From 041220fe4b91bcd1765b839949b938906e117294 Mon Sep 17 00:00:00 2001
From: Chris Fields <cjfields@bioperl.org>
Date: Tue, 3 Sep 2013 22:17:27 -0500
Subject: [PATCH] skip tests if Bio::DB::Sam is present but samtools not in
 PATH

---
 t/Assembly/IO/bowtie.t | 138 +++++++++++++++++++++++++------------------------
 1 file changed, 71 insertions(+), 67 deletions(-)
 rewrite t/Assembly/IO/bowtie.t (73%)

diff --git a/t/Assembly/IO/bowtie.t b/t/Assembly/IO/bowtie.t
dissimilarity index 73%
index 581aae562..f51c92265 100644
--- a/t/Assembly/IO/bowtie.t
+++ b/t/Assembly/IO/bowtie.t
@@ -1,67 +1,71 @@
-use strict;
-use warnings;
-my %ASSEMBLY_TESTS;
-
-BEGIN {
-    use lib '.';
-    use Bio::Root::Test;
-
-    test_begin( -tests => 796,
-                -requires_modules => [
-                    'DB_File',
-                    'Bio::DB::Sam',
-                    'Bio::Tools::Run::Samtools',
-                   ],
-               );
-
-    use_ok('Bio::Seq');
-    use_ok('Bio::LocatableSeq');
-    use_ok('Bio::Seq::Quality');
-    use_ok('Bio::Assembly::IO');
-    use_ok('Bio::Assembly::Singlet');
-
-}
-
-use Bio::Root::IO;
-
-my ($aio, $assembly, @contig_seq_ids, @singlet_ids, @contig_ids, @all_seq_ids);
-
-my $file = 'test.bowtie';
-my $refdb = 'test.ref.fas';
-ok $aio = Bio::Assembly::IO->new( -file => test_input_file($file),
-                  -index => test_input_file($refdb),
-                  -format => 'bowtie' ), "init bowtie IO object";
-isa_ok($aio, 'Bio::Assembly::IO');
-$aio->_current_refseq_id( ($aio->sam->seq_ids)[0] ); # kludge
-
-while (my $contig = $aio->next_contig) {
-isa_ok($contig, 'Bio::Assembly::Contig');
-}
-ok $aio = Bio::Assembly::IO->new( -file => test_input_file($file),
-                  -index => test_input_file($refdb),
-                  -format => 'bowtie' ),"reopen";
-ok $assembly = $aio->next_assembly, "get sam assy";
-is( $assembly->get_nof_contigs, 23, "got all contigs");
-
-ok(@contig_seq_ids = $assembly->get_contig_seq_ids, "get_contig_seq_ids");
-is(@contig_seq_ids, 312);
-for my $contig_seq_id (@contig_seq_ids) {
-ok ($contig_seq_id =~ m/^SRR/i);
-}
-ok(@contig_ids = $assembly->get_contig_ids, "get_contig_ids");
-is(@contig_ids, 23);
-for my $contig_id (@contig_ids) {
-ok ($contig_id =~ m/sam_assy/i);
-}
-ok(@singlet_ids = $assembly->get_singlet_ids, "get_singlet_ids");
-is(@singlet_ids, 36);
-for my $singlet_id (@singlet_ids) {
-ok ($singlet_id =~ m/^sam_assy/i);
-}
-ok(@all_seq_ids = $assembly->get_all_seq_ids, "get_all_seq_ids");
-for my $seq_id (@all_seq_ids) {
-ok ($seq_id =~ m/^SRR/i);
-}
-is(@all_seq_ids, 348);
-
-exit;
+use strict;
+use warnings;
+my %ASSEMBLY_TESTS;
+
+BEGIN {
+    use lib '.';
+    use Bio::Root::Test;
+
+    test_begin( -tests => 796,
+                -requires_modules => [
+                    'DB_File',
+                    'Bio::DB::Sam',
+                    'Bio::Tools::Run::Samtools',
+                   ],
+               );
+
+    use_ok('Bio::Seq');
+    use_ok('Bio::LocatableSeq');
+    use_ok('Bio::Seq::Quality');
+    use_ok('Bio::Assembly::IO');
+    use_ok('Bio::Assembly::Singlet');
+
+}
+
+use Bio::Root::IO;
+
+SKIP: {
+    skip("SAMTOOLSDIR not set, skipping", 791) unless exists $ENV{SAMTOOLSDIR};
+
+    my ($aio, $assembly, @contig_seq_ids, @singlet_ids, @contig_ids, @all_seq_ids);
+
+    my $file = 'test.bowtie';
+    my $refdb = 'test.ref.fas';
+    ok $aio = Bio::Assembly::IO->new( -file => test_input_file($file),
+                      -index => test_input_file($refdb),
+                      -format => 'bowtie' ), "init bowtie IO object";
+    isa_ok($aio, 'Bio::Assembly::IO');
+    $aio->_current_refseq_id( ($aio->sam->seq_ids)[0] ); # kludge
+
+    while (my $contig = $aio->next_contig) {
+    isa_ok($contig, 'Bio::Assembly::Contig');
+    }
+    ok $aio = Bio::Assembly::IO->new( -file => test_input_file($file),
+                      -index => test_input_file($refdb),
+                      -format => 'bowtie' ),"reopen";
+    ok $assembly = $aio->next_assembly, "get sam assy";
+    is( $assembly->get_nof_contigs, 23, "got all contigs");
+
+    ok(@contig_seq_ids = $assembly->get_contig_seq_ids, "get_contig_seq_ids");
+    is(@contig_seq_ids, 312);
+    for my $contig_seq_id (@contig_seq_ids) {
+    ok ($contig_seq_id =~ m/^SRR/i);
+    }
+    ok(@contig_ids = $assembly->get_contig_ids, "get_contig_ids");
+    is(@contig_ids, 23);
+    for my $contig_id (@contig_ids) {
+    ok ($contig_id =~ m/sam_assy/i);
+    }
+    ok(@singlet_ids = $assembly->get_singlet_ids, "get_singlet_ids");
+    is(@singlet_ids, 36);
+    for my $singlet_id (@singlet_ids) {
+    ok ($singlet_id =~ m/^sam_assy/i);
+    }
+    ok(@all_seq_ids = $assembly->get_all_seq_ids, "get_all_seq_ids");
+    for my $seq_id (@all_seq_ids) {
+    ok ($seq_id =~ m/^SRR/i);
+    }
+    is(@all_seq_ids, 348);
+
+}
+exit;
-- 
2.11.4.GIT