[med-svn] r22254 - in trunk/packages/conservation-code/trunk/debian: . tests

[Tatiana Malygina]

Author: latticetower-guest
Date: 2016-06-29 10:12:35 +0000 (Wed, 29 Jun 2016)
New Revision: 22254

Modified:
   trunk/packages/conservation-code/trunk/debian/README.test
   trunk/packages/conservation-code/trunk/debian/changelog
   trunk/packages/conservation-code/trunk/debian/tests/non-default-params-test
Log:
simplified debian/tests/non-default-params-test, but made more verbose debian/README.test

Modified: trunk/packages/conservation-code/trunk/debian/README.test
===================================================================
--- trunk/packages/conservation-code/trunk/debian/README.test	2016-06-29 08:48:28 UTC (rev 22253)
+++ trunk/packages/conservation-code/trunk/debian/README.test	2016-06-29 10:12:35 UTC (rev 22254)
@@ -7,3 +7,47 @@
     sh non-default-params-test
 
 in order to confirm its integrity.
+
+To test manually, cd to some dir where you have write permissions
+and do
+
+    cp -a /usr/share/doc/conservation-code/examples/* .
+    ln -s 1G6C_A_jsd.scores conservation_data/1G6C_C_jsd.scores
+    ln -s 1G6C_B_jsd.scores conservation_data/1G6C_D_jsd.scores
+    score_conservation -o alignment.scores 2plc__hssp-filtered.aln
+
+Algorithm uses BLOSUM62 [1] alignment matrix, located at 
+/usr/share/conservation-code/matrix/blosum62.bla.
+If you want to use specify other alignment matrix, you can do it like so:
+
+    ln -s /usr/share/conservation-code/matrix/blosum100.bla blosum100.bla
+    score_conservation -m blosum100.bla -o alignment.scores 2plc__hssp-filtered.aln
+
+For other parameters and their usage type "man score_conservation" in terminal.
+
+Program tries to get some results even when numeric parameters are incorrect or
+some data can't be found. If you provide matrix file which doesn't exist, it shows 
+similar message:
+
+  Could not load similarity matrix: /usr/share/conservation-code/matrix/blosum63.bla. Using identity matrix...
+
+Identity matrix [2] makes everything work, but sequence alignment will look 
+sparser than you expect when using blosum matrix.
+
+If you provide incorrect distribution file, `score_conservation` shows similar 
+message:
+
+  [Errno 2] No such file or directory: '/usr/share/conservation-code/distributions/swissprot1.distribution' Using default (BLOSUM62) background.
+
+These messages are written to stderr, but they simply inform you that your set
+of parameters differs from those used in actual data processing. 
+
+In contrast, if you see message with "Error:" text [2], it means that some
+unprocessed errors appeared during program call and resulting file probably 
+will not contain any sensible results.
+
+References:
+
+  [1]: BLOSUM alignment matrices https://en.wikipedia.org/wiki/BLOSUM
+  [1]: https://en.wikipedia.org/wiki/Identity_matrix
+  [3]: https://docs.python.org/2/tutorial/errors.html

Modified: trunk/packages/conservation-code/trunk/debian/changelog
===================================================================
--- trunk/packages/conservation-code/trunk/debian/changelog	2016-06-29 08:48:28 UTC (rev 22253)
+++ trunk/packages/conservation-code/trunk/debian/changelog	2016-06-29 10:12:35 UTC (rev 22254)
@@ -10,6 +10,8 @@
   * allow-stderr for testsuite to allow test pass instead of fail when matrix 
     file is not found
   * verbose output in test + check distributions usage
+  * simplified debian/tests/non-default-params-test, but made more verbose 
+    debian/README.test
 
   [ Andreas Tille ]
   * install link to /usr/bin rather than copy of Python file

Modified: trunk/packages/conservation-code/trunk/debian/tests/non-default-params-test
===================================================================
--- trunk/packages/conservation-code/trunk/debian/tests/non-default-params-test	2016-06-29 08:48:28 UTC (rev 22253)
+++ trunk/packages/conservation-code/trunk/debian/tests/non-default-params-test	2016-06-29 10:12:35 UTC (rev 22254)
@@ -20,16 +20,7 @@
 score_conservation -m /usr/share/${pkg}/matrix/blosum100.bla -o alignment.scores 2plc__hssp-filtered.aln
 [ -e alignment.scores ]
 
-# following call has invalid matrix file as a parameter -> script tries to use identity matrix instead
-# can produce error
-score_conservation -m /usr/share/${pkg}/matrix/blosum63.bla -o alignment2.scores 2plc__hssp-filtered.aln
-[ -e alignment2.scores ]
-
 echo "Checking distribution file usage"
 #with valid distribution file name
-score_conservation -d /usr/share/${pkg}/distributions/swissprot.distribution -o alignment3.scores 2plc__hssp-filtered.aln
-[ -e alignment3.scores ]
-
-#with invalid distribution file name - produces output to stderr:
-score_conservation -d /usr/share/${pkg}/distributions/swissprot1.distribution -o alignment4.scores 2plc__hssp-filtered.aln
-[ -e alignment4.scores ] # and still produces output
+score_conservation -d /usr/share/${pkg}/distributions/swissprot.distribution -o alignment2.scores 2plc__hssp-filtered.aln
+[ -e alignment2.scores ]