Author: latticetower-guest Date: 2017-01-19 11:17:56 +0000 (Thu, 19 Jan 2017) New Revision: 23642
Modified: trunk/packages/metastudent/trunk/debian/README.Debian trunk/packages/metastudent/trunk/debian/README.test trunk/packages/metastudent/trunk/debian/changelog Log: add details on package testsuite failure to README.Debian, update README.test Modified: trunk/packages/metastudent/trunk/debian/README.Debian =================================================================== --- trunk/packages/metastudent/trunk/debian/README.Debian 2017-01-18 16:34:53 UTC (rev 23641) +++ trunk/packages/metastudent/trunk/debian/README.Debian 2017-01-19 11:17:56 UTC (rev 23642) @@ -3,3 +3,47 @@ metastudent searches through large data files (>200M compressed) in order to predict gene ontology terms. These data files are available from the metastudent-data package or [1], and are released under the GPL-2+. [1] ftp://rostlab.org/metastudent/metastudent-data_[0-9.]+.tar.gz + + +Metastudent currently works correctly only with legacy version of blast. It is + stated in metastudent development repository here: + + 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. + +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 2017-01-18 16:34:53 UTC (rev 23641) +++ trunk/packages/metastudent/trunk/debian/README.test 2017-01-19 11:17:56 UTC (rev 23642) @@ -7,7 +7,24 @@ in order to confirm its integrity. -To test manually, cd to some dir where you have write permissions and do +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. + +There are several necessary steps to run it now, if you expect correct results: + +1. Install legacy blast from NCBI website. + I recommend using legacy blast 2.2.26, since I checked metastudent results + with this specific version). +2. Copy metastudentrc.default config file from metastudent dir to location + where you have write permissions. +3. Find "blastpgp" file in legacy blast installation. Edit your + metastudentrc.default copy to point to this file in line starting with + "BLASTPGP_EXE_PATH". + +After that, do cp /usr/share/doc/metastudent/examples/test.fasta . - metastudent -i test.fasta -o test.result --temp-dir=. + metastudent -i test.fasta -o test.result --temp-dir=. --config=metastudentrc.default + +The result files produced by metastudent should appear in working dir. Modified: trunk/packages/metastudent/trunk/debian/changelog =================================================================== --- trunk/packages/metastudent/trunk/debian/changelog 2017-01-18 16:34:53 UTC (rev 23641) +++ trunk/packages/metastudent/trunk/debian/changelog 2017-01-19 11:17:56 UTC (rev 23642) @@ -2,6 +2,9 @@ * Team upload. * add allow-stderr restriction to debian/tests/control + * add details on package testsuite failure to REAMDE.Debian, + add to README.test how to test manually (currently metastudent supports + legacy blast only and fails on blast+ output parsing). -- Tatiana Malygina <[email protected]> Sat, 16 Jul 2016 09:24:57 +0300 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
