Commit 0407b781 authored by Carsten Kemena's avatar Carsten Kemena

adding test

parent 396bb27e
Pipeline #635 failed with stage
in 3 minutes and 37 seconds
......@@ -225,14 +225,14 @@ main(int argc, char *argv[])
fs::path queryDomainFile, querySeqFile, outFile, domainDB;
string prefix;
vector<std::string> q, domains;
//string radsVersion = "2.0.0";
unsigned short nThreads;
po::options_description allOpts("rads " + version + " (C) 2015-2017 Carsten Kemena\nThis program comes with ABSOLUTELY NO WARRANTY;\n\nAllowed options are displayed below.");
po::options_description allOpts("rads " + version + " (C) 2015-2018 Carsten Kemena\nThis program comes with ABSOLUTELY NO WARRANTY;\n\nAllowed options are displayed below.");
po::options_description general("General options");
general.add_options()
("help,h", "Produces this help message")
("db,d", po::value<string>(&prefix)->required(), "The database prefix")
("out,o", po::value<fs::path>(&outFile), "The output file")
("out,o", po::value<fs::path>(&outFile)->value_name("FILE"), "The output file")
("threads,n", po::value<unsigned short>(&nThreads)->default_value(1), "The number of threads to use")
;
......@@ -248,9 +248,9 @@ main(int argc, char *argv[])
fs::path matrixName;
po::options_description scoreOpts("Scoring options");
scoreOpts.add_options()
("matrix,m", po::value<fs::path>(&matrixName), "The domain similarity matrix")
("gop", po::value<int>(&gop)->default_value(-50), "Gap opening costs")
("gep", po::value<int>(&gep)->default_value(-10), "Gap extension costs")
("matrix,m", po::value<fs::path>(&matrixName)->value_name("FILE"), "The domain similarity matrix")
("gop", po::value<int>(&gop)->default_value(-50)->value_name("INT"), "Gap opening costs")
("gep", po::value<int>(&gep)->default_value(-10)->value_name("INT"), "Gap extension costs")
;
bool all;
......
......@@ -36,3 +36,24 @@
rm interPro.db interPro.da
}
@test "run RADS Test - 2" {
run ../../build/makeRadsDB -I ../data/match_small2.xml -o interPro-test -d PFAM
[ $status == 0 ]
run ../../build/rads -D PF00001 PF00002 PF00003 -m pfam-31.dsm -d interPro-test -a -o test2Res.txt
[ $status == 0 ]
run diff <(grep -v '#' test2Res.txt) <(grep -v '#' results/test2Res.txt)
[ $status == 0 ]
run ../../build/rads -D PF00001 PF00002 PF00003 -m pfam-31.dsm -d interPro-test -o test3Res.txt
[ $status == 0 ]
run diff <(grep -v '#' test3Res.txt) <(grep -v '#' results/test3Res.txt)
[ $status == 0 ]
rm interPro-test.db interPro-test.da
}
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