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if $gthtestdata then
files="-genomic #{$gthtestdata}ngasp32/test_regions.fa " +
"-cdna #{$gthtestdata}ngasp32/rna_matches.fa " +
"-protein #{$gthtestdata}ngasp32/protein_matches.fa"
opts="-bssm #{$gthtestdata}ngasp/ngasp -dpminintronlen 10 " +
"-gcmaxgapwidth 22000 -enrichchains -scoreminexonlen 1 -maskpolyatails"
Name "nGASP (gene prediction, complete)"
Keywords "gth ngasp diss md5ids"
Test do
run "#{$bin}gth #{files} #{opts} -minalignmentscore 0.85 -startcodon yes " +
"-skipalignmentout -gff3out -md5ids -o ngasp.gff3", :maxtime => 3600
run "diff --strip-trailing-cr ngasp.gff3 #{$gthtestdata}ngasp/ngasp.gff3"
end
Name "nGASP (gene prediction, intermediate)"
Keywords "gth ngasp diss md5ids"
Test do
run "#{$bin}gth #{files} #{opts} -intermediate " +
"-xmlout -gzip -o ngasp.inter.gz", :maxtime => 3600
run "#{$bin}gthconsensus -minalignmentscore 0.85 -startcodon yes " +
"-skipalignmentout -gff3out -md5ids " +
"-o ngasp.inter.gff3 ngasp.inter.gz ", :maxtime => 1200
run "diff --strip-trailing-cr ngasp.inter.gff3 #{$gthtestdata}ngasp32/ngasp.inter.gff3"
end
end
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