[med-svn] [Git][med-team/diamond-aligner][master] 2 commits: Autopkgtest: ignore warnings about the C2 sequences looking like DNA

[Michael R. Crusoe (@crusoe)]

Michael R. Crusoe pushed to branch master at Debian Med / diamond-aligner


Commits:
11111f9b by Michael R. Crusoe at 2021-09-14T12:19:35+02:00
Autopkgtest: ignore warnings about the C2 sequences looking like DNA

- - - - -
2191758d by Michael R. Crusoe at 2021-09-14T12:20:33+02:00
routine-update: Ready to upload to unstable

- - - - -


2 changed files:

- debian/changelog
- debian/tests/diamond-calls


Changes:

=====================================
debian/changelog
=====================================
@@ -1,10 +1,17 @@
-diamond-aligner (2.0.11-1) UNRELEASED; urgency=medium
+diamond-aligner (2.0.11-1) unstable; urgency=medium
 
+  * Team upload.
+
+  [ Andreas Tille ]
   * Fix watchfile to detect new versions on github (routine-update)
   * New upstream version
   * Standards-Version: 4.6.0 (routine-update)
 
- -- Andreas Tille <tille at debian.org>  Wed, 01 Sep 2021 06:46:50 +0200
+  [ Michael R. Crusoe ]
+  * Autopkgtest: pass "--ignore-warnings" when needed due to a protein sequence
+    that looks like a DNA sequence
+
+ -- Michael R. Crusoe <crusoe at debian.org>  Tue, 14 Sep 2021 12:20:33 +0200
 
 diamond-aligner (2.0.7-1) unstable; urgency=medium
 


=====================================
debian/tests/diamond-calls
=====================================
@@ -1,48 +1,50 @@
 #!/bin/sh
 set -e
 set -x
-# Test sxcript obtained from proteinortho (see bug #9580909
+# Test sxcript obtained from proteinortho (see bug #958090
 
 TESTDIR=`mktemp -d`
 
-#TODO: 10 DONE: 0 Running: 4 -> 14
-diamond blastp --threads 1 --db 'test/C.faa.diamond' --query 'test/E.faa' --out $TESTDIR/E.faa.vs.C.faa.diamond -e 1e-05 --outfmt 6 --sensitive 2>/dev/null
-diamond blastp --threads 1 --db 'test/E.faa.diamond' --query 'test/C.faa' --out $TESTDIR/C.faa.vs.E.faa.diamond -e 1e-05 --outfmt 6 --sensitive 2>/dev/null
+# ./proteinortho6.pl -debug  -force -project=test_diamond -p=diamond test/*.faa -cpus=1 -verbose=2
 
-#TODO: 10 DONE: 1 Running: 3 -> 12
-diamond blastp --threads 1 --db 'test/C.faa.diamond' --query 'test/L.faa' --out $TESTDIR/L.faa.vs.C.faa.diamond -e 1e-05 --outfmt 6 --sensitive 2>/dev/null
-diamond blastp --threads 1 --db 'test/L.faa.diamond' --query 'test/C.faa' --out $TESTDIR/C.faa.vs.L.faa.diamond -e 1e-05 --outfmt 6 --sensitive 2>/dev/null
+# DONE: 0 Running: 1 -> 11
+diamond blastp --threads 1 --db 'test/C.faa.diamond' --query 'test/E.faa' --out $TESTDIR/E.faa.vs.C.faa.diamond -e 1e-05 --outfmt 6 --sensitive
+diamond blastp --threads 1 --db 'test/E.faa.diamond' --query 'test/C.faa' --out $TESTDIR/C.faa.vs.E.faa.diamond -e 1e-05 --outfmt 6 --sensitive
 
-#TODO: 10 DONE: 1 Running: 3 -> 12
-diamond blastp --threads 1 --db 'test/C.faa.diamond' --query 'test/M.faa' --out $TESTDIR/M.faa.vs.C.faa.diamond -e 1e-05 --outfmt 6 --sensitive 2>/dev/null
+# DONE: 1 Running: 0 -> 9
+diamond blastp --threads 1 --db 'test/C.faa.diamond' --query 'test/L.faa' --out $TESTDIR/L.faa.vs.C.faa.diamond -e 1e-05 --outfmt 6 --sensitive
+diamond blastp --threads 1 --db 'test/L.faa.diamond' --query 'test/C.faa' --out $TESTDIR/C.faa.vs.L.faa.diamond -e 1e-05 --outfmt 6 --sensitive
 
-# TODO: 10 DONE: 1 Running: 3 -> 12
-diamond blastp --threads 1 --db 'test/C.faa.diamond' --query 'test/C2.faa' --out $TESTDIR/C2.faa.vs.C.faa.diamond -e 1e-05 --outfmt 6 --sensitive 2>/dev/null
+# DONE: 2 Running: 0 -> 8
+diamond blastp --threads 1 --db 'test/C.faa.diamond' --query 'test/M.faa' --out $TESTDIR/M.faa.vs.C.faa.diamond -e 1e-05 --outfmt 6 --sensitive
+diamond blastp --threads 1 --db 'test/M.faa.diamond' --query 'test/C.faa' --out $TESTDIR/C.faa.vs.M.faa.diamond -e 1e-05 --outfmt 6 --sensitive
 
-# TODO: 10 DONE: 1 Running: 3 -> 12
-diamond blastp --threads 1 --db 'test/E.faa.diamond' --query 'test/L.faa' --out $TESTDIR/L.faa.vs.E.faa.diamond -e 1e-05 --outfmt 6 --sensitive 2>/dev/null
+# DONE: 3 Running: 0 -> 7
+diamond blastp --ignore-warnings --threads 1 --db 'test/C.faa.diamond' --query 'test/C2.faa' --out $TESTDIR/C2.faa.vs.C.faa.diamond -e 1e-05 --outfmt 6 --sensitive
+diamond blastp --threads 1 --db 'test/C2.faa.diamond' --query 'test/C.faa' --out $TESTDIR/C.faa.vs.C2.faa.diamond -e 1e-05 --outfmt 6 --sensitive
 
-# TODO: 10 DONE: 2 Running: 3 -> 11
-diamond blastp --threads 1 --db 'test/E.faa.diamond' --query 'test/M.faa' --out $TESTDIR/M.faa.vs.E.faa.diamond -e 1e-05 --outfmt 6 --sensitive 2>/dev/null
-diamond blastp --threads 1 --db 'test/C2.faa.diamond' --query 'test/C.faa' --out $TESTDIR/C.faa.vs.C2.faa.diamond -e 1e-05 --outfmt 6 --sensitive 2>/dev/null
-diamond blastp --threads 1 --db 'test/M.faa.diamond' --query 'test/C.faa' --out $TESTDIR/C.faa.vs.M.faa.diamond -e 1e-05 --outfmt 6 --sensitive 2>/dev/null
+# DONE: 4 Running: 0 -> 6
+diamond blastp --threads 1 --db 'test/E.faa.diamond' --query 'test/L.faa' --out $TESTDIR/L.faa.vs.E.faa.diamond -e 1e-05 --outfmt 6 --sensitive
+diamond blastp --threads 1 --db 'test/L.faa.diamond' --query 'test/E.faa' --out $TESTDIR/E.faa.vs.L.faa.diamond -e 1e-05 --outfmt 6 --sensitive
 
-# TODO: 10 DONE: 3 Running: 3 -> 10
-diamond blastp --threads 1 --db 'test/E.faa.diamond' --query 'test/C2.faa' --out $TESTDIR/C2.faa.vs.E.faa.diamond -e 1e-05 --outfmt 6 --sensitive 2>/dev/null
-diamond blastp --threads 1 --db 'test/C2.faa.diamond' --query 'test/E.faa' --out $TESTDIR/E.faa.vs.C2.faa.diamond -e 1e-05 --outfmt 6 --sensitive 2>/dev/null
+# DONE: 5 Running: 0 -> 5
+diamond blastp --threads 1 --db 'test/E.faa.diamond' --query 'test/M.faa' --out $TESTDIR/M.faa.vs.E.faa.diamond -e 1e-05 --outfmt 6 --sensitive
+diamond blastp --threads 1 --db 'test/M.faa.diamond' --query 'test/E.faa' --out $TESTDIR/E.faa.vs.M.faa.diamond -e 1e-05 --outfmt 6 --sensitive
 
-# TODO: 10 DONE: 4 Running: 3 -> 9
-diamond blastp --threads 1 --db 'test/L.faa.diamond' --query 'test/M.faa' --out $TESTDIR/M.faa.vs.L.faa.diamond -e 1e-05 --outfmt 6 --sensitive 2>/dev/null
+# DONE: 6 Running: 0 -> 4
+diamond blastp --ignore-warnings --threads 1 --db 'test/E.faa.diamond' --query 'test/C2.faa' --out $TESTDIR/C2.faa.vs.E.faa.diamond -e 1e-05 --outfmt 6 --sensitive
+diamond blastp --threads 1 --db 'test/C2.faa.diamond' --query 'test/E.faa' --out $TESTDIR/E.faa.vs.C2.faa.diamond -e 1e-05 --outfmt 6 --sensitive
 
-# TODO: 10 DONE: 5 Running: 3 -> 8
-diamond blastp --threads 1 --db 'test/L.faa.diamond' --query 'test/C2.faa' --out $TESTDIR/C2.faa.vs.L.faa.diamond -e 1e-05 --outfmt 6 --sensitive 2>/dev/null
-diamond blastp --threads 1 --db 'test/C2.faa.diamond' --query 'test/L.faa' --out $TESTDIR/L.faa.vs.C2.faa.diamond -e 1e-05 --outfmt 6 --sensitive 2>/dev/null
-diamond blastp --threads 1 --db 'test/L.faa.diamond' --query 'test/E.faa' --out $TESTDIR/E.faa.vs.L.faa.diamond -e 1e-05 --outfmt 6 --sensitive 2>/dev/null
-diamond blastp --threads 1 --db 'test/M.faa.diamond' --query 'test/E.faa' --out $TESTDIR/E.faa.vs.M.faa.diamond -e 1e-05 --outfmt 6 --sensitive 2>/dev/null
+# DONE: 7 Running: 0 -> 3
+diamond blastp --threads 1 --db 'test/L.faa.diamond' --query 'test/M.faa' --out $TESTDIR/M.faa.vs.L.faa.diamond -e 1e-05 --outfmt 6 --sensitive
+diamond blastp --threads 1 --db 'test/M.faa.diamond' --query 'test/L.faa' --out $TESTDIR/L.faa.vs.M.faa.diamond -e 1e-05 --outfmt 6 --sensitive
 
-#TODO: 10 DONE: 6 Running: 3 -> 7
-diamond blastp --threads 1 --db 'test/M.faa.diamond' --query 'test/C2.faa' --out $TESTDIR/C2.faa.vs.M.faa.diamond -e 1e-05 --outfmt 6 --sensitive 2>/dev/null
-diamond blastp --threads 1 --db 'test/C2.faa.diamond' --query 'test/M.faa' --out $TESTDIR/M.faa.vs.C2.faa.diamond -e 1e-05 --outfmt 6 --sensitive 2>/dev/null
-diamond blastp --threads 1 --db 'test/M.faa.diamond' --query 'test/L.faa' --out $TESTDIR/L.faa.vs.M.faa.diamond -e 1e-05 --outfmt 6 --sensitive 2>/dev/null
+# DONE: 8 Running: 0 -> 2
+diamond blastp --ignore-warnings --threads 1 --db 'test/L.faa.diamond' --query 'test/C2.faa' --out $TESTDIR/C2.faa.vs.L.faa.diamond -e 1e-05 --outfmt 6 --sensitive
+diamond blastp --threads 1 --db 'test/C2.faa.diamond' --query 'test/L.faa' --out $TESTDIR/L.faa.vs.C2.faa.diamond -e 1e-05 --outfmt 6 --sensitive
+
+# DONE: 9 Running: 0 -> 1
+diamond blastp --ignore-warnings --threads 1 --db 'test/M.faa.diamond' --query 'test/C2.faa' --out $TESTDIR/C2.faa.vs.M.faa.diamond -e 1e-05 --outfmt 6 --sensitive
+diamond blastp --threads 1 --db 'test/C2.faa.diamond' --query 'test/M.faa' --out $TESTDIR/M.faa.vs.C2.faa.diamond -e 1e-05 --outfmt 6 --sensitive
 
 rm -rf $TESTDIR



View it on GitLab: https://salsa.debian.org/med-team/diamond-aligner/-/compare/97ab99e8662381954b090b8eba75410b629f9392...2191758da105d2093f10337b9db2b1fb0ea9c57c

-- 
View it on GitLab: https://salsa.debian.org/med-team/diamond-aligner/-/compare/97ab99e8662381954b090b8eba75410b629f9392...2191758da105d2093f10337b9db2b1fb0ea9c57c
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