Commit 968f4d6e authored by Shayan Doust's avatar Shayan Doust
Browse files

Fix test_bestalphabet binary. Now works. 

This is used within autopkgtest
parent cf05c791

debian/patches/fix_tests.patch

+26 −2
Original line number Diff line number Diff line
@@ -6,8 +6,8 @@ Last-Update: 2019-07-20 


Index: mmseqs2/src/test/TestScoreMatrixSerialization.cpp

===================================================================

--- mmseqs2.orig/src/test/TestScoreMatrixSerialization.cpp	2019-07-20 16:32:20.107321242 +0100

+++ mmseqs2/src/test/TestScoreMatrixSerialization.cpp	2019-07-20 16:32:58.363643912 +0100

--- mmseqs2.orig/src/test/TestScoreMatrixSerialization.cpp	2019-07-20 17:51:23.891331720 +0100

+++ mmseqs2/src/test/TestScoreMatrixSerialization.cpp	2019-07-20 17:51:23.879331619 +0100

@@ -18,10 +18,12 @@

     ScoreMatrix* unserialized = ScoreMatrix::unserialize(serialized, subMat.alphabetSize, 3);
@@ -25,3 +25,27 @@ Index: mmseqs2/src/test/TestScoreMatrixSerialization.cpp 
+   

     return EXIT_SUCCESS;

 }

Index: mmseqs2/src/test/TestBestAlphabet.cpp

===================================================================

--- mmseqs2.orig/src/test/TestBestAlphabet.cpp	2019-07-20 08:12:45.250499276 +0100

+++ mmseqs2/src/test/TestBestAlphabet.cpp	2019-07-20 17:52:58.384128682 +0100

@@ -58,7 +58,7 @@

     /////////                                 |   ////////////////

     ///////// Choose substitution matrix here V ! ////////////////

     //SubstitutionMatrix subMat("/Users/soeding/Projects/MMseqs2/MMseqs2/data/blosum100.out", 2.0, -0.0f);

-    SubstitutionMatrix subMat("/Users/soeding/Projects/MMseqs2/MMseqs2/data/PAM70.out", 2.0, -0.0f);

+    SubstitutionMatrix subMat("../example-data/PAM70.out", 2.0, -0.0f);

 

     const size_t numAAs = subMat.alphabetSize-1;    // size of original alphabet

     const size_t numKmers = pow(numAAs,kmerSize);

@@ -72,8 +72,8 @@

     //////////////////////////////////////////////////////////////////////////////////////////////

     // Compute probabilities for all 20^k k-mers in a sequence database "seqDB"

 

-    std::string dbPath = "seqDB";

-    std::string dbIndexPath = "seqDB.index";

+    std::string dbPath = "../example-data/DB";

+    std::string dbIndexPath = "../example-data/DB.index";

     DBReader<unsigned int> seqDb(dbPath.c_str(), dbIndexPath.c_str(), 1, DBReader<unsigned int>::USE_DATA|DBReader<unsigned int>::USE_INDEX);

     seqDb.open(DBReader<unsigned int>::NOSORT);

debian/tests/run-unit-test

+10 −0
Original line number Diff line number Diff line
@@ -9,6 +9,14 @@ if [ "${AUTOPKGTEST_TMP}" = "" ] ; then 
fi



cp -r /usr/lib/${pkg}/test "${AUTOPKGTEST_TMP}"

cp -r /usr/share/doc/${pkg}/example-data "${AUTOPKGTEST_TMP}"



# Build some data for the test binaries as prerequisites

cd "${AUTOPKGTEST_TMP}"/example-data

gunzip *.gz



mmseqs createdb DB.fasta DB

mmseqs createindex DB tmp



cd "${AUTOPKGTEST_TMP}"/test
@@ -57,3 +65,5 @@ echo "Invoking test_util" 
./test_util

echo "Invoking test_scorematrixserialization"

./test_scorematrixserialization

echo "Invoking test_bestalphabet"

./test_bestalphabet