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Name "fastdp 01"
Keywords "gth fastdp"
Test do
run_test "#{$bin}gth -genomic #{$testdata}U89959_genomic.fas " +
"-cdna #{$testdata}gth/fastdp_01.fas -fastdp"
end
Name "fastdp (U89959)"
Keywords "gth fastdp"
Test do
run_test "#{$bin}gth -species arabidopsis " +
"-genomic #{$testdata}U89959_genomic.fas " +
"-cdna #{$testdata}U89959_ests.fas -gff3out -intermediate " +
"-fastdp", :maxtime => 300
run "diff --strip-trailing-cr #{$last_stdout} #{$testdata}U89959_sas_fast.gff3"
end
Name "fastdp (U89959, introncutout)"
Keywords "gth fastdp"
Test do
run_test "#{$bin}gth -species arabidopsis " +
"-genomic #{$testdata}U89959_genomic.fas " +
"-cdna #{$testdata}U89959_ests.fas -gff3out -intermediate " +
"-fastdp -introncutout", :maxtime => 300
run "diff --strip-trailing-cr #{$last_stdout} #{$testdata}U89959_sas_fast_ic.gff3"
end
if $gthtestdata then
Name "fastdp (unused)"
Keywords "gth fastdp diss"
Test do
run_test "#{$bin}gth -bssm #{$gthtestdata}ngasp/ngasp -enrichchains " +
"-scoreminexonlen 1 -maskpolyatails -dpminintronlen 10 " +
"-gcmaxgapwidth 22000 -gff3out -intermediate " +
"-genomic #{$gthtestdata}ngasp32/training_regions.fa " +
"-cdna #{$gthtestdata}ngasp32/rna_small.fa", :maxtime => 300
run "diff --strip-trailing-cr #{$last_stdout} #{$gthtestdata}ngasp/rna_small.gff3"
end
Name "fastdp (-fastdp)"
Keywords "gth fastdp diss"
Test do
run_test "#{$bin}gth -bssm #{$gthtestdata}ngasp/ngasp -enrichchains " +
"-scoreminexonlen 1 -maskpolyatails -dpminintronlen 10 " +
"-gcmaxgapwidth 22000 -gff3out -intermediate " +
"-genomic #{$gthtestdata}ngasp32/training_regions.fa " +
"-cdna #{$gthtestdata}ngasp32/rna_small.fa -fastdp",
:maxtime => 120
run "diff --strip-trailing-cr #{$last_stdout} #{$gthtestdata}ngasp/rna_small_fast.gff3"
end
Name "fastdp (-introncutout)"
Keywords "gth fastdp diss"
Test do
run_test "#{$bin}gth -bssm #{$gthtestdata}ngasp/ngasp -enrichchains " +
"-scoreminexonlen 1 -maskpolyatails -dpminintronlen 10 " +
"-gcmaxgapwidth 22000 -gff3out -intermediate " +
"-genomic #{$gthtestdata}ngasp32/training_regions.fa " +
"-cdna #{$gthtestdata}ngasp32/rna_small.fa -introncutout",
:maxtime => 120
run "diff --strip-trailing-cr #{$last_stdout} #{$gthtestdata}ngasp/rna_small_ic.gff3"
end
Name "fastdp (-fastdp -introncutout)"
Keywords "gth fastdp diss"
Test do
run_test "#{$bin}gth -bssm #{$gthtestdata}ngasp/ngasp -enrichchains " +
"-scoreminexonlen 1 -maskpolyatails -dpminintronlen 10 " +
"-gcmaxgapwidth 22000 -gff3out -intermediate " +
"-genomic #{$gthtestdata}ngasp32/training_regions.fa " +
"-cdna #{$gthtestdata}ngasp32/rna_small.fa -fastdp -introncutout"
run "diff --strip-trailing-cr #{$last_stdout} #{$gthtestdata}ngasp/rna_small_fast_ic.gff3"
end
end
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