metastudent_2.0.1-5_all.deb


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Description

metastudent - predictor of Gene Ontology terms from protein sequence

Property Value
Distribution Ubuntu 18.04 LTS (Bionic Beaver)
Repository Ubuntu Universe amd64
Package filename metastudent_2.0.1-5_all.deb
Package name metastudent
Package version 2.0.1
Package release 5
Package architecture all
Package type deb
Category universe/science
Homepage https://rostlab.org/owiki/index.php/Metastudent
License -
Maintainer Ubuntu Developers <ubuntu-devel-discuss@lists.ubuntu.com>
Download size 5.71 MB
Installed size 92.76 MB
Often, only the sequence of a protein is known, but
not its functions. Metastudent will try to predict
missing functional annotations through homology searches (BLAST).
All predicted functions correspond to Gene Ontology (GO)
terms from the Molecular Function (MFO), the Biological Process
(BPO) and the Cellular Component Ontology (CCO) and are associated
with a reliability score.

Alternatives

Package Version Architecture Repository
metastudent_2.0.1-5_all.deb 2.0.1 all Ubuntu Universe
metastudent - - -

Requires

Name Value
blast2 -
default-jre -
libfile-chdir-perl -
libgo-perl >= 0.15-3
libgraphviz-perl -
libipc-run-perl -
metastudent-data >= 2.0.0
perl:any -
python -
python:any >= 2.7.5-5~
python:any << 2.8

Download

Type URL
Mirror archive.ubuntu.com
Binary Package metastudent_2.0.1-5_all.deb
Source Package metastudent

Install Howto

  1. Update the package index:
    # sudo apt-get update
  2. Install metastudent deb package:
    # sudo apt-get install metastudent

Files

Path
/etc/metastudentrc
/usr/bin/metastudent
/usr/lib/python2.7/dist-packages/metastudent-2.0.1.egg-info
/usr/lib/python2.7/dist-packages/metastudentPkg/BlastWrapper.py
/usr/lib/python2.7/dist-packages/metastudentPkg/Logger.py
/usr/lib/python2.7/dist-packages/metastudentPkg/__init__.py
/usr/lib/python2.7/dist-packages/metastudentPkg/commons.py
/usr/lib/python2.7/dist-packages/metastudentPkg/generateTermNameMapping.py
/usr/lib/python2.7/dist-packages/metastudentPkg/runMethods.py
/usr/lib/python2.7/dist-packages/metastudentPkg/version.py
/usr/lib/python2.7/dist-packages/metastudentPkg/lib/groupA/report.txt
/usr/lib/python2.7/dist-packages/metastudentPkg/lib/groupA/DataPreprocessing/splitDB.py
/usr/lib/python2.7/dist-packages/metastudentPkg/lib/groupA/GOSSIP/.classpath
/usr/lib/python2.7/dist-packages/metastudentPkg/lib/groupA/GOSSIP/.project
/usr/lib/python2.7/dist-packages/metastudentPkg/lib/groupA/GOSSIP/temp.fasta
/usr/lib/python2.7/dist-packages/metastudentPkg/lib/groupA/GOSSIP/.settings/org.eclipse.core.resources.prefs
/usr/lib/python2.7/dist-packages/metastudentPkg/lib/groupA/GOSSIP/.settings/org.eclipse.jdt.core.prefs
/usr/lib/python2.7/dist-packages/metastudentPkg/lib/groupA/GOSSIP/.settings/org.eclipse.jdt.ui.prefs
/usr/lib/python2.7/dist-packages/metastudentPkg/lib/groupA/GO_Parser/GO_Parents.2014.txt
/usr/lib/python2.7/dist-packages/metastudentPkg/lib/groupA/GO_Parser/GO_Parents.txt
/usr/lib/python2.7/dist-packages/metastudentPkg/lib/groupA/GO_Parser/src/.classpath
/usr/lib/python2.7/dist-packages/metastudentPkg/lib/groupA/GO_Parser/src/.project
/usr/lib/python2.7/dist-packages/metastudentPkg/lib/groupA/Validation/GO_Table.txt
/usr/lib/python2.7/dist-packages/metastudentPkg/lib/groupA/Validation/SIMPLECOUNT_0.8.val
/usr/lib/python2.7/dist-packages/metastudentPkg/lib/groupA/Validation/SIMPLECOUNT_0.9.val
/usr/lib/python2.7/dist-packages/metastudentPkg/lib/groupA/parser/group2_blastParser.py
/usr/lib/python2.7/dist-packages/metastudentPkg/lib/groupA/parser/group2_goParserSwissprot.py
/usr/lib/python2.7/dist-packages/metastudentPkg/lib/groupA/parser/group2_goStatistics.py
/usr/lib/python2.7/dist-packages/metastudentPkg/lib/groupA/parser/group4_blastParser.pl
/usr/lib/python2.7/dist-packages/metastudentPkg/lib/groupA/parser/group4_swissProtParser.pl
/usr/lib/python2.7/dist-packages/metastudentPkg/lib/groupB/data/besthit.dist
/usr/lib/python2.7/dist-packages/metastudentPkg/lib/groupB/data/goterm2014.txt
/usr/lib/python2.7/dist-packages/metastudentPkg/lib/groupB/data/goterm2term.txt
/usr/lib/python2.7/dist-packages/metastudentPkg/lib/groupB/data/transitiveClosure2014.txt
/usr/lib/python2.7/dist-packages/metastudentPkg/lib/groupB/data/unweighted.dist
/usr/lib/python2.7/dist-packages/metastudentPkg/lib/groupB/data/weighted.dist
/usr/lib/python2.7/dist-packages/metastudentPkg/lib/groupB/java/bla.tabularresults
/usr/lib/python2.7/dist-packages/metastudentPkg/lib/groupB/java/META-INF/MANIFEST.MF
/usr/lib/python2.7/dist-packages/metastudentPkg/lib/groupB/perl/GOaddpath.pl
/usr/lib/python2.7/dist-packages/metastudentPkg/lib/groupB/perl/GOeval.pl
/usr/lib/python2.7/dist-packages/metastudentPkg/lib/groupB/perl/GOfunctions.pm
/usr/lib/python2.7/dist-packages/metastudentPkg/lib/groupB/perl/GOmultifiles.pl
/usr/lib/python2.7/dist-packages/metastudentPkg/lib/groupB/perl/addGO2BLAST.pl
/usr/lib/python2.7/dist-packages/metastudentPkg/lib/groupB/perl/build_splitsets.rb
/usr/lib/python2.7/dist-packages/metastudentPkg/lib/groupB/perl/cafa_format_checker_2.pl
/usr/lib/python2.7/dist-packages/metastudentPkg/lib/groupB/perl/call_build_splitsets.readme
/usr/lib/python2.7/dist-packages/metastudentPkg/lib/groupB/perl/evaluate.pl
/usr/lib/python2.7/dist-packages/metastudentPkg/lib/groupB/perl/filter_fasta.pl
/usr/lib/python2.7/dist-packages/metastudentPkg/lib/groupB/perl/go_filter_cc.pl
/usr/lib/python2.7/dist-packages/metastudentPkg/lib/groupB/perl/make_percent.pl
/usr/lib/python2.7/dist-packages/metastudentPkg/lib/groupB/perl/make_splits.pl
/usr/lib/python2.7/dist-packages/metastudentPkg/lib/groupB/perl/parse_GO_hierarchy.xslt
/usr/lib/python2.7/dist-packages/metastudentPkg/lib/groupB/perl/parse_GO_terms.xslt
/usr/lib/python2.7/dist-packages/metastudentPkg/lib/groupB/perl/parse_blast.pl
/usr/lib/python2.7/dist-packages/metastudentPkg/lib/groupB/perl/readme.txt
/usr/lib/python2.7/dist-packages/metastudentPkg/lib/groupB/perl/splitall.sh
/usr/lib/python2.7/dist-packages/metastudentPkg/lib/groupB/perl/splitall_clusters.sh
/usr/lib/python2.7/dist-packages/metastudentPkg/lib/groupB/perl/swissprot_extract_go.pl
/usr/lib/python2.7/dist-packages/metastudentPkg/lib/groupB/perl/test2eval.pl
/usr/lib/python2.7/dist-packages/metastudentPkg/lib/groupB/pp2/.classpath
/usr/lib/python2.7/dist-packages/metastudentPkg/lib/groupB/pp2/.project
/usr/lib/python2.7/dist-packages/metastudentPkg/lib/groupB/pp2/tools/cafa_format_checker_2.pl
/usr/lib/python2.7/dist-packages/metastudentPkg/lib/groupB/run/knn_weighted
/usr/lib/python2.7/dist-packages/metastudentPkg/lib/groupB/run/run_knn_weighted
/usr/lib/python2.7/dist-packages/metastudentPkg/lib/groupC/CafaWrapper1.pl
/usr/lib/python2.7/dist-packages/metastudentPkg/lib/groupC/CafaWrapper2.pl
/usr/lib/python2.7/dist-packages/metastudentPkg/lib/groupC/CafaWrapper3.pl
/usr/lib/python2.7/dist-packages/metastudentPkg/lib/groupC/CafaWrapper3_new.pl
/usr/lib/python2.7/dist-packages/metastudentPkg/lib/groupC/Report.doc
/usr/lib/python2.7/dist-packages/metastudentPkg/lib/groupC/Report.pdf
/usr/lib/python2.7/dist-packages/metastudentPkg/lib/groupC/exercise3.pl
/usr/lib/python2.7/dist-packages/metastudentPkg/lib/groupC/transitiveClosure2014.txt
/usr/lib/python2.7/dist-packages/metastudentPkg/lib/groupC/treehandler.pl
/usr/lib/python2.7/dist-packages/metastudentPkg/lib/groupC/treehandler_new.pl
/usr/lib/python2.7/dist-packages/metastudentPkg/lib/groupC/validate.pl
/usr/share/doc/metastudent/README.Debian
/usr/share/doc/metastudent/README.test
/usr/share/doc/metastudent/changelog.Debian.gz
/usr/share/doc/metastudent/copyright
/usr/share/doc/metastudent/installation-test
/usr/share/doc/metastudent/examples/test.fasta
/usr/share/doc/metastudent/examples/test.result.BPO.txt
/usr/share/doc/metastudent/examples/test.result.CCO.txt
/usr/share/doc/metastudent/examples/test.result.MFO.txt
/usr/share/man/man1/metastudent.1.gz
/usr/share/metastudent/blastfilep.jar
/usr/share/metastudent/gossip.jar
/usr/share/metastudent/metastudentrc.default
/usr/share/metastudent/pp2.jar

Changelog

2017-11-15 - Andreas Tille <tille@debian.org>
metastudent (2.0.1-5) unstable; urgency=medium
* Team upload.
* Moved packaging from SVN to Git
* debhelper 10
* Standards-Version: 4.1.1
* d/rules: do not parse d/changelog
2017-02-05 - Tatiana Malygina <merlettaia@gmail.com>
metastudent (2.0.1-4) unstable; urgency=medium
* Team upload
* 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).
* add patch to parse blast+ output correctly (closes: #848903).
* update debian/README.Debian and debian/README.test
2016-07-16 - Tatiana Malygina <merlettaia@gmail.com>
metastudent (2.0.1-3) unstable; urgency=medium
* Team upload.
* add allow-stderr restriction to debian/tests/control
2016-07-13 - Tatiana Malygina <merlettaia@gmail.com>
metastudent (2.0.1-2) unstable; urgency=medium
[ Tatiana Malygina ]
* Team upload.
* cme fix dpkg-control
* cme fix dpkg-copyright
* add hardening
* add testsuite, debian/README.test, debian/docs
[ Andreas Tille ]
* Copy configuration file to /etc/metastudentrc that overrides default
configuration to enable local user adjusting data path
* Fix sequence of copyright paragraphs to follow DEP5
* Add versioned Depends libgo-perl (>= 0.15-3)
2015-03-20 - Tobias Hamp <hampt@rostlab.org>
metastudent (2.0.1-1) unstable; urgency=low
* Added Cellular Component Ontology
* Updated GO annotations databases
* Updated Gene Ontology
* Predictions are now fully propagated to the root
* Updated URL for image generation
* fixed setup.py
2014-09-14 - Laszlo Kajan <lkajan@debian.org>
metastudent (1.0.11-2) unstable; urgency=medium
* Fixed VCS URL.
* Fixed python2 dependency handling.
2013-12-13 - Tobias Hamp <hampt@rostlab.org>
metastudent (1.0.11-1) unstable; urgency=low
* New upstream release.
2013-06-08 - Tobias Hamp <hampt@rostlab.org>
metastudent (1.0.10-1) unstable; urgency=low
* New upstream release.
2013-06-05 - Tobias Hamp <hampt@rostlab.org>
metastudent (1.0.9-1) unstable; urgency=low
* New upstream release.
2013-05-08 - Laszlo Kajan <lkajan@rostlab.org>
metastudent (1.0.8-2) unstable; urgency=low
* This version depends on data packaged as metastudent-data.

See Also

Package Description
metche_1.2.4-1_all.deb configuration monitor to ease collective administration
meterbridge_0.9.2-13_amd64.deb Collection of Audio meters for the JACK audio server
meterec_0.9.2~ds0-2build1_amd64.deb minimalistic multi track recorder
metis_5.1.0.dfsg-5_amd64.deb Serial Graph Partitioning and Fill-reducing Matrix Ordering. Binaries
metview-data_5.0.0~beta.1-1build1_all.deb Data needed for the Metview data analysis environment
metview_5.0.0~beta.1-1build1_amd64.deb Interactive data visualization and analysis environment,
mew-beta-bin_7.0.50~6.7+0.20170719-1_amd64.deb external commands for Mew (development version)
mew-beta_7.0.50~6.7+0.20170719-1_all.deb mail reader supporting PGP/MIME for Emacs (development version)
mew-bin_6.7-4_amd64.deb external commands for Mew
mew_6.7-4_all.deb mail reader supporting PGP/MIME for Emacs
mffm-fftw-dev_1.7-4_amd64.deb C++ wrapper for the fftw.org C library (version 3)
mffm-fftw1_1.7-4_amd64.deb C++ wrapper for the fftw.org C library (version 3)
mftrace_1.2.19-1_amd64.deb Converts Metafont fonts into Type1 fonts
mg_20171014-1_amd64.deb microscopic GNU Emacs-style editor
mgba-common_0.5.2+dfsg1-3_all.deb Game Boy Advance emulator (common files for mGBA)
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