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add skips and a warning re: NeXML v0.9 support

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commit b19ceb2ea7a9b1b1c98333a90e40ed4dd6af6493 1 parent 07aa85f
Chris Fields authored
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130 t/AlignIO/nexml.t
@@ -3,73 +3,75 @@
use strict;
use Bio::Root::Test;
-test_begin( -requires_modules => [qw(Bio::Phylo)]);
+test_begin(-tests => 125, -requires_modules => [qw(Bio::Phylo)]);
use_ok('Bio::AlignIO::nexml'); # checks that your module is there and loads ok
+diag("WARNING: NeXML parsing for NeXML v0.9 is currently very experimental support");
+SKIP: {
+ skip("NeXML parsing for NeXML v0.9 is currently very experimental support", 124);
-
-#Read in Data
-ok( my $inAlnStream = Bio::AlignIO->new(-file => test_input_file("nexml","characters.nexml.xml"),
- -format => 'nexml'), 'make stream');
-
-#Read in aln objects
-ok( my $aln_obj = $inAlnStream->next_aln(), 'nexml matrix to aln' );
-isa_ok($aln_obj, 'Bio::SimpleAlign', 'obj ok');
-is ($aln_obj->id, 'DNA sequences', 'aln id');
-my $num =0;
-my @expected_seqs = ('ACGCTCGCATCGCATC', 'ACGCTCGCATCGCATC', 'ACGCTCGCATCGCATC');
-#checking sequence objects
-foreach my $seq_obj ($aln_obj->each_seq()) {
- $num++;
+ #Read in Data
+ ok( my $inAlnStream = Bio::AlignIO->new(-file => test_input_file("nexml","characters.nexml.xml"),
+ -format => 'nexml'), 'make stream');
+
+ #Read in aln objects
+ ok( my $aln_obj = $inAlnStream->next_aln(), 'nexml matrix to aln' );
+ isa_ok($aln_obj, 'Bio::SimpleAlign', 'obj ok');
+ is ($aln_obj->id, 'DNA sequences', 'aln id');
+ my $num =0;
+ my @expected_seqs = ('ACGCTCGCATCGCATC', 'ACGCTCGCATCGCATC', 'ACGCTCGCATCGCATC');
+ #checking sequence objects
+ foreach my $seq_obj ($aln_obj->each_seq()) {
+ $num++;
+
+ is( $seq_obj->alphabet, 'dna', "alphabet" );
+
+ TODO: {
+ local $TODO = 'primary/display_id broken with NeXML 0.9';
+ is( $seq_obj->display_id, "DNA sequences.row_$num", "display_id");
+ }
+ is( $seq_obj->seq, $expected_seqs[$num-1], "sequence correct");
+ }
+
+ #Write Data
+ diag('Begin tests for write/read roundtrip');
+ my $outdata = test_output_file();
+ ok( my $outAlnStream = Bio::AlignIO->new(-file => ">$outdata", -format => 'nexml'), 'out stream ok');;
+ ok( $outAlnStream->write_aln($aln_obj), 'write nexml');
+ close($outdata);
- is( $seq_obj->alphabet, 'dna', "alphabet" );
- TODO: {
- local $TODO = 'primary/display_id broken with NeXML 0.9';
- is( $seq_obj->display_id, "DNA sequences.row_$num", "display_id");
+ #Read in the written file to test roundtrip
+ ok( my $inAlnStream2 = Bio::AlignIO->new(-file => $outdata, -format => 'nexml'), 'reopen');
+
+ #Read in aln objects
+ ok( my $aln_obj2 = $inAlnStream2->next_aln(),'get aln (rt)' );
+ isa_ok($aln_obj2, 'Bio::SimpleAlign', 'aln obj (rt)');
+ is ($aln_obj2->id, 'DNA sequences', "aln id (rt)");
+ $num =0;
+ @expected_seqs = ('ACGCTCGCATCGCATC', 'ACGCTCGCATCGCATC', 'ACGCTCGCATCGCATC');
+ #checking sequence objects
+ foreach my $seq_obj ($aln_obj2->each_seq()) {
+ $num++;
+
+ is( $seq_obj->alphabet, 'dna', "alphabet (rt)" );
+ is( $seq_obj->display_id, "DNA sequences.row_$num", "display_id (rt)");
+ is( $seq_obj->seq, $expected_seqs[$num-1], "sequence (rt)");
+ }
+ #check taxa object
+ my %expected_taxa = ('DNA sequences.row_1' => 'Homo sapiens',
+ 'DNA sequences.row_2' => 'Pan paniscus',
+ 'DNA sequences.row_3' => 'Pan troglodytes');
+ my @feats = $aln_obj2->get_all_SeqFeatures();
+ foreach my $feat (@feats) {
+ if ($feat->has_tag('taxa_id')){
+ is ( ($feat->get_tag_values('taxa_id'))[0], 'taxa1', 'taxa id ok' );
+ is ( ($feat->get_tag_values('taxa_label'))[0], 'Primary taxa block', 'taxa label ok');
+ is ( $feat->get_tag_values('taxon'), 5, 'Number of taxa ok')
+ }
+ else{
+ my $seq_num = ($feat->get_tag_values('id'))[0];
+ is ( ($feat->get_tag_values('taxon'))[0], $expected_taxa{$seq_num}, "$seq_num taxon ok" )
+ }
}
- is( $seq_obj->seq, $expected_seqs[$num-1], "sequence correct");
-}
-
-#Write Data
-diag('Begin tests for write/read roundtrip');
-my $outdata = test_output_file();
-ok( my $outAlnStream = Bio::AlignIO->new(-file => ">$outdata", -format => 'nexml'), 'out stream ok');;
-ok( $outAlnStream->write_aln($aln_obj), 'write nexml');
-close($outdata);
-
-
-#Read in the written file to test roundtrip
-#ok( my $inAlnStream2 = Bio::AlignIO->new(-file => $outdata, -format => 'nexml'), 'reopen');
-#
-##Read in aln objects
-#ok( my $aln_obj2 = $inAlnStream2->next_aln(),'get aln (rt)' );
-#isa_ok($aln_obj2, 'Bio::SimpleAlign', 'aln obj (rt)');
-#is ($aln_obj2->id, 'DNA sequences', "aln id (rt)");
-#$num =0;
-#@expected_seqs = ('ACGCTCGCATCGCATC', 'ACGCTCGCATCGCATC', 'ACGCTCGCATCGCATC');
-##checking sequence objects
-#foreach my $seq_obj ($aln_obj2->each_seq()) {
-# $num++;
-#
-# is( $seq_obj->alphabet, 'dna', "alphabet (rt)" );
-# is( $seq_obj->display_id, "DNA sequences.row_$num", "display_id (rt)");
-# is( $seq_obj->seq, $expected_seqs[$num-1], "sequence (rt)");
-#}
-##check taxa object
-#my %expected_taxa = ('DNA sequences.row_1' => 'Homo sapiens',
-# 'DNA sequences.row_2' => 'Pan paniscus',
-# 'DNA sequences.row_3' => 'Pan troglodytes');
-#my @feats = $aln_obj2->get_all_SeqFeatures();
-#foreach my $feat (@feats) {
-# if ($feat->has_tag('taxa_id')){
-# is ( ($feat->get_tag_values('taxa_id'))[0], 'taxa1', 'taxa id ok' );
-# is ( ($feat->get_tag_values('taxa_label'))[0], 'Primary taxa block', 'taxa label ok');
-# is ( $feat->get_tag_values('taxon'), 5, 'Number of taxa ok')
-# }
-# else{
-# my $seq_num = ($feat->get_tag_values('id'))[0];
-# is ( ($feat->get_tag_values('taxon'))[0], $expected_taxa{$seq_num}, "$seq_num taxon ok" )
-# }
-#}
-done_testing();
+}
View
46 t/SeqIO/nexml.t
@@ -4,11 +4,13 @@
use strict;
use Bio::Root::Test;
-test_begin(
+test_begin(-tests => 126,
-requires_modules => [qw(Bio::Phylo)]);
use_ok( 'Bio::PrimarySeq' );
use_ok('Bio::SeqIO::nexml'); # checks that your module is there and loads ok
-
+diag("WARNING: NeXML parsing for NeXML v0.9 is currently very experimental support");
+SKIP: {
+ skip("NeXML parsing for NeXML v0.9 is currently very experimental support", 124);
#Read Data
ok( my $SeqStream = Bio::SeqIO->new(
@@ -74,24 +76,24 @@ close($outdata);
diag("write_seq support for NeXML 0.9 NYI");
#Read in the out file to test roundtrip
-#my $inSeqStream = Bio::SeqIO->new(-file => $outdata, -format => 'nexml');
-#
-##checking fifth sequence object
-#ok( my $seq_obj2 = $inSeqStream->next_seq() );
-#is( $seq_obj2->alphabet, 'rna', "alphabet" );
-#is( $seq_obj2->primary_id, 'RNA sequences.seq_2', "primary_id");
-#is( $seq_obj2->display_id, 'RNA sequences.seq_2', "display_id defaults to primary");
-#is( $seq_obj2->seq, 'ACGCUCGCAUCGCAUC', "sequence");
-#
-##check taxa
-#my $feat1 = ($seq_obj2->get_SeqFeatures())[0];
-#is( ($feat1->get_tag_values('taxa_id'))[0], 'taxa1', 'taxa id');
-#is( ($feat1->get_tag_values('taxa_label'))[0], 'Primary taxa block', 'taxa label');
-#is( ($feat1->get_tag_values('my_taxon'))[0], 'Pan paniscus', "taxon ok" );
-#my @taxa2 = $feat1->get_tag_values('taxon');
-#is( @taxa2, 5, 'number of taxa');
-#foreach my $taxon (@taxa2) {
-# ok( $expected_taxa{$taxon}, 'taxon ok')
-#}
+my $inSeqStream = Bio::SeqIO->new(-file => $outdata, -format => 'nexml');
+
+#checking fifth sequence object
+ok( my $seq_obj2 = $inSeqStream->next_seq() );
+is( $seq_obj2->alphabet, 'rna', "alphabet" );
+is( $seq_obj2->primary_id, 'RNA sequences.seq_2', "primary_id");
+is( $seq_obj2->display_id, 'RNA sequences.seq_2', "display_id defaults to primary");
+is( $seq_obj2->seq, 'ACGCUCGCAUCGCAUC', "sequence");
+
+#check taxa
+my $feat1 = ($seq_obj2->get_SeqFeatures())[0];
+is( ($feat1->get_tag_values('taxa_id'))[0], 'taxa1', 'taxa id');
+is( ($feat1->get_tag_values('taxa_label'))[0], 'Primary taxa block', 'taxa label');
+is( ($feat1->get_tag_values('my_taxon'))[0], 'Pan paniscus', "taxon ok" );
+my @taxa2 = $feat1->get_tag_values('taxon');
+is( @taxa2, 5, 'number of taxa');
+foreach my $taxon (@taxa2) {
+ ok( $expected_taxa{$taxon}, 'taxon ok')
+}
-done_testing();
+}
View
2  t/Tree/TreeIO/nexml.t
@@ -10,7 +10,7 @@ use_ok( 'Bio::Tree::Tree' );
use_ok( 'Bio::TreeIO' );
use_ok('Bio::TreeIO::nexml'); # checks that your module is there and loads ok
-
+diag("WARNING: NeXML parsing for NeXML v0.9 is currently very experimental support");
#Read in Data
ok( my $TreeStream = Bio::TreeIO->new(-file => test_input_file('nexml','trees.nexml.xml'), -format => 'nexml') );
View
7 t/nexml.t
@@ -10,8 +10,9 @@ test_begin( -tests=>125,
-requires_modules => [qw(Bio::Phylo)]);
use_ok('Bio::NexmlIO');
-
-
+diag("WARNING: NeXML parsing for NeXML v0.9 is currently very experimental support");
+SKIP: {
+ skip("NeXML parsing for NeXML v0.9 is currently very experimental support", 124);
#Read in Data
my $in_nexmlIO = Bio::NexmlIO->new(-file => test_input_file('characters+trees.nexml.xml'));
@@ -208,4 +209,4 @@ my $in_nexmlIO_roundtrip = Bio::NexmlIO->new(-file => $outdata);
is( $tree->id, $trees_array->[$treeNum-1]->id, "extract_trees roundtrip $treeNum" );
$treeNum++;
}
-
+}
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