debian/0000755000000000000000000000000012207572017007171 5ustar debian/control0000644000000000000000000000335012207570206010573 0ustar Source: profphd Maintainer: Debian Med Packaging Team Uploaders: Laszlo Kajan , Andreas Tille Section: science Priority: extra Build-Depends: cdbs, debhelper (>= 7.0.50~), perl, rsync Standards-Version: 3.9.4 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/rostlab/profphd/trunk/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/rostlab/profphd/trunk/ Homepage: http://predictprotein.org/ Package: profphd Architecture: all Depends: ${perl:Depends}, ${misc:Depends}, librg-utils-perl (>= 1.0.16), profnet-prof, profphd-utils, profphd-net Recommends: pp-popularity-contest Conflicts: profphd-data, profphd-perl Replaces: profphd-data, profphd-perl Description: secondary structure and solvent accessibility predictor This package provides prof(1), the protein secondary structure, accessibility and transmembrane helix predictor from Burkhard Rost. Prediction is either done from protein sequence alone or from an alignment - the latter should be used for optimal performance. . How well does prof(1) perform? . * Secondary structure is predicted at an expected average accuracy > 72% for the three states helix, strand and loop. . * Solvent accessibility is predicted at a correlation coefficient (correlation between experimentally observed and predicted relative solvent accessibility) of 0.54 . * Transmembrane helix prediction has an expected per-residue accuracy of about 95%. The number of false positives, i.e., transmembrane helices predicted in globular proteins, is about 2%. debian/rules0000755000000000000000000000057212146711441010253 0ustar #!/usr/bin/make -f include /usr/share/cdbs/1/rules/debhelper.mk include /usr/share/cdbs/1/class/makefile.mk # Add here any variable or target overrides you need. DEB_MAKE_BUILD_TARGET = prefix=/usr all DEB_MAKE_INSTALL_TARGET = prefix=/usr DESTDIR=$(CURDIR)/debian/tmp/ install get-orig-source: mkdir -p ../tarballs uscan --verbose --force-download --destdir=../tarballs debian/profphd.install0000644000000000000000000000000611641774446012232 0ustar usr/* debian/watch0000644000000000000000000000013412033761366010224 0ustar version=3 opts=pasv ftp://rostlab.org/profphd/profphd-([0-9.]+)\.tar\.[a-z]z debian uupdate debian/upstream0000644000000000000000000000153411752037525010763 0ustar Name: profphd Reference: - Author: Rost, B. and Sander, C. Title: 'Combining evolutionary information and neural networks to predict protein secondary structure.' Journal: Proteins Volume: 19 Number: 1 Pages: 55-72 Year: 1994 URL: http://www.ncbi.nlm.nih.gov/pubmed/8066087 PMID: 8066087 - Author: Rost, B. and Sander, C. Title: 'Conservation and prediction of solvent accessibility in protein families.' Journal: Proteins Volume: 20 Number: 3 Pages: 216-26 Year: 1994 URL: http://www.ncbi.nlm.nih.gov/pubmed/7892171 PMID: 7892171 - Author: Rost, B. and Casadio, R. and Fariselli, P. and Sander, C. Title: 'Transmembrane helices predicted at 95% accuracy.' Journal: Protein Sci Volume: 4 Number: 3 Pages: 521-33 Year: 1995 URL: http://www.ncbi.nlm.nih.gov/pubmed/7795533 PMID: 7795533 debian/copyright0000644000000000000000000000472512146711441011132 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: profphd Upstream-Contact: Laszlo Kajan Source: ftp://rostlab.org/profphd/ Files: src/prof/embl/scr/ctime.pl src/prof/embl/scr/lib/ctime.pl Copyright: 1988 Waldemar Kebsch March 1990, Feb 1991 Marion Hakanson , Oregon Graduate Institute of Science and Technology License: GPL-1+ or Artistic Files: debian/* Copyright: 2009 Laszlo Kajan License: GPL-2+ Files: * Copyright: 1998 B. Rost EMBL, CUBIC (Columbia University, NY, USA) and LION Biosciences (Heidelberg, DE) C. Sander P. Fariselli R. Casadio J. Liu 2009-2013 G. Yachdav CUBIC (Columbia University, NY, USA) and Technical University Munich (Munich, DE) 2009-2013 L. Kajan Laszlo Kajan Technical University Munich (Munich, DE) License: GPL-2+ License: GPL-2+ This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. . This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. . You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. . On Debian systems, the complete text of the GNU General Public License version 2 can be found in `/usr/share/common-licenses/GPL-2'. License: GPL-1+ This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 1, or (at your option) any later version. . On Debian systems, the complete text of version 1 of the GNU General Public License can be found in `/usr/share/common-licenses/GPL-1'. License: Artistic This program is free software; you can redistribute it and/or modify it under the terms of the Artistic License, which comes with Perl. . On Debian systems, the complete text of the Artistic License can be found in `/usr/share/common-licenses/Artistic'. debian/source/0000755000000000000000000000000012207567205010474 5ustar debian/source/format0000644000000000000000000000001411641774446011712 0ustar 3.0 (quilt) debian/README.Debian0000644000000000000000000000123411641774446011245 0ustar profphd for Debian ------------------ profphd predicts protein secondary structure, accessibility and transmembrane helices with high accuracy. References ========== * Rost, B. and Sander, C. (1994a). Combining evolutionary information and neural networks to predict protein secondary structure. Proteins, 19(1), 55-72. * Rost, B. and Sander, C. (1994b). Conservation and prediction of solvent accessibility in protein families. Proteins, 20(3), 216-26. * Rost, B., Casadio, R., Fariselli, P., and Sander, C. (1995). Transmembrane helices predicted at 95% accuracy. Protein Sci, 4(3), 521-33. -- Laszlo Kajan Tue, 17 Nov 2009 10:50:19 +0100 debian/changelog0000644000000000000000000001761112207572017011051 0ustar profphd (1.0.40-1) unstable; urgency=low [ Laszlo Kajan ] * New upstream release. [ Gregor Herrmann ] * Fix "FTBFS with perl 5.18: POD failure": add patch to fix POD (Closes: #720497) [ Andreas Tille ] * cme fix dpkg-control * anonscm in Vcs fields -- Andreas Tille Thu, 29 Aug 2013 08:52:49 +0200 profphd (1.0.39-1) unstable; urgency=low [ Andreas Tille ] * debian/upstream: Make author field BibTeX compliant [ Laszlo Kajan ] * New upstream release. (Closes: #684857) -- Laszlo Kajan Tue, 14 Aug 2012 19:50:34 +0200 profphd (1.0.38-1) unstable; urgency=low [ Laszlo Kajan ] * New upstream release [ Andreas Tille ] * debian/control: Added rsync to Build-Depends Closes: #646662 * debian/watch: Stripped unneeded comments * debian/patches: Deleted empty dir -- Andreas Tille Wed, 26 Oct 2011 08:09:27 +0200 profphd (1.0.37-1) unstable; urgency=low * Initial release in Debian (Closes: #643324) * New upstream release -- Laszlo Kajan Wed, 28 Sep 2011 14:51:19 +0200 profphd (1.0.36-1) UNRELEASED; urgency=low * New upstream release -- Laszlo Kajan Wed, 28 Sep 2011 12:31:43 +0200 profphd (1.0.35-1) UNRELEASED; urgency=low * added Replaces and Conflicts to control file for profphd-perl and profphd-data -- Laszlo Kajan Tue, 27 Sep 2011 11:05:27 +0200 profphd (1.0.34) unstable; urgency=low * fixed "HTMTOP_RID :-10.942" bug in src/prof/scr/lib/lib-prof.pl -- Laszlo Kajan Fri, 20 May 2011 21:09:41 +0200 profphd (1.0.33) unstable; urgency=low * use warnings in phd.pl -- Laszlo Kajan Tue, 01 Mar 2011 16:00:23 +0100 profphd (1.0.32) unstable; urgency=low * copyright corrected to GPL -- Laszlo Kajan Fri, 26 Nov 2010 16:49:36 +0100 profphd (1.0.31) unstable; urgency=low * Makefile update - works now on Ubuntu as well (/bin/sh bug) -- Laszlo Kajan Fri, 26 Nov 2010 16:49:36 +0100 profphd (1.0.29) * [A-Z.~_!] in src/prof/scr/lib/lib-col.pl -- Laszlo Kajan Wed, 20 Oct 2010 14:28:49 +0200 profphd (1.0.28) * provide NORM_EXP for Selenocysteine: $NORM_EXP{"U"} = $NORM_EXP{"C"}; # U - Selenocysteine # lkajan quick hack -- Laszlo Kajan Wed, 20 Oct 2010 13:54:03 +0200 profphd (1.0.27) * fasta AA pattern now [A-Z.~_!] -- Laszlo Kajan Wed, 20 Oct 2010 11:54:27 +0200 profphd (1.0.26) * Documented `optJury' * prof in debug mode now dumps final parameter values before starting actual work * Proper error reporting when input file is empty -- Laszlo Kajan Thu, 07 Oct 2010 08:48:44 +0200 profphd (1.0.25) * work dir now automatically set to temp dir when not given * introduced translate-jobid-in-param-values param to suppress unexpected file name (and other) conversions - now you have to explicitly ask for this behaviour -- Laszlo Kajan Fri, 27 Aug 2010 17:33:30 +0200 profphd (1.0.24) * Man page syntax corrected * Better debugging output -- Laszlo Kajan Fri, 27 Aug 2010 17:33:30 +0200 profphd (1.0.23) * Now the default is to no change nice level * Documented para3 paraBoth paraSec paraAcc numresMin nresPerLineAli riSubSec riSubAcc riSubSym -- Laszlo Kajan Mon, 23 Aug 2010 20:48:29 +0200 profphd (1.0.22) * Documented a phd.pl call * Fixed overzealous ID substitution in src/prof/embl/scr/lib-phd.pl -- Laszlo Kajan Mon, 05 Jul 2010 12:25:14 +0200 profphd (1.0.21) * Fixed verbosity bug that lead to incorrect call to hssp_filter.pl -- Laszlo Kajan Thu, 24 Jun 2010 14:54:11 +0200 profphd (1.0.20) * Changed default to silent mode from verbose -- Laszlo Kajan Thu, 24 Jun 2010 11:56:26 +0200 profphd (1.0.19) * Added param dirWork to prof/scr/lib/lib-prof.pl exeCopf call * Markus' failing sequence now works ('ARCH' in file name problem) * Weird prof/scr/lib/lib-prof.pl $fileOut{1,$kwd} constructs eliminated * Resolved bug 9 'prof creates tmp files into current directory (where it is run from)' -- Laszlo Kajan Sat, 15 May 2010 13:38:56 +0200 profphd (1.0.18) * resolved bug #10 html formatting of ouput -- Guy Yachdav Sun, 02 May 2010 13:28:27 +0200 profphd (1.0.17) * Much more efficient install Makefile target * Produces gold standard for tsnap_query.fasta * Able to use dirWork now: read-only input file dir is now OK * Command line options now correctly documented: no leading - * sed --in-place -> -i, --in-place is not understood by Mac sed -- Laszlo Kajan Sat, 15 May 2010 13:38:41 +0200 profphd (1.0.16) * corrected faulty file name extension matching: escapes '.' now -- Laszlo Kajan Tue, 09 Feb 2010 18:18:43 +0100 profphd (1.0.15) * removed pub blast - it was not in use -- Laszlo Kajan Sat, 16 Jan 2010 11:03:59 +0100 profphd (1.0.14) * moved ./src/prof/scr/safFilterRed.pl to librg-utils-perl -- Laszlo Kajan Fri, 15 Jan 2010 16:00:43 +0100 profphd (1.0.13) * Modifications now allow usage of RG::Utils::* modules -- Laszlo Kajan Thu, 14 Jan 2010 21:10:39 +0100 profphd (1.0.12) * added debugging for system()-like calls to scr/pack/hssp_filter.pm * added more examples: DMD_HUMAN.hssp is huge; PSA2_HUMAN.safFil has xxxx_a and xxxx_A sequences; * increased MAXCORE to 16777216 in filter_hssp.f in order to allow a big alignment to fit (DMD_HUMAN.hssp example) * Made sequence names case sensitive for READ_MSF routine - solves bug with 3h4p_A and 3h4p_a chains mistaken for the same thing -- Laszlo Kajan Tue, 12 Jan 2010 11:52:56 +0100 profphd (1.0.11) * Fixed hssp_filter 'gyachdav' path bug -- Laszlo Kajan Fri, 08 Jan 2010 12:49:19 +0100 profphd (1.0.10) * Removed faulty executable checks that did not take PATH into account -- Laszlo Kajan Thu, 07 Jan 2010 18:24:46 +0100 profphd (1.0.9) * Removed bin dependency of make all target because the binary utilities are distributed in a separate package -- Laszlo Kajan Thu, 07 Jan 2010 15:06:40 +0100 profphd (1.0.8) * Removed $ARCH extension from src/prof/scr/pack/copf.pm exeConvertSeq and exeConvertSeqBig -- Laszlo Kajan Thu, 07 Jan 2010 10:18:44 +0100 profphd (1.0.7) * Fixed saf issue due to copf path problem -- Laszlo Kajan Wed, 06 Jan 2010 17:01:59 +0100 profphd (1.0.6) * Changed prof to the gold-standard: the prof from SNAP (now snapfun) * Introduces __PREFIX__ where necessary -- Laszlo Kajan Tue, 05 Jan 2010 21:51:16 +0100 profphd (1.0.5) * Moved prof and phd fortran sources to profnet package * Added facilities for making a Debian source package out of src-lib * Changed prof to the gold-standard: the prof from SNAP (now snapfun) * Introduces __PREFIX__ where necessary -- Laszlo Kajan Tue, 05 Jan 2010 21:51:16 +0100 profphd (1.0.4) * Added -fbounds-check to Fortran compilation options * Removed .LINUX from binary names * Fixed string bounds problem at line 327 of file lib-phd.f -- Laszlo Kajan Tue, 15 Dec 2009 23:57:05 +0100 profphd (1.0.3) * Adjusted buffer size for reading in network data. Allows for analysis of large (>2000 residues) sequences -- Guy Yachdav Tue, 24 Nov 2009 12:22:17 +0200 profphd (1.0.2) * Compilation failure when profphd is installed on system issue resolved. * Man page example changed to work in default installation scenario. -- Laszlo Kajan Fri, 20 Nov 2009 08:15:04 +0100 debian/patches/0000755000000000000000000000000012207567441010625 5ustar debian/patches/fix-pod.patch0000644000000000000000000000063312207567441013216 0ustar Description: perl 5.18 doesn't allow numbers after =item, so mask it Origin: vendor Bug-Debian: http://bugs.debian.org/720497 Forwarded: no Author: gregor herrmann Last-Update: 2013-08-23 --- a/src/prof/prof +++ b/src/prof/prof @@ -238,7 +238,7 @@ See each keyword for more help. Most of alternative connectivity patterns (default=3) -=item 3 +=item Z<>3 predict sec + acc + htm debian/patches/series0000644000000000000000000000001612207567416012041 0ustar fix-pod.patch debian/compat0000644000000000000000000000000211641774446010402 0ustar 7