[med-svn] r23668 - trunk/packages/metastudent/trunk/debian

[Tatiana Malygina]

Author: latticetower-guest
Date: 2017-02-05 11:53:28 +0000 (Sun, 05 Feb 2017)
New Revision: 23668

Modified:
   trunk/packages/metastudent/trunk/debian/README.Debian
   trunk/packages/metastudent/trunk/debian/README.test
Log:
update debian/README.Debian and debian/README.test

Modified: trunk/packages/metastudent/trunk/debian/README.Debian
===================================================================
--- trunk/packages/metastudent/trunk/debian/README.Debian	2017-02-05 11:47:36 UTC (rev 23667)
+++ trunk/packages/metastudent/trunk/debian/README.Debian	2017-02-05 11:53:28 UTC (rev 23668)
@@ -11,39 +11,8 @@
     https://github.com/Rostlab/MetaStudent
 
 Since the moment when blast2 package is resolved as blast+ set of programs,
-autopkgtest testsuite began to fail. The main reason is that blast+ programs
-produce slightly different output. Particularly, in some lines of these files
-number of space characters differs from those found in legacy blast output,
-this leads to the main problem that regular expressions, used by metastudent 
-to parse these lines, don't parse them correctly. This leads to incorrect
-metastudent output. 
+autopkgtest testsuite began to fail. Blast file parsing result
+in all metastudent stages was observed (as a result of metastudent run with
+--keep-temp flag), parsing was fixed to produce meaningful output in each
+stage. 
  
-Another problem, which is the reason why Bug #848903 appeared, is also related
-to difference in programs output. When legacy versions of blast produce output
-for several input .fasta sequences, at the beginning of each sequence's input
-set they contain line starting with "BLASTP" substring (that's a program name
-used by legacy blast). Metastudent searches for this substring and considers
-data following this line to be related to next protein sequence in input .fasta
-file. This is relatively simplier to fix, since it produces only 1 exception
-which is the reason of Bug #848903. 
-
-Problem with blast output parsing appears in several places of metastudent,
-since different code is used to parsing in "studentA" and "studentB" parts.
-
-Currently there is also a problem with test files, since the result files
-provided by upstream and named "test.result.BPO.txt", "test.result.CCO.txt"
-and "test.result.MFO.txt" - contain result of metastudent run only for
-1 sequence (instead of full output for 3 sequences given in "test.fasta").
-
-Necessary steps to fix everything to produce correct results with new version
-of blast2 package (work in progress):
-
-1. Add patch for fixing bug #848903
-2. Run metastudent with legacy blast 2.2.26 and save all results, including
-temporary, for latest version of metastudent-data package. They should be
-similar to expected results produced by blast+ on the same version of
-metastudent-data package and might be used as a reference while fixing package.
-3. Metastudent runs in 3 stages, and they use different code for parsing blast
-run output. Check them one by one and fix regular expressions, at each stage
-compare temporary results with those produced by metastudent run with
-legacy blast.

Modified: trunk/packages/metastudent/trunk/debian/README.test
===================================================================
--- trunk/packages/metastudent/trunk/debian/README.test	2017-02-05 11:47:36 UTC (rev 23667)
+++ trunk/packages/metastudent/trunk/debian/README.test	2017-02-05 11:53:28 UTC (rev 23668)
@@ -7,12 +7,24 @@
 
 in order to confirm its integrity.
 
-Currently metastudent supports only legacy version of blast (for additional
-details see README.Debian). That's why currently autopkgtest fails and this
-package should be tested and run manually.
+To test manually, cd to some dir where you have write permissions and do
 
-There are several necessary steps to run it now, if you expect correct results:
+    cp /usr/share/doc/metastudent/examples/test.fasta .
+    metastudent -i test.fasta -o test.result --temp-dir=.
 
+If you believe that results are incorrect, you can run metastudent with
+additional parameter to see temporary output for different stages. 
+Just run it with --keep-temp flag like this:
+
+    metastudent -i test.fasta -o test.result --temp-dir=. --keep-temp
+
+As a result of this call, temporary directory will be present in work dir.
+The most informative files you can find there are named "logA.txt", 
+"logB.txt", "logC.txt" - they contain logs for different stages. 
+
+To run metastudent with legacy version of blast (or any different version,
+installed manually), you should do the following:
+
 1. Install legacy blast from NCBI website. 
   I recommend using legacy blast 2.2.26, since I checked metastudent results
   with this specific version).