[Bioperl-guts-l] [15430] bioperl-network/trunk/t: removed extraneous syntax; better use of Bio::Root::Test syntax
Senduran Balasubramaniam
sendu at dev.open-bio.org
Thu Jan 22 06:07:51 EST 2009
Revision: 15430
Author: sendu
Date: 2009-01-22 06:07:51 -0500 (Thu, 22 Jan 2009)
Log Message:
-----------
removed extraneous syntax; better use of Bio::Root::Test syntax
Modified Paths:
--------------
bioperl-network/trunk/t/Edge.t
bioperl-network/trunk/t/Graph-Articulation.x
bioperl-network/trunk/t/Graph-MD5.t
bioperl-network/trunk/t/Graph-Seq.t
bioperl-network/trunk/t/IO_dip_tab.t
bioperl-network/trunk/t/IO_psi10.t
bioperl-network/trunk/t/IO_psi25.t
bioperl-network/trunk/t/Interaction.t
bioperl-network/trunk/t/Node.t
bioperl-network/trunk/t/ProteinNet.t
Modified: bioperl-network/trunk/t/Edge.t
===================================================================
--- bioperl-network/trunk/t/Edge.t 2009-01-22 10:50:52 UTC (rev 15429)
+++ bioperl-network/trunk/t/Edge.t 2009-01-22 11:07:51 UTC (rev 15430)
@@ -2,16 +2,12 @@
# Bioperl Test Harness Script for Modules
# $Id$
-use vars qw($NUMTESTS $DEBUG $ERROR);
use strict;
-$DEBUG = $ENV{'BIOPERLDEBUG'} || 0;
BEGIN {
-
- use lib ".";
use Bio::Root::Test;
- test_begin(-tests => 11,
- -requires_module => 'Graph');
+ test_begin(-tests => 10,
+ -requires_module => 'Graph');
use_ok('Bio::Network::ProteinNet');
use_ok('Bio::Network::Edge');
@@ -19,11 +15,8 @@
use_ok('Bio::Seq');
}
-my $verbose = 0;
-$verbose = 1 if $DEBUG;
+my $verbose = test_debug();
-ok 1;
-
my $seq1 = Bio::Seq->new(-seq => "aaaaaaa");
my $seq2 = Bio::Seq->new(-seq => "ttttttt");
my $seq3 = Bio::Seq->new(-seq => "ccccccc");
Modified: bioperl-network/trunk/t/Graph-Articulation.x
===================================================================
--- bioperl-network/trunk/t/Graph-Articulation.x 2009-01-22 10:50:52 UTC (rev 15429)
+++ bioperl-network/trunk/t/Graph-Articulation.x 2009-01-22 11:07:51 UTC (rev 15430)
@@ -2,23 +2,18 @@
# Bioperl Test Harness Script for Modules
# $Id: Node.t 14466 2008-02-04 05:15:58Z bosborne $
-use vars qw($NUMTESTS $DEBUG $ERROR);
use strict;
-$DEBUG = $ENV{'BIOPERLDEBUG'} || 0;
BEGIN {
-
- use lib ".";
use Bio::Root::Test;
test_begin(-tests => 53,
- -requires_module => 'Graph');
+ -requires_module => 'Graph');
use_ok('Bio::Network::IO');
use_ok('Bio::Network::Node');
}
-my $verbose = 0;
-$verbose = 1 if $DEBUG;
+my $verbose = test_debug();
# tests for Graph's problematic articulation_points()
# As of 2/2008 this test suite is still not reliably passing -
@@ -30,7 +25,7 @@
#
my $io = Bio::Network::IO->new(
-format => 'dip_tab',
- -file => Bio::Root::IO->catfile("t","data","tab1part.tab"),
+ -file => test_input_file("tab1part.tab"),
-threshold => 0.6);
ok(defined $io);
ok my $g1 = $io->next_network();
@@ -45,7 +40,7 @@
#
$io = Bio::Network::IO->new
(-format => 'psi10',
- -file => Bio::Root::IO->catfile("t","data","bovin_small_intact.xml"));
+ -file => test_input_file("bovin_small_intact.xml"));
my $g = $io->next_network();
@nodes = $g->nodes;
@@ -73,7 +68,7 @@
#
ok $io = Bio::Network::IO->new
(-format => 'psi10',
- -file => Bio::Root::IO->catfile("t", "data", "arath_small-02.xml"));
+ -file => test_input_file("arath_small-02.xml"));
ok $g1 = $io->next_network();
ok $g1->nodes == 73;
ok $g1->interactions == 516;
Modified: bioperl-network/trunk/t/Graph-MD5.t
===================================================================
--- bioperl-network/trunk/t/Graph-MD5.t 2009-01-22 10:50:52 UTC (rev 15429)
+++ bioperl-network/trunk/t/Graph-MD5.t 2009-01-22 11:07:51 UTC (rev 15430)
@@ -2,16 +2,12 @@
# Bioperl Test Harness Script for Modules#
# $Id$
-use vars qw($NUMTESTS $DEBUG $ERROR);
use strict;
-$DEBUG = $ENV{'BIOPERLDEBUG'} || 0;
BEGIN {
-
- use lib ".";
use Bio::Root::Test;
test_begin(-tests => 23,
- -requires_module => 'Digest::MD5' );
+ -requires_module => 'Digest::MD5');
use_ok('Graph::Undirected');
}
Modified: bioperl-network/trunk/t/Graph-Seq.t
===================================================================
--- bioperl-network/trunk/t/Graph-Seq.t 2009-01-22 10:50:52 UTC (rev 15429)
+++ bioperl-network/trunk/t/Graph-Seq.t 2009-01-22 11:07:51 UTC (rev 15430)
@@ -2,16 +2,12 @@
# Bioperl Test Harness Script for Modules#
# $Id$
-use vars qw($NUMTESTS $DEBUG $ERROR);
use strict;
-$DEBUG = $ENV{'BIOPERLDEBUG'} || 0;
BEGIN {
-
- use lib ".";
use Bio::Root::Test;
test_begin(-tests => 21,
- -requires_module => 'Graph');
+ -requires_module => 'Graph');
use_ok('Graph::Undirected');
use_ok('Graph::Traversal::DFS');
Modified: bioperl-network/trunk/t/IO_dip_tab.t
===================================================================
--- bioperl-network/trunk/t/IO_dip_tab.t 2009-01-22 10:50:52 UTC (rev 15429)
+++ bioperl-network/trunk/t/IO_dip_tab.t 2009-01-22 11:07:51 UTC (rev 15430)
@@ -2,16 +2,12 @@
# Bioperl Test Harness Script for Modules
# $Id$
-use vars qw($NUMTESTS $DEBUG $ERROR);
use strict;
-$DEBUG = $ENV{'BIOPERLDEBUG'} || 0;
BEGIN {
-
- use lib ".";
use Bio::Root::Test;
- test_begin(-tests => 20,
- -requires_module => 'Graph');
+ test_begin(-tests => 19,
+ -requires_module => 'Graph');
use_ok('Bio::Network::IO');
use_ok('Bio::Network::Edge');
@@ -19,17 +15,14 @@
use_ok('Bio::Seq');
}
-my $verbose = 0;
-$verbose = 1 if $DEBUG;
+my $verbose = test_debug();
-ok 1;
-
#
# read new DIP format
#
my $io = Bio::Network::IO->new(
-format => 'dip_tab',
- -file => Bio::Root::IO->catfile("t","data","tab4part.tab"));
+ -file => test_input_file("tab4part.tab"));
my $g1 = $io->next_network();
ok $g1->edges == 5;
ok $g1->vertices == 7;
@@ -38,7 +31,7 @@
#
$io = Bio::Network::IO->new(
-format => 'dip_tab',
- -file => Bio::Root::IO->catfile("t","data","tab1part.tab"),
+ -file => test_input_file("tab1part.tab"),
-threshold => 0.6);
ok(defined $io);
ok $g1 = $io->next_network();
@@ -54,9 +47,10 @@
#
# test write to filehandle...
#
+my $out_file = test_output_file();
my $out = Bio::Network::IO->new(
-format => 'dip_tab',
- -file => ">". Bio::Root::IO->catfile("t","data","out.tab"));
+ -file => ">".$out_file);
ok(defined $out);
ok $out->write_network($g1);
#
@@ -64,7 +58,7 @@
#
my $io2 = Bio::Network::IO->new(
-format => 'dip_tab',
- -file => Bio::Root::IO->catfile("t","data","out.tab"));
+ -file => $out_file);
ok defined $io2;
ok my $g2 = $io2->next_network();
ok $node = $g2->get_nodes_by_id('PIR:A64696');
Modified: bioperl-network/trunk/t/IO_psi10.t
===================================================================
--- bioperl-network/trunk/t/IO_psi10.t 2009-01-22 10:50:52 UTC (rev 15429)
+++ bioperl-network/trunk/t/IO_psi10.t 2009-01-22 11:07:51 UTC (rev 15430)
@@ -2,32 +2,25 @@
# Bioperl Test Harness Script for Modules#
# $Id$
-use vars qw($NUMTESTS $DEBUG $ERROR);
use strict;
-$DEBUG = $ENV{'BIOPERLDEBUG'} || 0;
BEGIN {
-
- use lib ".";
use Bio::Root::Test;
- test_begin(-tests => 22,
- -requires_module => 'Graph',
- -requires_module => 'XML::Twig' );
+ test_begin(-tests => 21,
+ -requires_module => 'Graph',
+ -requires_module => 'XML::Twig');
use_ok('Bio::Network::IO');
}
-my $verbose = 0;
-$verbose = 1 if $DEBUG;
+my $verbose = test_debug();
-ok 1;
-
#
# PSI XML from DIP
#
ok my $io = Bio::Network::IO->new
(-format => 'psi10',
- -file => Bio::Root::IO->catfile("t", "data", "psi_xml.dat"));
+ -file => test_input_file("psi_xml.dat"));
ok my $g1 = $io->next_network();
ok $g1->edge_count == 3;
ok $g1->node_count == 4;
@@ -47,7 +40,7 @@
#
ok $io = Bio::Network::IO->new
(-format => 'psi10',
- -file => Bio::Root::IO->catfile("t", "data", "sv40_small.xml"));
+ -file => test_input_file("sv40_small.xml"));
ok $g1 = $io->next_network();
ok $g1->edge_count == 3;
ok $g1->node_count == 5;
@@ -81,7 +74,7 @@
#
ok $io = Bio::Network::IO->new
(-format => 'psi10',
- -file => Bio::Root::IO->catfile("t", "data", "00001.xml"));
+ -file => test_input_file("00001.xml"));
# ok $g1 = $io->next_network();
# The individual files from HPRD are not standard PSI, problems parsing them
Modified: bioperl-network/trunk/t/IO_psi25.t
===================================================================
--- bioperl-network/trunk/t/IO_psi25.t 2009-01-22 10:50:52 UTC (rev 15429)
+++ bioperl-network/trunk/t/IO_psi25.t 2009-01-22 11:07:51 UTC (rev 15430)
@@ -2,31 +2,25 @@
# Bioperl Test Harness Script for Modules#
# $Id$
-use vars qw($NUMTESTS $DEBUG $ERROR);
use strict;
-$DEBUG = $ENV{'BIOPERLDEBUG'} || 0;
BEGIN {
- use lib ".";
use Bio::Root::Test;
- test_begin(-tests => 10,
- -requires_module => 'Graph',
- -requires_module => 'XML::Twig' );
+ test_begin(-tests => 9,
+ -requires_module => 'Graph',
+ -requires_module => 'XML::Twig');
use_ok('Bio::Network::IO');
}
-my $verbose = 0;
-$verbose = 1 if $DEBUG;
+my $verbose = test_debug();
-ok 1;
-
#
# PSI XML from IntAct
#
ok my $io = Bio::Network::IO->new
(-format => 'psi25',
- -file => Bio::Root::IO->catfile("t", "data", "human_small-01.xml"),
+ -file => test_input_file("human_small-01.xml"),
-verbose => $verbose );
ok my $g1 = $io->next_network();
ok $g1->node_count == 646;
@@ -37,7 +31,7 @@
#
ok $io = Bio::Network::IO->new
(-format => 'psi25',
- -file => Bio::Root::IO->catfile("t", "data", "Viruses.psi25.xml"),
+ -file => test_input_file("Viruses.psi25.xml"),
-verbose => $verbose );
ok $g1 = $io->next_network();
ok $g1->node_count == 521;
Modified: bioperl-network/trunk/t/Interaction.t
===================================================================
--- bioperl-network/trunk/t/Interaction.t 2009-01-22 10:50:52 UTC (rev 15429)
+++ bioperl-network/trunk/t/Interaction.t 2009-01-22 11:07:51 UTC (rev 15430)
@@ -2,15 +2,12 @@
# Bioperl Test Harness Script for Modules
# $Id$
-use vars qw($NUMTESTS $DEBUG $ERROR);
use strict;
-$DEBUG = $ENV{'BIOPERLDEBUG'} || 0;
BEGIN {
- use lib ".";
use Bio::Root::Test;
- test_begin(-tests => 23,
- -requires_module => 'Graph');
+ test_begin(-tests => 22,
+ -requires_module => 'Graph');
use_ok('Bio::Network::ProteinNet');
use_ok('Bio::Network::Interaction');
@@ -20,11 +17,8 @@
use_ok('Bio::Annotation::OntologyTerm');
}
-my $verbose = 0;
-$verbose = 1 if $DEBUG;
+my $verbose = test_debug();
-ok 1;
-
my $g = Bio::Network::ProteinNet->new();
my $seq1 = Bio::Seq->new(-seq => "aaaaaaa");
Modified: bioperl-network/trunk/t/Node.t
===================================================================
--- bioperl-network/trunk/t/Node.t 2009-01-22 10:50:52 UTC (rev 15429)
+++ bioperl-network/trunk/t/Node.t 2009-01-22 11:07:51 UTC (rev 15430)
@@ -2,26 +2,20 @@
# Bioperl Test Harness Script for Modules
# $Id$
-use vars qw($NUMTESTS $DEBUG $ERROR);
use strict;
-$DEBUG = $ENV{'BIOPERLDEBUG'} || 0;
BEGIN {
- use lib ".";
use Bio::Root::Test;
- test_begin(-tests => 33,
- -requires_module => 'Graph');
@@ Diff output truncated at 10000 characters. @@
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