Shayan Doust pushed to branch master at Debian Med / mmseqs2
Commits:
968f4d6e by Shayan Doust at 2019-07-20T17:09:47Z
Fix test_bestalphabet binary. Now works.
This is used within autopkgtest
- - - - -
2 changed files:
- debian/patches/fix_tests.patch
- debian/tests/run-unit-test
Changes:
=====================================
debian/patches/fix_tests.patch
=====================================
@@ -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
=====================================
@@ -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
View it on GitLab:
https://salsa.debian.org/med-team/mmseqs2/commit/968f4d6ec81844e7d448281bfed3a52b3b01fba1
--
View it on GitLab:
https://salsa.debian.org/med-team/mmseqs2/commit/968f4d6ec81844e7d448281bfed3a52b3b01fba1
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