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Name "gthbssmtrain (examples from manual)"
Keywords "gthbssmtrain"
Test do
run_test "#{$bin}gth -genomic #{$testdata}U89959_genomic.fas " +
"-cdna #{$testdata}U89959_ests.fas -gff3out -skipalignmentout " +
"-md5ids -o arab.gff3", :maxtime => 600
run "diff --strip-trailing-cr arab.gff3 #{$testdata}arab.gff3"
run_test "#{$bin}gthbssmtrain -seed 1238225656 " +
"-seqfile #{$testdata}U89959_genomic.fas arab.gff3"
run_test "#{$bin}gthbssmbuild -gtdonor -agacceptor -datapath training_data " +
"-bssmfile arab.bssm"
run "diff --strip-trailing-cr arab.bssm #{$testdata}arab.bssm"
run_test "#{$bin}gth -bssm arab -genomic #{$testdata}U89959_genomic.fas " +
"-cdna #{$testdata}U89959_ests.fas", :maxtime => 300
end
Name "gthbssmtrain (file, no introns)"
Keywords "gthbssmtrain"
Test do
run_test "#{$bin}gthbssmtrain -seqfile #{$testdata}U89959_genomic.fas " +
"-matchdesc -seed 913609837 #{$testdata}U89959_csas.gff3"
run "diff --strip-trailing-cr #{$last_stdout} #{$testdata}gthbssmtrain.out"
run "rm -f training_data/gthbssmtrain.run"
run "diff --strip-trailing-cr -r training_data #{$testdata}training_data"
end
Name "gthbssmtrain (file, introns)"
Keywords "gthbssmtrain"
Test do
run_test "#{$bin}gthbssmtrain -seqfile #{$testdata}U89959_genomic.fas " +
"-matchdesc -seed 913609837 #{$testdata}U89959_csas_introns.gff3"
run "diff --strip-trailing-cr #{$last_stdout} #{$testdata}gthbssmtrain.out"
run "rm -f training_data/gthbssmtrain.run"
run "diff --strip-trailing-cr -r training_data #{$testdata}training_data"
end
Name "gthbssmtrain (stdin, no introns)"
Keywords "gthbssmtrain"
Test do
run_test "gt gff3 " +
"#{$testdata}U89959_csas.gff3 | " +
"#{$bin}gthbssmtrain -seqfile #{$testdata}U89959_genomic.fas " +
"-matchdesc -seed 913609837 -"
run "diff --strip-trailing-cr #{$last_stdout} #{$testdata}gthbssmtrain.out"
run "rm -f training_data/gthbssmtrain.run"
run "diff --strip-trailing-cr -r training_data #{$testdata}training_data"
end
Name "gthbssmtrain (stdin, introns)"
Keywords "gthbssmtrain"
Test do
run_test "gt gff3 " +
"#{$testdata}U89959_csas_introns.gff3 | " +
"#{$bin}gthbssmtrain -seqfile #{$testdata}U89959_genomic.fas " +
"-matchdesc -seed 913609837 -"
run "diff --strip-trailing-cr #{$last_stdout} #{$testdata}gthbssmtrain.out"
run "rm -f training_data/gthbssmtrain.run"
run "diff --strip-trailing-cr -r training_data #{$testdata}training_data"
end
Name "gthbssmtrain (short intron)"
Keywords "gthbssmtrain"
Test do
run_test "#{$bin}gthbssmtrain -seqfile #{$testdata}U89959_genomic.fas " +
"-matchdesc #{$testdata}short_intron.gff3"
grep $last_stderr, "ignoring intron of length < 2 for sequence ID " +
"'md5:063b1024d68e26716b7f38caf958316f:1877523'"
end
if $gthtestdata then
Name "gthbssmtrain (arabidopsis)"
Keywords "gthbssmtrain"
Test do
run_test "gt gff3 -sort " +
"#{$gthtestdata}gthbssmtrain/22329272.gff3 " +
"#{$gthtestdata}gthbssmtrain/22330780.gff3"
run_test "gt csa #{$last_stdout}"
run_test "gt cds -regionmapping " +
"#{$gthtestdata}gthbssmtrain/mapping.lua -minorflen 1 " +
"-startcodon yes -finalstopcodon yes #{$last_stdout}",
:maxtime => 300
run "diff --strip-trailing-cr #{$last_stdout} #{$gthtestdata}gthbssmtrain/bssmtrain_input.gff3"
FileUtils.mkdir_p("training_data")
run_test "#{$bin}gthbssmtrain " +
"-gcdonor no -goodexoncount 3 " +
"-seed 4067582214 -intermediate -regionmapping " +
"#{$gthtestdata}gthbssmtrain/mapping.lua "+
"#{$gthtestdata}gthbssmtrain/bssmtrain_input.gff3"
run "rm -f training_data/gthbssmtrain.run"
run "diff --strip-trailing-cr -r training_data #{$gthtestdata}gthbssmtrain/training_data"
end
Name "gthbssmtrain (22329272 input)"
Keywords "gthbssmtrain"
Test do
run_test "#{$bin}gth -species arabidopsis -introncutout " +
"-genomic #{$gthtestdata}gthbssmtrain/22329272.fas " +
"-cdna #{$testdata}U89959_ests.fas -intermediate -gff3out",
:maxtime => 300
run "diff --strip-trailing-cr #{$last_stdout} #{$gthtestdata}gthbssmtrain/22329272.gff3"
end
Name "gthbssmtrain (22330780 input)"
Keywords "gthbssmtrain"
Test do
run_test "#{$bin}gth -species arabidopsis -introncutout " +
"-genomic #{$gthtestdata}gthbssmtrain/22330780.fas " +
"-cdna #{$testdata}U89959_ests.fas -intermediate -gff3out",
:maxtime => 300
run "diff --strip-trailing-cr #{$last_stdout} #{$gthtestdata}gthbssmtrain/22330780.gff3"
end
end
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