Commit c0e72a7a authored by Andreas Tille's avatar Andreas Tille

New upstream version 1.0.10

parent 7ba57954
Authors:
See details in source files.
Reinhard Schneider <schneider@lion-ag.de>
Ulrike Goebel
C. Sander
Burkhard Rost <rost@rostlab.org>
Bug fixes and enhancements by Laszlo Kajan <lkajan@rostlab.org> and Guy Yachdav <gyachdav@rostlab.org>
Copyright:
See details in source files.
Copyright 1998-2011 by Burkhard Rost <rost@rostlab.org> EMBL, CUBIC (Columbia University, NY, USA) and LION Biosciences (Heidelberg, DE)
Copyright 1994 by C. Sander MPIMF (Heidelberg, DE)
Copyright 2009-2011 by Guy Yachdav <gyachdav@rostlab.org> CUBIC (Columbia University, NY, USA), Technical University Munich (Munich, DE), Biosof LLC (USA)
Copyright 2009-2011 by Laszlo Kajan <lkajan@rostlab.org> Technical University Munich (Munich, DE)
Copyright 1988,1991,1997 by Reinhard Schneider LION Biosciences (Heidelberg, DE)
Copyright 1997 by Ulrike Goebel LION Biosciences (Heidelberg, DE)
This diff is collapsed.
profphd-utils (1.0.10) unstable; urgency=low
* Removed CONTACT and AVAILABLE fields from output. These were outdated and
incorrect.
-- Laszlo Kajan <lkajan@rostlab.org> Tue, 14 Aug 2012 09:19:02 +0200
profphd-utils (1.0.9) unstable; urgency=low
* -fbacktrace in make file
* convert_seq.f: increased parameter MAX_NAME_LEN to 1024
* lib-maxhom.f and lib-convert.f: in SUBROUTINE GETCHAR(KCHAR,CHARARR,CTEXT):
changed LINE from fixed value to: CHARACTER*(KCHAR) - KCHAR was not
used in this SUB before.
* fixed gfortran warnings, added LDFLAGS
-- Laszlo Kajan <lkajan@rostlab.org> Mon, 28 Nov 2011 18:43:44 +0100
profphd-utils (1.0.8) unstable; urgency=low
* dash safe Makefile
-- Laszlo Kajan <lkajan@rostlab.org> Tue, 27 Sep 2011 18:40:48 +0200
profphd-utils (1.0.7) unstable; urgency=low
* added man pages for convert_seq and filter_hssp
-- Laszlo Kajan <lkajan@rostlab.org> Tue, 27 Sep 2011 10:07:47 +0200
PACKAGE := profphd-utils
VERSION := 1.0.10
DISTDIR := $(PACKAGE)-$(VERSION)
mandir := $(prefix)/share/man
man1dir := $(mandir)/man1
ARCH = LINUX
F77 = gfortran
AM_FFLAGS := -O2 -fbounds-check -Wuninitialized -fbacktrace -g
#AM_FFLAGS := $(AM_FFLAGS) -Wall -Wno-unused -Wtabs
BINARIES=convert_seq filter_hssp
MAN1 := convert_seq.1 filter_hssp.1
MANS := $(MAN1)
all: $(BINARIES) $(MANS)
%.1 : %.pod Makefile
pod2man -c 'User Commands' -r "$(VERSION)" -name $(shell echo "$(basename $@)" | tr '[:lower:]' '[:upper:]') "$<" "$@"
convert_seq filter_hssp : maxhom.common maxhom.param
convert_seq : convert_seq.f lib-maxhom.f lib-sys-$(ARCH).f
$(F77) $(CPPFLAGS) $(AM_FFLAGS) $(FFLAGS) $(LDFLAGS) -o $@ convert_seq.f lib-maxhom.f lib-sys-$(ARCH).f
filter_hssp : filter_hssp.f lib-maxhom.f lib-sys-$(ARCH).f
$(F77) $(CPPFLAGS) $(AM_FFLAGS) $(FFLAGS) $(LDFLAGS) -o $@ filter_hssp.f lib-maxhom.f lib-sys-$(ARCH).f
#lib-maxhom.o : maxhom.common maxhom.param
install:
mkdir -p $(DESTDIR)$(prefix)/bin && \
cp $(BINARIES) $(DESTDIR)$(prefix)/bin/
mkdir -p $(DESTDIR)$(man1dir) && \
cp $(MAN1) $(DESTDIR)$(man1dir)/
clean:
rm -f *.o convert_seq filter_hssp convert_seq.1 filter_hssp.1
dist: $(DISTDIR)
tar -c -f - "$(DISTDIR)" | gzip -c >$(DISTDIR).tar.gz
rm -rf $(DISTDIR)
$(DISTDIR): distclean
rm -rf $(DISTDIR) && mkdir -p $(DISTDIR) && \
rsync -avC \
--exclude /*-stamp \
--exclude .*.swp \
AUTHORS \
ChangeLog \
compile_macintel.csh \
compile.pl \
convert_seq.f \
convert_seq.pod \
COPYING \
dead.f \
filter_hssp.f \
filter_hssp.pod \
lib-convert.f \
lib-maxhom.f \
lib-maxhom-node-pvm3.f \
lib-metr.f \
lib-metr-sys.f \
lib-sys-LINUX.f \
long.msf \
Makefile \
maxhom.common \
maxhom.default \
maxhom.f \
maxhom.param \
metr2st_make.f \
$(PACKAGE).spec \
ReadMe \
ReadMe-linux \
ReadMe-mac \
$(DISTDIR)/;
distclean: clean
rm -rf\
$(DISTDIR) \
$(DISTDIR).tar.gz
help:
@echo "all*: convert_seq filter_hssp"
@echo "convert_seq"
@echo "filter_hssp"
@echo "install"
@echo
@echo "VARIABLES"
@echo "prefix - prefix all paths with 'prefix'"
@echo "DESTDIR - installation directory prefix"
.PHONY: all clean dist distclean help install
*----------------------------------------------------------------------*
* Burkhard Rost Aug, 1998 version 0.1 *
* EMBL/LION http://www.embl-heidelberg.de/~rost/ *
* D-69012 Heidelberg rost@embl-heidelberg.de *
*----------------------------------------------------------------------*
* ------------------------------ *
* This directory contains: *
* ------------------------------ *
* *
* - all FORTRAN tools needed : 1 convert_seq.f *
* : 2 filter_hssp.f *
* : 3 maxhom.f *
* - FORTRAN include files : 1 maxhom.para *
* : 2 maxhom.common *
* - all FORTRAN libs : *
* convert_seq : lib-maxhom.f + lib-sys-ARCH.f *
* filter_hssp : lib-maxhom.f + lib-sys-ARCH.f *
* maxhom : lib-maxhom.f + lib-sys-ARCH.f *
* : + lib-maxhom-node-pvm3.f *
* - general perl make script : (compile.pl) *
* run this script with no argument for help! *
* - make-files : (mat/make_*) *
* *
* ------------------------------ *
* to DO for compile: *
* ------------------------------ *
* *
* compile.pl -> gives help *
* compile.pl auto -> DOES it.. *
* *
* *
*----------------------------------------------------------------------*
#on oak
/usr/pub/pgi/linux86/bin/pgf77 -o maxhom.LINUX -O3 -C maxhom.f lib-sys-LINUX.f lib-maxhom.f lib-maxhom-node-pvm3.f
/usr/pub/pgi/linux86/bin/pgf77 -o filter_hssp.LINUX -O3 -C filter_hssp.f lib-sys-LINUX.f lib-maxhom.f
/usr/pub/pgi/linux86/bin/pgf77 -o convert_seq.LINUX -O3 -C convert_seq.f lib-sys-LINUX.f lib-convert.f
/usr/pub/pgi/linux86/bin/pgf77 -o profile_make.LINUX -O3 -C profile_make.f lib-sys-LINUX.f lib-profile-make.f
# gnu gfortran compiler - only on INTEL MAC
/usr/local/bin/gfortran -o maxhom.MACINTEL -O3 -C maxhom.f lib-sys-MAC.f lib-maxhom.f lib-maxhom-node-pvm3.f
/usr/local/bin/gfortran -o convert_seq.MACINTEL -O3 -C convert_seq.f lib-sys-MAC.f lib-convert.f
/usr/local/bin/gfortran -o filter_hssp.MACINTEL -O3 -C filter_hssp.f lib-sys-MAC.f lib-maxhom.f
/usr/local/bin/gfortran -o profile_make.MACINTEL -O3 -C profile_make.f lib-sys-MAC.f lib-profile-make.f
# gnu g77 compiler
g77 -o maxhom.MAC -O3 -C maxhom.f lib-sys-MAC.f lib-maxhom.f lib-maxhom-node-pvm3.f
g77 -o convert_seq.MAC -O3 -C convert_seq.f lib-sys-MAC.f lib-convert.f
g77 -o filter_hssp.MAC -O3 -C filter_hssp.f lib-sys-MAC.f lib-maxhom.f
g77 -o profile_make.MAC -O3 -C profile_make.f lib-sys-MAC.f lib-profile-make.f
# IBM compiler
setenv PATH /opt/ibmcmp/xlf/8.1/bin:/usr/pub/bin:/usr/local/bin:/bin:/sbin:/usr/bin:/usr/sbin:/usr/etc:/sbin:/usr/local/bin
/opt/ibmcmp/xlf/8.1/bin/f77 -o maxhom.IBM -O3 -C maxhom.f lib-sys-MACIBM.f lib-maxhom.f lib-maxhom-node-pvm3.f
/opt/ibmcmp/xlf/8.1/bin/f77 -o convert_seq.IBM -O3 -C convert_seq.f lib-sys-MACIBM.f lib-convert.f
/opt/ibmcmp/xlf/8.1/bin/f77 -o filter_hssp.IBM -O3 -C filter_hssp.f lib-sys-MACIBM.f lib-maxhom.f
#!/bin/env perl
##!/usr/local/bin/perl -w
#
#
$scrName=$0;$scrName=~s/^.*\/|\.pl//g;
$scrGoal="compile PHD FORTRAN tools programs (convert_seq, filter_hssp)";
#$scrGoal="compile PHD FORTRAN tools programs (convert_seq, filter_hssp, maxhom ?)";
#
#
$[ =1 ;
$dirMake= "mat/";
# for PHD
$fileMake{"convert"}="make_convert_seq.ARCH";
$fileMake{"filter"}= "make_filter_hssp.ARCH";
# for TOPITS
$fileMake{"metr2st"}="make_metr2st_make.ARCH";
# for MaxHom
$fileMake{"maxhom"}= "make_maxhom.ARCH";
$fileMake{"profile"}="make_profile_make.ARCH";
$exe{"convert"}= "convert_seq.". "ARCH";
$exe{"filter"}= "filter_hssp.". "ARCH";
$exe{"metr2st"}= "metr2st_make.". "ARCH";
$exe{"maxhom"}= "maxhom.". "ARCH";
$exe{"profile"}= "profile_make.". "ARCH";
$LnotMaxhome= 1;
#$LnotMaxhome= 0;
@all=("convert","filter","metr2st","maxhom","profile");
# ------------------------------
if ($#ARGV<1){ # help
print "goal: $scrGoal\n";
print "use: '$scrName <auto|filter|convert|metr2st|maxhom|profile>'\n";
print "opt: (pass the following arguments like '$scrName arg=val')\n";
# 'keyword' 'value' 'description'
printf " %-12s=%-10s %-22s %-s\n","." x 10, "." x 10, "." x 15, "." x 20;
printf " %-12s=%-10s %-22s %-s\n","keyword", "value", "default", "explanation";
printf " %-12s=%-10s %-22s %-s\n","." x 10, "." x 10, "." x 15, "." x 20;
printf " %-12s=%-10s %-22s %-s\n","ARCH", "ALPHA", "",
"system arch: SGI64|SGI32|SGI5|ALPHA|SUNMP";
printf " %-12s=%-10s %-22s %-s\n","dir", "mat",$dirMake, "directory with make file";
foreach $kwd (@all){
next if ($LnotMaxhom && $kwd eq "maxhom");
printf " %-12s=%-10s %-22s %-s\n","exe_".$kwd,"x", $exe{$kwd}, "name of executable"; }
foreach $kwd (@all){
next if ($LnotMaxhom && $kwd eq "maxhom");
printf " %-12s=%-10s %-22s %-s\n","make_".$kwd,"x", $fileMake{$kwd},"make file";}
foreach $kwd (@all){
next if ($LnotMaxhom && $kwd eq "maxhom");
printf " %-12s %-10s %-22s %-s\n",$kwd, "no value", "1","compiles $kwd";}
exit;
}
foreach $kwd (@all) {
$do{$kwd}=0;}
$Lopted=0;
# ------------------------------
# read command line
foreach $arg (@ARGV){
next if ($arg eq $ARGV[1] && $arg =~ /^(auto|do)$/);
if ($arg=~/^ARCH=(.*)$/i) { $ARCH=$1;}
elsif ($arg=~/^make_(.*)=(.*)$/) { $fileMake{$1}=$2;}
elsif ($arg=~/^exe_(.*)=(.*)$/) { $exe{$1}=$2;}
elsif ($arg=~/^conv(ert)?$/) { $do{"convert"}=1; $Lopted=1;}
elsif ($arg=~/^fil(ter)?$/) { $do{"filter"}= 1; $Lopted=1;}
elsif ($arg=~/^metr(2st)?$/) { $do{"metr2st"}=1; $Lopted=1;}
elsif ($arg=~/^max(hom)?$/) { $do{"maxhom"}= 1; $Lopted=1;}
elsif ($arg=~/^prof(ile)?$/) { $do{"profile"}=1; $Lopted=1;}
elsif ($arg=~/^dir=(.*)$/) { $dirMake=$1;}
# elsif ($arg=~/^=(.*)$/){ $=$1;}
else { print "*** ERROR $scrName: wrong command line arg '$arg'\n";
die;}}
$ARCH= $ARCH || $ENV{'ARCH'};
$dirMake.="/" if ($dirMake !~/\// && length($dirMake)>=1);
if (! defined $ARCH) {
$ansr=
&get_in_keyboardLoc("ARCH","",$scrName);
$ARCH=$ansr; }
if ($ARCH !~ /ALPHA|SGI(64|32|5)|SUNMP|SUN4SOL|LINUX/){
print "--- $scrName: ARCH must be either of the following :\n";
print "--- "." " x length($scrName)." ALPHA|SGI64|SGI32|SGI5|SUNMP|SUN4SOL\n";
$ansr=
&get_in_keyboardLoc("ARCH","",$scrName);
$ARCH=$ansr; }
if ($ARCH !~ /ALPHA|SGI(64|32|5)|SUNMP|SUN4SOL|LINUX/){
print "*** ERROR $scrName: ARCH really must be either of the following :\n";
print "*** "." " x length($scrName)." ALPHA|SGI64|SGI32|SGI5|SUNMP|SUN4SOL\n";
die; }
# default: do all 3 compilations
if (! $Lopted){
foreach $kwd (@all){
next if ($LnotMaxhom && $kwd eq "maxhom");
$do{$kwd}=1;}}
foreach $kwd (@all) {
next if (! $do{$kwd});
$fileMake{$kwd}=~s/ARCH/$ARCH/ if ($fileMake{$kwd} =~ /ARCH/);
$fileMake{$kwd}=$dirMake.$fileMake{$kwd} if ($fileMake{$kwd} !~ /$dirMake/);
$fileMake=$fileMake{$kwd};
undef $exeOut;
if (defined $exe{$kwd}) {
$exeOut= $exe{$kwd};
$exeOut=~s/ARCH/$ARCH/ if ($exeOut=~/ARCH/);}
$exeDef= "convert_seq.". $ARCH if ($kwd eq "convert");
$exeDef= "filter_hssp.". $ARCH if ($kwd eq "filter");
$exeDef= "maxhom." . $ARCH if ($kwd eq "maxhom");
$exeDef= "metr2st_make.".$ARCH if ($kwd eq "metr2st");
$exeDef= "profile_make.".$ARCH if ($kwd eq "profile");
# local copy of make file
$fileMakeTmp="make_".$kwd."_tmp_".$$.".".$ARCH;
print "--- $scrName: system '\\cp $fileMake $fileMakeTmp '\n";
system("\\cp $fileMake $fileMakeTmp");
# compile
print "--- $scrName: system 'make -f $fileMakeTmp'\n";
system("make -f $fileMakeTmp");
if (-e $exeDef && defined $exeOut && ($exeDef ne $exeOut)) {
print "--- $scrName: system '\\mv $exeDef $exeOut'\n";
system("\\mv $exeDef $exeOut");
$exeDef=$exeOut; }
print "--- $scrName: expected executable: $exeDef\n" if (-e $exeDef);
if (! -e $exeDef) {
print "*** ERROR $scrName: never made '$exeDef'\n";
print "*** keyword assigned to executable?? check code!\n";}
unlink($fileMakeTmp);
}
exit;
#===============================================================================
sub get_in_keyboardLoc {
local($des,$def,$pre,$Lmirror)=@_;local($txt);
#--------------------------------------------------------------------------------
# get_in_keyboardLoc gets info from keyboard
# in: $des : keyword to get
# in: $def : default settings
# in: $pre : text string beginning screen output
# default '--- '
# in: $Lmirror: if true, the default is mirrored
# out: $val : value obtained
#--------------------------------------------------------------------------------
$pre= "---" if (! defined $pre);
$Lmirror=0 if (! defined $Lmirror || ! $Lmirror);
$txt=""; # ini
printf "%-s %-s\n", $pre,"-" x (79 - length($pre));
printf "%-s %-15s:%-s\n", $pre,"type value for",$des;
if (defined $def){
printf "%-s %-15s:%-s\n",$pre,"type RETURN to enter value, or to keep default";
printf "%-s %-15s>%-s\n",$pre,"default value",$def;}
else {
printf "%-s %-15s>%-s\n",$pre,"type RETURN to enter value"; }
$txt=$def if ($Lmirror); # mirror it
printf "%-s %-15s>%-s", $pre,"type",$txt;
while(<STDIN>){
$txt.=$_;
last if ($_=~/\n/);} $txt=~s/^\s+|\s+$//g;
$txt=$def if (length($txt) < 1);
printf "%-s %-15s>%-s\n", $pre,"--> you chose",$txt;
return ($txt);
} # end of get_in_keyboardLoc
echo "--- now Maxhom: "
echo "/usr/local/bin/gfortran -o maxhom.MACINTEL -O3 -C maxhom.f lib-sys-MAC.f lib-maxhom.f lib-maxhom-node-pvm3.f "
/usr/local/bin/gfortran -o maxhom.MACINTEL -O3 -C maxhom.f lib-sys-MAC.f lib-maxhom.f lib-maxhom-node-pvm3.f
echo "--- now convert_seq: "
echo "/usr/local/bin/gfortran -o convert_seq.MACINTEL -O3 -C convert_seq.f lib-sys-MAC.f lib-convert.f"
/usr/local/bin/gfortran -o convert_seq.MACINTEL -O3 -C convert_seq.f lib-sys-MAC.f lib-convert.f
echo "--- now filter_hssp:"
echo "/usr/local/bin/gfortran -o filter_hssp.MACINTEL -O3 -C filter_hssp.f lib-sys-MAC.f lib-maxhom.f"
/usr/local/bin/gfortran -o filter_hssp.MACINTEL -O3 -C filter_hssp.f lib-sys-MAC.f lib-maxhom.f
echo "--- exit before profile_make! "
echo "--- "
echo "--- stay cool IS ok!!"
echo "--- "
exit
echo "--- now profile_make:"
echo "/usr/local/bin/gfortran -o profile_make.MACINTEL -O3 -C profile_make.f lib-sys-MAC.f lib-profile-make.f"
/usr/local/bin/gfortran -o profile_make.MACINTEL -O3 -C profile_make.f lib-sys-MAC.f lib-profile-make.f
This diff is collapsed.
=pod
=head1 NAME
convert_seq - conversion of sequence and alignment formats
=head1 SYNOPSIS
convert_seq [OPTION]
=head1 DESCRIPTION
convert_seq is used for sequence and alignment format conversion. Instead of using command line arguments it starts a conversation with the user where the desired function can be invoked by answering questions.
This program is used by the prof(1) secondary structure, accessibility and transmembrane helix predictor from Burkhard Rost.
=head1 OPTIONS
None. Answer questions printed on STDOUT by typing your choice into STDIN.
=head1 AUTHORS
=over
=item Reinhard Schneider Mar, 1991 version 1.0 LION http://www.lion-ag/ Heidelberg
=item Ulrike Goebel Mar, 1997 version 1.1 LION http://www.lion-ag/ Heidelberg
=item Reinhard Schneider Mar, 1997 version 2.0 LION http://www.lion-ag/ Heidelberg
=item Burkhard Rost May, 1998 version 2.1 EMBL/LION Heidelberg
=item Burkhard Rost Oct, 1998 version 2.2
=item Laszlo Kajan <lkajan@rostlab.org> TU Muenchen, Germany
=item Guy Yachdav <gyachdav@rostlab.org> CUBIC (Columbia University, NY, USA), Technical University Munich (Munich, DE), BioSof LLC (USA)
=back
=head1 SEE ALSO
prof(1), filter_hssp(1)
=cut
This diff is collapsed.
profphd-utils for Debian
------------------------
This package presents the binary utilities for profphd.
-- Laszlo Kajan <lkajan@rostlab.org> Fri, 18 Dec 2009 23:42:34 +0100
profphd-utils for Debian
========================
lintian warnings
----------------
W: profphd-utils: hardening-no-fortify-functions usr/bin/convert_seq
W: profphd-utils: hardening-no-fortify-functions usr/bin/filter_hssp
These binaries are compiled from gfortran source only. As far as I can tell, all the flags are set. blhc(1) does not report problems. I think these are false positives, but I do not want to override the warning, in order maintain awareness of this issue.
Notes on how this package can be tested.
────────────────────────────────────────
This package can be tested by executing
sh convert-seq-test
sh filter-hssp-test
in order to confirm its integrity.
To test manually, run one of these executables:
convert_seq
filter_hssp
They both work in interactive mode (as described in man pages), testsuite
simply emulates one of the possible sequences of user input commands.
Each `\n` in tests corresponds to moving forward to next command.
As stated in man pages for `convert_seq` and `filter_hssp`, these programs
write output to STDOUT. It means that in normal situation no errors should
be produced.
Example files for this testsuite were taken from `profphd` source package.
profphd-utils (1.0.10-3) unstable; urgency=medium
* Team upload.
* add debian/examples/ to use with testsuite
* add profphd-utils.examples
* add testsuite for autopkgtest
* add files in debian/examples/ to debian/copyright,
* run cme fix dpkg-copyright
* add debian/docs
* add debian/README.test
* cme fix dpkg-control
* add hardening
-- Tatiana Malygina <merlettaia@gmail.com> Fri, 08 Jul 2016 17:03:18 +0300
profphd-utils (1.0.10-2) unstable; urgency=medium
* Add myself to Uploaders
* cme fix dpkg-control
* Priority: optional
* debhelper 9
* d/copyright converted to DEP5
-- Andreas Tille <tille@debian.org> Fri, 08 Jan 2016 16:16:28 +0100
profphd-utils (1.0.10-1) unstable; urgency=low
* New upstream release.
-- Laszlo Kajan <lkajan@rostlab.org> Tue, 14 Aug 2012 09:29:31 +0200
profphd-utils (1.0.9-1) unstable; urgency=low
* New upstream release.
* Changed from cdbs to dh.
-- Laszlo Kajan <lkajan@rostlab.org> Fri, 01 Jun 2012 12:56:21 +0200
profphd-utils (1.0.8-1) unstable; urgency=low
* Initial release in Debian (Closes: #643323)
-- Laszlo Kajan <lkajan@rostlab.org> Tue, 27 Sep 2011 10:08:18 +0200
profphd-utils (1.0.6) unstable; urgency=low
* Debian native now
-- Laszlo Kajan <lkajan@rostlab.org> Mon, 28 Feb 2011 15:50:38 +0100
profphd-utils (1.0.5)
* Introduced AM_FFLAGS; FFLAGS now can be used on the command line/ENV as expected
-- Laszlo Kajan <lkajan@rostlab.org> Thu, 01 Apr 2010 11:53:35 +0200
profphd-utils (1.0.4)
* 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 <lkajan@rostlab.org> Tue, 12 Jan 2010 12:17:03 +0100
profphd-utils (1.0.3)
* Removed unnecessary directories; made not to install *.{LINUX,ALPHA,etc} files
* lib-sys-linux.f was duplicate of lib-sys-LINUX.f - lib-sys-linux.f removed
* Distribute only .LINUX version of lib-sys-*.f
-- Laszlo Kajan <lkajan@rostlab.org> Tue, 05 Jan 2010 23:18:07 +0100
profphd-utils (1.0.2)
* Fixed uninitialized variables without -flocal-init-zero
-- Laszlo Kajan <lkajan@rostlab.org> Tue, 05 Jan 2010 23:18:07 +0100
profphd-utils (1.0.1)
* Initial version
-- Laszlo Kajan <lkajan@rostlab.org> Fri, 18 Dec 2009 23:23:21 +0100
Source: profphd-utils
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Laszlo Kajan <lkajan@rostlab.org>,
Andreas Tille <tille@debian.org>
Section: science
Priority: optional
Build-Depends: debhelper (>= 9),
gfortran
Standards-Version: 3.9.8
Vcs-Browser: https://anonscm.debian.org/viewvc/debian-med/trunk/packages/rostlab/profphd-utils/trunk/
Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/rostlab/profphd-utils/trunk/
Homepage: http://www.rostlab.org/
Package: profphd-utils
Architecture: any
Depends: ${shlibs:Depends},
${misc:Depends}
Recommends: profphd
Description: profphd helper utilities convert_seq and filter_hssp
The package provides the following binary utilities: convert_seq, filter_hssp.
These are used by prof from the profphd package: a secondary structure,
accessibility and transmembrane helix predictor from Burkhard Rost.
Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: profphd-utils
Upstream-Contact: Reinhard Schneider <schneider@lion-ag.de>
Source: ftp://rostlab.org/profphd-utils/
Files: *
Copyright: 1998-2011 by Burkhard Rost <rost@rostlab.org> EMBL, CUBIC (Columbia University, NY, USA) and LION Biosciences (Heidelberg, DE)
1994 by C. Sander MPIMF (Heidelberg, DE)
2009-2011 by Guy Yachdav <gyachdav@rostlab.org> CUBIC (Columbia University, NY, USA), Technical University Munich (Munich, DE), Biosof LLC (USA)
2009-2011 by Laszlo Kajan <lkajan@rostlab.org> Technical University Munich (Munich, DE)
1988,1991,1997 by Reinhard Schneider LION Biosciences (Heidelberg, DE)
1997 by Ulrike Goebel LION Biosciences (Heidelberg, DE)
License: GPL-2+
Files: debian/*
Copyright: 2009-2012 Laszlo Kajan <lkajan@rostlab.org>
License: GPL-2+
Files: debian/examples/*
Copyright:
1998 B. Rost <rost@rostlab.org> EMBL, CUBIC (Columbia University, NY, USA) and LION Biosciences (Heidelberg, DE)
C. Sander
P. Fariselli
R. Casadio
J. Liu
2009-2013 G. Yachdav <gyachdav@rostlab.org> CUBIC (Columbia University, NY, USA) and Technical University Munich (Munich, DE)
2009-2013 L. Kajan <lkajan@rostlab.org> Laszlo Kajan <lkajan@rostlab.org> Technical University Munich (Munich, DE)
License: GPL-2+
Comment: example files are used in testsuite for autopkgtest. They were taken
from `profphd` source package to remove profphd package dependency in
debian/control.
.
In profphd upstream these files were found in the following locations:
1ppt.hssp - in src/prof/exa/ folder,
Maxhom_GCG.metric - in src/prof/mat/ folder.
License: GPL-2+
This package 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 package 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 package; if not, write to the Free Software
Foundation, Inc., 51 Franklin St, 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'.
debian/README.test
debian/tests/convert-seq-test
debian/tests/filter-hssp-test
This diff is collapsed.
#****************************************************************** MAXHOM AMINO ACID EXCHANGE MATRIX ***************************************
# table used by the GCG-package
# see: Gribskov and Burgess NAR 14(16) 6745-6763
# minimal value: -1.2 ; maximal value: 1.5
# symbols: "-X!" added
# Dayhoff table (Schwartz, R. M. and Dayhoff, M. O. [1979] in Atlas of Protein Sequence and Structure, Dayhoff, M. O. Ed,
# pp. 353-358, National Biomedical Research Foundation, Washington D.C.) rescaled by dividing each value by the sum of its row
# and column, and normalizing to a mean of 0 and standard deviation of 1.0. The value for FY (Phe-Tyr) = RW =1.425.
# Perfect matches are set to 1.5 and no matches on any row are better than perfect matches.
#============================================================================================================================================
STRUCTURE-STATES: 1
I/O-STATES: 1
#============================================================================================================================================
AA STR I/O V L I M F W Y G A P S T C H R K Q E N D B Z
V 1.50 0.80 1.10 0.60 0.20 -0.80 -0.10 0.20 0.20 0.10 -0.10 0.20 0.20 -0.30 -0.30 -0.20 -0.20 -0.20 -0.30 -0.20 -0.20 -0.20
L 0.80 1.50 0.80 1.30 1.20 0.50 0.30 -0.50 -0.10 -0.30 -0.40 -0.10 -0.80 -0.20 -0.40 -0.30 -0.10 -0.30 -0.40 -0.50 -0.50 -0.20
I 1.10 0.80 1.50 0.60 0.70 -0.50 0.10 -0.30 0.00 -0.20 -0.10 0.20 0.20 -0.30 -0.30 -0.20 -0.30 -0.20 -0.30 -0.20 -0.20 -0.20
M 0.60 1.30 0.60 1.50 0.50 -0.30 -0.10 -0.30 0.00 -0.20 -0.30 0.00 -0.60 -0.30 0.20 0.20 0.00 -0.20 -0.30 -0.40 -0.30 -0.10
F 0.20 1.20 0.70 0.50 1.50 1.30 1.40 -0.60 -0.50 -0.70 -0.30 -0.30 -0.10 -0.10 -0.50 -0.70 -0.80 -0.70 -0.50 -1.00 -0.70 -0.70
W -0.80 0.50 -0.50 -0.30 1.30 1.50 1.10 -1.00 -0.80 -0.80 0.30 -0.60 -1.20 -0.10 1.40 0.10 -0.50 -1.10 -0.30 -1.10 -0.70 -0.80
Y -0.10 0.30 0.10 -0.10 1.40 1.10 1.50 -0.70 -0.30 -0.80 -0.40 -0.30 1.00 0.30 -0.60 -0.60 -0.60 -0.50 -0.10 -0.50 -0.30 -0.60
G 0.20 -0.50 -0.30 -0.30 -0.60 -1.00 -0.70 1.50 0.70 0.30 0.60 0.40 0.20 -0.20 -0.30 -0.10 0.20 0.50 0.40 0.70 0.60 0.30
A 0.20 -0.10 0.00 0.00 -0.50 -0.80 -0.30 0.70 1.50 0.50 0.40 0.40 0.30 -0.10 -0.30 0.00 0.20 0.30 0.20 0.30 0.20 0.20
P 0.10 -0.30 -0.20 -0.20 -0.70 -0.80 -0.80 0.30 0.50 1.50 0.40 0.30 0.10 0.20 0.30 0.10 0.30 0.10 0.00 0.10 0.10 0.20
S -0.10 -0.40 -0.10 -0.30 -0.30 0.30 -0.40 0.60 0.40 0.40 1.50 0.30 0.70 -0.20 0.10 0.20 -0.10 0.20 0.30 0.20 0.30 0.00
T 0.20 -0.10 0.20 0.00 -0.30 -0.60 -0.30 0.40 0.40 0.30 0.30 1.50 0.20 -0.10 -0.10 0.20 -0.10 0.20 0.20 0.20 0.20 0.10
C 0.20 -0.80 0.20 -0.60 -0.10 -1.20 1.00 0.20 0.30 0.10 0.70 0.20 1.50 -0.10 -0.30 -0.60 -0.60 -0.60 -0.30 -0.50 -0.40 -0.60
H -0.30 -0.20 -0.30 -0.30 -0.10 -0.10 0.30 -0.20 -0.10 0.20 -0.20 -0.10 -0.10 1.50 0.50 0.10 0.70 0.40 0.50 0.40 0.40 0.50
R -0.30 -0.40 -0.30 0.20 -0.50 1.40 -0.60 -0.30 -0.30 0.30 0.10 -0.10 -0.30 0.50 1.50 0.80 0.40 0.00 0.10 0.00 0.10 0.20
K -0.20 -0.30 -0.20 0.20 -0.70 0.10 -0.60 -0.10 0.00 0.10 0.20 0.20 -0.60 0.10 0.80 1.50 0.40 0.30 0.40 0.30 0.40 0.40
Q -0.20 -0.10 -0.30 0.00 -0.80 -0.50 -0.60 0.20 0.20 0.30 -0.10 -0.10 -0.60 0.70 0.40 0.40 1.50 0.70 0.40 0.70 0.50 1.10
E -0.20 -0.30 -0.20 -0.20 -0.70 -1.10 -0.50 0.50 0.30 0.10 0.20 0.20 -0.60 0.40 0.00 0.30 0.70 1.50 0.50 1.00 0.70 1.10
N -0.30 -0.40 -0.30 -0.30 -0.50 -0.30 -0.10 0.40 0.20 0.00 0.30 0.20 -0.30 0.50 0.10 0.40 0.40 0.50 1.50 0.70 1.10 0.40
D -0.20 -0.50 -0.20 -0.40 -1.00 -1.10 -0.50 0.70 0.30 0.10 0.20 0.20 -0.50 0.40 0.00 0.30 0.70 1.00 0.70 1.50 1.10 0.90
B -0.20 -0.50 -0.20 -0.30 -0.70 -0.70 -0.30 0.60 0.20 0.10 0.30 0.20 -0.40 0.40 0.10 0.40 0.50 0.70 1.10 1.10 1.10 0.60
Z -0.20 -0.20 -0.20 -0.10 -0.70 -0.80 -0.60 0.30 0.20 0.20 0.00 0.10 -0.60 0.50 0.20 0.40 1.10 1.10 0.40 0.90 0.60 1.10
#!/usr/bin/make -f
# Uncomment this to turn on verbose mode.
#export DH_VERBOSE=1
export DEB_BUILD_MAINT_OPTIONS = hardening=+all
export CPPFLAGS:=$(shell dpkg-buildflags --get CPPFLAGS)
export FFLAGS:=$(shell dpkg-b