Minor edits

bioperl · Oct 10, 2011 · c360fe1 · c360fe1
1 parent f135c87
commit c360fe1
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Showing 2 changed files with 7 additions and 13 deletions.
diff --git a/t/Njtree.t b/t/Njtree.t
@@ -1,7 +1,6 @@
 # This is -*-Perl-*- code
 ## Bioperl Test Harness Script for Modules
 ##
-# $Id$
 
 # Before `make install' is performed this script should be runnable with
 # `make test'. After `make install' it should work as `perl test.t'
@@ -25,13 +24,11 @@ SKIP: {
 			  -tests => 1);
 
 	my $alignio = Bio::AlignIO->new(-format => 'fasta',
-									-file   => 't/data/njtree_aln2.nucl.mfa');
-
+									-file   => test_input_file('njtree_aln2.nucl.mfa'));
 	my $aln = $alignio->next_aln;
 
 	my $treeio = Bio::TreeIO->new(
-		-format => 'nhx', -file => 't/data/species_tree_njtree.nh');
-
+		-format => 'nhx', -file => test_input_file('species_tree_njtree.nh'));
 	my $tree = $treeio->next_tree;
 
 	$njtree_best->alignment($aln);

diff --git a/t/ProtPars.t b/t/ProtPars.t
@@ -1,6 +1,5 @@
 # -*-Perl-*-
 ## Bioperl Test Harness Script for Modules
-## $Id$
 
 use vars qw($DEBUG );
 $DEBUG = test_debug();
@@ -33,7 +32,6 @@ SKIP: {
 	my $new_outgroup= $tree_factory->outgroup();
 	is $new_outgroup, 3, "set factory parameter";
 
-
 	my $jumble = "7,5";
 	$tree_factory->jumble($jumble);
 
@@ -67,18 +65,17 @@ SKIP: {
 		$tree = $tree_factory->create_tree($aln);
 
 		@nodes = sort { defined $a->id && defined $b->id && $a->id cmp $b->id } $tree->get_nodes();
-		is (scalar(@nodes),5,
-			"creating tree by protpars");
+		is (scalar(@nodes),5, "creating tree by protpars");
 
 		# test name preservation and restoration:
 		@params = ('threshold'=>10,'jumble'=>'7,5',outgroup=>2,'idlength'=>10);
 		$tree_factory = Bio::Tools::Run::Phylo::Phylip::ProtPars->new(@params);
 		$tree_factory->quiet($bequiet);  # Suppress protpars messages to terminal 
 		$inputfilename = test_input_file("longnames.aln");
-		$aln = Bio::AlignIO->new(-file=>$inputfilename, -format=>'clustalw')->next_aln;
-		my ($aln_safe, $ref_name) =$aln->set_displayname_safe(3);
-		$tree = $tree_factory->create_tree($aln_safe);
-		@nodes = sort { $a->id cmp $b->id } $tree->get_nodes();
+		my $aln2 = Bio::AlignIO->new(-file=>$inputfilename, -format=>'clustalw')->next_aln;
+		my ($aln_safe, $ref_name) = $aln2->set_displayname_safe(3);
+		my $tree2 = $tree_factory->create_tree($aln_safe);
+		@nodes = sort { $a->id cmp $b->id } $tree2->get_nodes();
 		is (scalar(@nodes),27,
 			"creating tree by protpars");
 		is ($nodes[12]->id, 'S01',"assign serial names");