ -27,7 +25,7 @@
ok($file);
ok(-e $file);
- if( $DEBUG ) {
+ if( test_debug() ) {
`gs $file`;
}
unlink($file);
@@ -44,7 +42,7 @@
ok($file);
ok(-e $file);
- if( $DEBUG ) {
+ if( test_debug() ) {
`gs $file`;
}
unlink($file);
Modified: bioperl-run/trunk/t/DrawTree.t
===================================================================
--- bioperl-run/trunk/t/DrawTree.t 2009-01-10 00:15:32 UTC (rev 15322)
+++ bioperl-run/trunk/t/DrawTree.t 2009-01-10 16:21:46 UTC (rev 15323)
@@ -3,9 +3,7 @@
## $Id$
use strict;
-use vars qw($DEBUG);
-$DEBUG = $ENV{'BIOPERLDEBUG'} || 0;
BEGIN {
use lib '.';
use Bio::Root::Test;
@@ -26,7 +24,7 @@
ok($file);
ok(-e $file);
- if( $DEBUG ) {
+ if( test_debug() ) {
`gs $file`;
} else {
unlink($file);
@@ -38,7 +36,7 @@
ok($file);
ok(-e $file);
- if( $DEBUG ) {
+ if( test_debug() ) {
`gs $file`;
} else {
unlink($file);
Modified: bioperl-run/trunk/t/EMBOSS.t
===================================================================
--- bioperl-run/trunk/t/EMBOSS.t 2009-01-10 00:15:32 UTC (rev 15322)
+++ bioperl-run/trunk/t/EMBOSS.t 2009-01-10 16:21:46 UTC (rev 15323)
@@ -106,9 +106,7 @@
my $cons = $factory->program('cons');
$cons->verbose(0);
$in = Bio::AlignIO->new(-format => 'msf',
- -file => Bio::Root::IO->catfile('t',
- 'data',
- 'cysprot.msf'));
+ -file => test_input_file('cysprot.msf'));
my $aln2 = $in->next_aln;
if( $version ge '2.8.0' ) {
$cons->run({ '-sequence' => $aln2,
@@ -155,9 +153,7 @@
%input = ( '-word' => 4,
'-incorrect_option' => 'no value',
- '-sequence' => Bio::Root::IO->catfile('t',
- 'data',
- 'dna1.fa'),
+ '-sequence' => test_input_file('dna1.fa'),
'-outfile' => $compseqoutfile);
eval {
$compseqapp->run(\%input);
Modified: bioperl-run/trunk/t/Genemark.hmm.prokaryotic.t
===================================================================
--- bioperl-run/trunk/t/Genemark.hmm.prokaryotic.t 2009-01-10 00:15:32 UTC (rev 15322)
+++ bioperl-run/trunk/t/Genemark.hmm.prokaryotic.t 2009-01-10 16:21:46 UTC (rev 15323)
@@ -2,12 +2,10 @@
# ## Bioperl Test Harness Script for Modules
# #
use strict;
-use vars qw($NTESTS);
BEGIN {
use Bio::Root::Test;
- $NTESTS = 98;
- test_begin(-tests => $NTESTS,
+ test_begin(-tests => 98,
-requires_modules => [qw(IPC::Run)]);
use_ok('Bio::Tools::Run::Genemark');
@@ -15,7 +13,7 @@
use_ok('Bio::Seq');
}
-my $verbose = 1 if $ENV{'BIOPERLDEBUG'};
+my $verbose = test_debug();
my $model_dir = $ENV{'GENEMARK_MODELS'} if $ENV{'GENEMARK_MODELS'};
SKIP: {
Modified: bioperl-run/trunk/t/Genewise.t
===================================================================
--- bioperl-run/trunk/t/Genewise.t 2009-01-10 00:15:32 UTC (rev 15322)
+++ bioperl-run/trunk/t/Genewise.t 2009-01-10 16:21:46 UTC (rev 15323)
@@ -4,102 +4,84 @@
use strict;
BEGIN {
- eval { require Test; };
- if( $@ ) {
- use lib 't';
- }
- use Test;
- use vars qw($NTESTS);
- $NTESTS = 18;
- plan tests => $NTESTS;
+ use lib '.';
+ use Bio::Root::Test;
+ test_begin(-tests => 20);
+ use_ok('Bio::Tools::Run::Genewise');
+ use_ok('Bio::Root::IO');
+ use_ok('Bio::Seq');
}
-use Bio::Tools::Run::Genewise;
-use Bio::Root::IO;
-use Bio::Seq;
-END {
- for ( $Test::ntest..$NTESTS ) {
- skip("genewise program not found. Skipping. (Be sure you have the wise package > 2.2.0)",1);
- }
-}
-
-ok(1);
-my $verbose = $ENV{BIOPERLDEBUG} ? 1 : -1;
+my $verbose = test_debug() || -1;
my @params = ('-verbose' => $verbose,
'silent' => 1,
'quiet' => 1);
my $factory = Bio::Tools::Run::Genewise->new(@params);
-unless ($factory->executable) {
- warn("Genewise program not found. Skipping tests $Test::ntest to $NTESTS.\n");
- exit 0;
-}
+SKIP:{
+ test_skip(-requires_executable => $factory, -tests => 17);
-my $version = $factory->version;
-warn("version is $version\n") if $verbose > 0;
-ok $factory->isa('Bio::Tools::Run::Genewise');
+ my $version = $factory->version;
+ warn("version is $version\n") if $verbose > 0;
+ isa_ok $factory,'Bio::Tools::Run::Genewise';
+
+ my $bequiet = 1;
+ $factory->quiet($bequiet); # Suppress pseudowise messages to terminal
+
+ #test with one file with 2 sequences
+ my $inputfilename = test_input_file('road.pep');
+ my $seqstream1 = Bio::SeqIO->new(-file => $inputfilename,
+ -format => 'fasta');
+ my $seq1 = Bio::Seq->new();
+ $seq1 = $seqstream1->next_seq();
+
+ $inputfilename = test_input_file('human.genomic');
+ my $seqstream2 = Bio::SeqIO->new(-file => $inputfilename,
+ -format => 'fasta');
+ my $seq2 = Bio::Seq->new();
+ $seq2 = $seqstream2->next_seq();
+
+ my ($genes) = $factory->predict_genes($seq1, $seq2);
+
+ my @transcripts = $genes->transcripts;
+ my @feat = $transcripts[0]->exons;
+ my $seqid = $feat[0]->seq_id;
+ is($seqid, 'HSHNRNPA');
+ my ($featpair)= $feat[0]->each_tag_value('supporting_feature');
+ is($featpair->feature2->seq_id,'roa1_drome');
+ is($featpair->feature1->seq_id,'HSHNRNPA');
+ if( defined $version && $version eq 'wise2-2-0' ) {
+ is($transcripts[0]->start, 1386);
+ is($transcripts[0]->end, 3963);
+ is($feat[0]->start, 1386);
+ is($feat[0]->end, 1493);
+ is($feat[0]->strand,1);
+ is($featpair->feature2->start,26);
+ is($featpair->feature2->end,61);
+ is($featpair->feature2->strand,1);
+ is($featpair->feature2->score,'253.10');
+ is($featpair->feature1->start,1386);
+ is($featpair->feature1->end,1493);
+ is($featpair->feature1->strand,1);
+ is($featpair->feature1->score,'253.10');
+ } else {
+ warn("These tests may fail because I'm not sure about your genewise version -- using wise 2.2.3-rc7 values\n");
+ is($transcripts[0]->start, 1386);
+ is($transcripts[0]->end, 4304);
+
+ is($feat[0]->start, 1386);
+ is($feat[0]->end, 1493);
+ is($feat[0]->strand,1);
+ is($featpair->feature2->start,26);
+ is($featpair->feature2->end,61);
+ is($featpair->feature2->strand,1);
+ is($featpair->feature2->score,'319.10');
+ is($featpair->feature1->start,1386);
+ is($featpair->feature1->end,1493);
+ is($featpair->feature1->strand,1);
+ is($featpair->feature1->score,'319.10');
+
+ }
-my $bequiet = 1;
-$factory->quiet($bequiet); # Suppress pseudowise messages to terminal
-
-#test with one file with 2 sequences
-my $inputfilename = Bio::Root::IO->catfile(qw(t data road.pep));
-my $seqstream1 = Bio::SeqIO->new(-file => $inputfilename,
- -format => 'fasta');
-my $seq1 = Bio::Seq->new();
-$seq1 = $seqstream1->next_seq();
-
-$inputfilename = Bio::Root::IO->catfile(qw(t data human.genomic));
-my $seqstream2 = Bio::SeqIO->new(-file => $inputfilename,
- -format => 'fasta');
-my $seq2 = Bio::Seq->new();
-$seq2 = $seqstream2->next_seq();
-
-my ($genes) = $factory->predict_genes($seq1, $seq2);
-
-my @transcripts = $genes->transcripts;
-my @feat = $transcripts[0]->exons;
-my $seqid = $feat[0]->seq_id;
-ok($seqid, 'HSHNRNPA');
-my ($featpair)= $feat[0]->each_tag_value('supporting_feature');
-ok($featpair->feature2->seq_id,'roa1_drome');
-ok($featpair->feature1->seq_id,'HSHNRNPA');
-if( defined $version && $version eq 'wise2-2-0' ) {
- ok($transcripts[0]->start, 1386);
- ok($transcripts[0]->end, 3963);
- ok($feat[0]->start, 1386);
@@ Diff output truncated at 10000 characters. @@
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