standardized tests

svn path=/bioperl-run/trunk/; revision=12912

t/Clustalw.t

@@ -1,3 +1,4 @@
+# -*-Perl-*-
 ## Bioperl Test Harness Script for Modules
 ##
 
@@ -23,7 +24,6 @@ BEGIN { $| = 1; print "1..9\n";
 	use vars qw($loaded); }
 # Modify following line as required to point to clustalw program directory on your system
 BEGIN { 
-    #$ENV{CLUSTALDIR} = '/home/peter/clustalw1.8/' if( !defined $ENV{CLUSTALDIR} ); 
 }
 
 END {print "not ok 1\n" unless $loaded;}
@@ -134,7 +134,3 @@ my $seq = $str2->next_seq();
 $aln = $factory->profile_align($aln1,$seq);
 
 test 9, $aln->{order}->{'1'} eq 'CATH_HUMAN-1-335', "failed adding new sequence to alignment";
-
-
-
-

t/TCoffee.t

@@ -0,0 +1,134 @@
+# -*-Perl-*-
+## Bioperl Test Harness Script for Modules
+##
+
+
+# Before `make install' is performed this script should be runnable with
+# `make test'. After `make install' it should work as `perl test.t'
+
+#-----------------------------------------------------------------------
+## perl test harness expects the following output syntax only!
+## 1..3
+## ok 1  [not ok 1 (if test fails)]
+## 2..3
+## ok 2  [not ok 2 (if test fails)]
+## 3..3
+## ok 3  [not ok 3 (if test fails)]
+##
+## etc. etc. etc. (continue on for each tested function in the .t file)
+#-----------------------------------------------------------------------
+
+
+## We start with some black magic to print on failure.
+BEGIN { $| = 1; print "1..9\n";
+	use vars qw($loaded); }
+# Modify following line as required to point to tcoffee program directory on your system
+BEGIN { 
+
+}
+
+END {print "not ok 1\n" unless $loaded;}
+
+use Bio::Tools::Alignment::TCoffee;
+use Bio::SimpleAlign;
+use Bio::AlignIO;
+use Bio::SeqIO;
+use strict;
+
+$loaded = 1;
+print "ok 1\n";    # 1st test passes.
+
+
+## End of black magic.
+##
+## Insert additional test code below but remember to change
+## the print "1..x\n" in the BEGIN block to reflect the
+## total number of tests that will be run. 
+
+
+sub test ($$;$) {
+    my($num, $true,$msg) = @_;
+    print($true ? "ok $num\n" : "not ok $num $msg\n");
+}
+
+## Create tcoffee alignment factory
+my @params = ('ktuple' => 2, 'matrix' => 'BLOSUM');
+my  $factory = Bio::Tools::Alignment::TCoffee->new(@params);
+
+test 2, $factory, " couldn't create alignment factory";
+
+## Set parameter test
+
+my $ktuple = 3;
+$factory->ktuple($ktuple);
+
+my $new_ktuple = $factory->ktuple();
+test 3, $new_ktuple == 3, " couldn't set factory parameter";
+
+## Get parameter test
+
+my $what_matrix = $factory->matrix();
+test 4, $what_matrix eq 'BLOSUM', "couldn't get factory parameter";
+
+## Alignment test (from fasta file)
+my $bequiet = 1;
+$factory->quiet($bequiet);  # Suppress tcoffee messages to terminal
+
+my $inputfilename = 't/cysprot.fa';
+my $aln;
+
+# If the tcoffee program isn't found and executable at the expected location,
+# there is no point in executing the remaining tests...
+
+my $coffee_present = Bio::Tools::Alignment::TCoffee->exists_tcoffee();
+unless ($coffee_present) {
+	warn "tcoffee program not found. Skipping tests 5 to 9.\n";
+    	print "ok 5\n", "ok 6\n", "ok 7\n", "ok 8\n", "ok 9\n";
+	exit 0;
+}
+$aln = $factory->align($inputfilename);
+
+test 5, $aln->{order}->{'0'} eq 'CYS1_DICDI-1-343', "failed tcoffee alignment using input file";
+## Alignment test (from BioSeq array)
+
+my $str = Bio::SeqIO->new(-file=> 't/cysprot.fa', '-format' => 'Fasta');
+my @seq_array =();
+
+while ( my $seq = $str->next_seq() ) {
+    push (@seq_array, $seq) ;
+}
+
+my $seq_array_ref = \@seq_array;
+
+$aln = $factory->align($seq_array_ref);
+
+test 6,$aln->{order}->{'0'} eq 'CYS1_DICDI-1-343', "failed tcoffee alignment using BioSeq array ";
+
+## Profile alignment test (from alignment files)
+
+
+my $profile1 = 't/cysprot1a.msf';
+my $profile2 = 't/cysprot1b.msf';
+$aln = $factory->profile_align($profile1,$profile2);
+
+test 7, $aln->{order}->{'1'} eq 'CATL_HUMAN-1-333', " failed tcoffee profile alignment using input file ". $aln->{order}->{'1'} ;
+
+## Profile alignment test (from SimpleAlign objects)
+
+my $str1 = Bio::AlignIO->new(-file=> 't/cysprot1a.msf');
+my $aln1 = $str1->next_aln();
+my $str2 = Bio::AlignIO->new(-file=> 't/cysprot1b.msf');
+my $aln2 = $str2->next_aln();
+
+$aln = $factory->profile_align($aln1,$aln2);
+test 8, $aln->{order}->{'1'} eq 'CATL_HUMAN-1-333', "failed tcoffee profile alignment using SimpleAlign input ". $aln->{order}->{'1'};
+
+## Test aligning (single) new sequence to an alignment
+
+$str1 = Bio::AlignIO->new(-file=> 't/cysprot1a.msf');
+$aln1 = $str1->next_aln();
+$str2 = Bio::SeqIO->new(-file=> 't/cysprot1b.fa');
+my $seq = $str2->next_seq();
+$aln = $factory->profile_align($aln1,$seq);
+
+test 9, $aln->{order}->{'1'} eq 'CATH_RAT-1-333', "failed adding new sequence to alignment ". $aln->{order}->{'1'};