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Name "gtpython: genome_stream bindings (output stream)"
Keywords "gt_python"
Test do
run_python "#{$testdata}gtpython/gff3.py #{$testdata}gff3_file_1_short.txt"
run "env LC_ALL=C sort #{last_stdout}"
run "diff #{last_stdout} #{$testdata}gff3_file_1_short_sorted.txt"
end
Name "gtpython: genome_visitor bindings (output stream)"
Keywords "gt_python"
Test do
run_python "#{$testdata}gtpython/genome_visitor.py #{$testdata}gff3_file_1_short.txt"
run "env LC_ALL=C sort #{last_stdout}"
run "diff #{last_stdout} #{$testdata}gff3_file_1_short_sorted.txt"
end
Name "gtpython: feature_index and feature_stream bindings"
Keywords "gt_python"
Test do
run_python "#{$testdata}gtpython/feature_stuff.py " +
"#{$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 $arguments["nocairo"] then
Name "gtpython: AnnotationSketch bindings (valid gff3 file)"
Keywords "gt_python"
Test do
run_python "#{$testdata}gtpython/sketch.py test.png " +
"#{$testdata}gff3_file_1_short.txt"
end
Name "gtpython: AnnotationSketch bindings (corrupt gff3 file)"
Keywords "gt_python"
Test do
run_python("#{$testdata}gtpython/sketch.py test.png #{$testdata}corrupt.gff3",
:retval => 1)
grep last_stderr, "GenomeTools error"
end
Name "gtpython: AnnotationSketch bindings (nonexistent gff3 file)"
Keywords "gt_python"
Test do
run_python("#{$testdata}gtpython/sketch.py test.png " +
"#{$testdata}nonexistent_file", :retval => 1)
grep last_stderr, "GenomeTools error"
end
Name "gtpython: AnnotationSketch bindings (simple sketch)"
Keywords "gt_python"
Test do
run_python "#{$testdata}gtpython/sketch_simple.py test.png " +
"#{$testdata}gff3_file_1_short.txt"
end
Name "gtpython: AnnotationSketch bindings (PNG stream)"
Keywords "gt_python"
Test do
run_python "#{$testdata}gtpython/sketch_stream.py test.png " +
"#{$testdata}gff3_file_1_short.txt"
end
Name "gtpython: AnnotationSketch bindings (TrackSelectorFunc)"
Keywords "gt_python"
Test do
run_python "#{$testdata}gtpython/block_stuff.py " +
"#{$testdata}gff3_file_1_short.txt"
run "env LC_ALL=C sort #{last_stdout}"
run "diff #{last_stdout} #{$testdata}standard_gene_as_tree.blocks"
end
Name "gtpython: AnnotationSketch bindings (style)"
Keywords "gt_python"
Test do
run_python "#{$testdata}gtpython/style.py #{$cur}/gtdata/sketch/default.style"
end
Name "gtpython: AnnotationSketch bindings (error reporting)"
Keywords "gt_python"
Test do
run_python "#{$testdata}gtpython/sketch-failures.py " +
"#{$testdata}gff3_file_1_short.txt"
end
Name "gtpython: AnnotationSketch bindings (Graphics)"
Keywords "gt_python"
Test do
run_python "#{$testdata}gtpython/graphics_stuff.py " +
"#{$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 #{$testdata}graphics_test.out"
end
Name "gtpython: AnnotationSketch bindings (FeatureNode(Iterator))"
Keywords "gt_python"
Test do
run_python "#{$testdata}gtpython/feature_node.py"
end
Name "gtpython: show_seqids"
Keywords "gt_python"
Test do
run_python "#{$testdata}gtpython/show_seqids.py #{$testdata}encode_known_genes_Mar07.gff3"
run "diff #{last_stdout} #{$testdata}encode_known_genes_Mar07.seqids"
end
Name "gtpython: used_types"
Keywords "gt_python"
Test do
run_python "#{$testdata}gtpython/used_types.py " +
"#{$testdata}standard_gene_as_tree.gff3"
run "diff #{last_stdout} #{$testdata}standard_gene_as_tree.types"
end
Name "gtpython: show_recmaps"
Keywords "gt_python showrecmaps"
Test do
run_python "#{$testdata}gtpython/show_recmaps.py " +
"#{$testdata}standard_gene_as_tree.gff3"
run "diff #{last_stdout} #{$testdata}standard_gene_as_tree.hotspots"
end
Name "gtpython: unicode strings"
Keywords "gt_python"
Test do
run_python("#{$testdata}gtpython/unicode_strings.py #{$cur}/gtdata/sketch/default.style test.png")
end
end
Name "gtpython: unittests"
Keywords "gt_python unittests"
Test do
run_python "#{$gtpython}/tests/__init__.py "
grep last_stderr, "OK"
end
|
