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|
Name "gtruby: genome_stream bindings (output stream)"
Keywords "gt_ruby"
Test do
run_ruby "#{$testdata}gtruby/gff3.rb #{$testdata}gff3_file_1_short.txt"
run "env LC_ALL=C sort #{last_stdout}"
run "diff #{last_stdout} #{$testdata}gff3_file_1_short_sorted.txt"
end
Name "gtruby: genome_visitor bindings (output stream)"
Keywords "gt_ruby"
Test do
run_ruby "#{$testdata}gtruby/genome_visitor.rb #{$testdata}gff3_file_1_short.txt"
run "env LC_ALL=C sort #{last_stdout}"
run "diff #{last_stdout} #{$testdata}gff3_file_1_short_sorted.txt"
end
Name "gtruby: feature_index and feature_stream bindings"
Keywords "gt_ruby"
Test do
run_ruby "#{$testdata}gtruby/feature_stuff.rb " +
"#{$testdata}gff3_file_1_short.txt"
run "env LC_ALL=C sort #{last_stdout}"
run "grep -v '^##sequence-region' #{$testdata}gff3_file_1_short_sorted.txt | diff #{last_stdout} -"
end
if not $arguments["nocairo"] then
Name "gtruby: AnnotationSketch bindings (valid gff3 file)"
Keywords "gt_ruby"
Test do
run_ruby "#{$testdata}gtruby/sketch.rb test.png " +
"#{$testdata}gff3_file_1_short.txt"
end
Name "gtruby: AnnotationSketch bindings (corrupt gff3 file)"
Keywords "gt_ruby"
Test do
run_ruby("#{$testdata}gtruby/sketch.rb test.png #{$testdata}corrupt.gff3",
:retval => 1)
grep last_stderr, "GenomeTools error"
end
Name "gtruby: AnnotationSketch bindings (nonexistent gff3 file)"
Keywords "gt_ruby"
Test do
run_ruby("#{$testdata}gtruby/sketch.rb test.png " +
"#{$testdata}nonexistent_file", :retval => 1)
grep last_stderr, "GenomeTools error"
end
Name "gtruby: AnnotationSketch bindings (PNG stream)"
Keywords "gt_ruby"
Test do
run_ruby "#{$testdata}gtruby/sketch_stream.rb test.png " +
"#{$testdata}gff3_file_1_short.txt"
end
Name "gtruby: AnnotationSketch bindings (TrackSelectorFunc)"
Keywords "gt_ruby"
Test do
run_ruby "#{$testdata}gtruby/block_stuff.rb " +
"#{$testdata}gff3_file_1_short.txt"
run "env LC_ALL=C sort #{last_stdout}"
run "diff #{last_stdout} #{$testdata}standard_gene_as_tree.blocks"
end
Name "gtruby: AnnotationSketch bindings (style)"
Keywords "gt_ruby"
Test do
run_ruby "#{$testdata}gtruby/style.rb #{$cur}/gtdata/sketch/default.style"
end
Name "gtruby: AnnotationSketch bindings (error reporting)"
Keywords "gt_ruby"
Test do
run_ruby "#{$testdata}gtruby/sketch-failures.rb " +
"#{$testdata}gff3_file_1_short.txt"
end
Name "gtruby: AnnotationSketch bindings (Graphics)"
Keywords "gt_ruby"
Test do
run_ruby "#{$testdata}gtruby/graphics_stuff.rb " +
"#{$testdata}graphics_curve_test_coords.txt " +
"out.svg"
# will fail e.g. if cairo toy font setup is different from test machine
# disabled for now
# run "diff out.svg #{$testdata}graphics_test.out"
end
Name "gtruby: AnnotationSketch bindings (FeatureNode(Iterator))"
Keywords "gt_ruby"
Test do
run_ruby "#{$testdata}gtruby/feature_node.rb"
end
Name "gtruby: show_recmaps"
Keywords "gt_ruby showrecmaps"
Test do
run_ruby "#{$testdata}gtruby/show_recmaps.rb " +
"#{$testdata}standard_gene_as_tree.gff3"
run "diff #{last_stdout} #{$testdata}standard_gene_as_tree.hotspots"
end
end
Name "gtruby: Encseq bindings"
Keywords "gt_ruby"
Test do
run_ruby "#{$testdata}gtruby/encseq.rb"
end
Name "gtruby: show_seqids"
Keywords "gt_ruby"
Test do
run_ruby "#{$testdata}gtruby/show_seqids.rb #{$testdata}encode_known_genes_Mar07.gff3"
run "diff #{last_stdout} #{$testdata}encode_known_genes_Mar07.seqids"
end
Name "gtruby: used_types"
Keywords "gt_ruby"
Test do
run_ruby "#{$testdata}gtruby/used_types.rb " +
"#{$testdata}standard_gene_as_tree.gff3"
run "diff #{last_stdout} #{$testdata}standard_gene_as_tree.types"
end
Name "gtruby: {Comment,Sequence,Region,Meta,EOF}Node classes"
Keywords "gt_ruby"
Test do
run_ruby "#{$testdata}gtruby/node_types.rb"
end
Name "gtruby: CustomStream/CustomVisitor basic tests"
Keywords "gt_ruby"
Test do
run_ruby "#{$testdata}gtruby/custom_stuff.rb #{$testdata}eden.gff3"
run "diff #{last_stdout} #{$testdata}custom_streams_ref.txt"
end
Name "gtruby: CustomStream/CustomVisitor all node types"
Keywords "gt_ruby"
Test do
run_ruby "#{$testdata}gtruby/custom_visitor.rb"
end
Name "gtruby: Range class"
Keywords "gt_ruby"
Test do
run_ruby "#{$testdata}gtruby/range.rb"
end
Name "gtruby: TypeChecker class"
Keywords "gt_ruby"
Test do
run_ruby "#{$testdata}gtruby/type_checker.rb #{$cur}/gtdata/obo_files/so.obo"
end
Name "gtruby: TypeChecker class (failure)"
Keywords "gt_ruby"
Test do
run_ruby "#{$testdata}gtruby/type_checker.rb #{$gtdata}/obo_files/so", :retval => 1
end
|
