New upstream version 1.1.09 (863084e3) · Commits · Debian Med / predictprotein

ChangeLog

+8 −0

Original line number	Diff line number	Diff line
		predictprotein (1.1.09) unstable; urgency=low

		* predbind(1) has been renamed to prona2019(1)
		* prona2019(1) target and output file have been renamed from
		'predbind' to 'prona'

		-- Timothy Karl <karl@rostlab.org> Mon, 18 Mar 2019 15:57:00 +0100

		predictprotein (1.1.08) unstable; urgency=low

		* Added predbind(1) prediction file handling.

MakefilePP.mk

+8 −8

Original line number	Diff line number	Diff line
		@@ -59,10 +59,10 @@ PHDFILE:=$(INFILE:%.in=%.phdPred)
		PHDRDBFILE:=$(INFILE:%.in=%.phdRdb)
		# lkajan: never make PHDNOTHTMFILE a target - its creation depends on whether phd found an HTM region or not: it isn't always created
		PHDNOTHTMFILE:=$(INFILE:%.in=%.phdNotHtm)
		PREDBINDFILE:=$(INFILE:%.in=%.predbind)
		PROFFILE:=$(INFILE:%.in=%.profRdb)
		# prof output generated explicitely from one sequence - NO alignment - Chris Schaefer initiated this - B approved
		PROF1FILE:=$(INFILE:%.in=%.prof1Rdb)
		PRONAFILE:=$(INFILE:%.in=%.prona)
		# lkajan: 20120816: profasp is now removed (https://rostlab.org/bugzilla3/show_bug.cgi?id=154)
		ASPFILE:=$(INFILE:%.in=%.asp)
		NORSFILE:=$(INFILE:%.in=%.nors)
		@@ -188,7 +188,7 @@ subcell-loc:
		#
		# Optional targets should never appear in other aggregate targets (such as 'interaction').
		.PHONY: optional
		optional: loctree3 metadisorder predbind psic tmhmm tmseg somena consurf
		optional: loctree3 metadisorder prona psic tmhmm tmseg somena consurf

		.PHONY: coiledcoils
		coiledcoils: $(COILSFILE)
		@@ -395,12 +395,12 @@ $(PROFTEXTFILE): $(PROFFILE)
		# conv_prof creates query.profAscii.tmp in case query.profAscii already exists - make sure it does not
		rm -f $(PROFTEXTFILE); $(PROFROOT)scr/conv_prof.pl $< fileOut=$@ ascii nohtml nodet nograph

		.PHONY: predbind
		predbind: $(PREDBINDFILE)
		.PHONY: prona
		prona: $(PRONAFILE)

		# Predbind needs .fasta .blastPsiMat .profbval .mdisorder .profRdb to run
		$(PREDBINDFILE): $(FASTAFILE) $(BLASTMATFILE) $(PROFBVALFILE) $(METADISORDERFILE) $(PROFFILE)
		predbind -p $(dir $(FASTAFILE)) -d $(BIG80BLASTDB) $(if $(DEBUG), -v True, ) -o $@
		# ProNA needs .fasta .blastPsiMat .profbval .mdisorder .profRdb to run
		$(PRONAFILE): $(FASTAFILE) $(BLASTMATFILE) $(PROFBVALFILE) $(METADISORDERFILE) $(PROFFILE)
		prona2019 -p $(dir $(FASTAFILE)) -d $(BIG80BLASTDB) $(if $(DEBUG), -v True, ) -o $@

		.PHONY: metastudent
		metastudent: $(METASTUDENTBPO) $(METASTUDENTCCO) $(METASTUDENTMPO)
		@@ -505,7 +505,7 @@ install:
		$(NORSFILE) $(NORSSUMFILE) \
		$(NORSNETFILE) \
		$(PHDFILE) $(PHDNOTHTMFILE) $(PHDRDBFILE) \
		$(PREDBINDFILE) \
		$(PRONAFILE) \
		$(PROFTEXTFILE) $(PROFFILE) $(PROF1FILE) \
		$(PROFBVALFILE) $(PROFB4SNAPFILE) \
		$(PROFTMBFILE) $(PROFTMBDATFILE) \

configure

+10 −10

Original line number	Diff line number	Diff line
		#! /bin/sh
		# Guess values for system-dependent variables and create Makefiles.
		# Generated by GNU Autoconf 2.69 for predictprotein 1.1.08.
		# Generated by GNU Autoconf 2.69 for predictprotein 1.1.09.
		#
		# Report bugs to <https://rostlab.org/bugzilla3/enter_bug.cgi?product=predictprotein>.
		#
		@@ -580,8 +580,8 @@ MAKEFLAGS=
		# Identity of this package.
		PACKAGE_NAME='predictprotein'
		PACKAGE_TARNAME='predictprotein'
		PACKAGE_VERSION='1.1.08'
		PACKAGE_STRING='predictprotein 1.1.08'
		PACKAGE_VERSION='1.1.09'
		PACKAGE_STRING='predictprotein 1.1.09'
		PACKAGE_BUGREPORT='https://rostlab.org/bugzilla3/enter_bug.cgi?product=predictprotein'
		PACKAGE_URL=''

		@@ -1202,7 +1202,7 @@ if test "$ac_init_help" = "long"; then
		# Omit some internal or obsolete options to make the list less imposing.
		# This message is too long to be a string in the A/UX 3.1 sh.
		cat <<_ACEOF
		\`configure' configures predictprotein 1.1.08 to adapt to many kinds of systems.
		\`configure' configures predictprotein 1.1.09 to adapt to many kinds of systems.

		Usage: $0 [OPTION]... [VAR=VALUE]...

		@@ -1268,7 +1268,7 @@ fi

		if test -n "$ac_init_help"; then
		case $ac_init_help in
		short \| recursive ) echo "Configuration of predictprotein 1.1.08:";;
		short \| recursive ) echo "Configuration of predictprotein 1.1.09:";;
		esac
		cat <<\_ACEOF

		@@ -1342,7 +1342,7 @@ fi
		test -n "$ac_init_help" && exit $ac_status
		if $ac_init_version; then
		cat <<\_ACEOF
		predictprotein configure 1.1.08
		predictprotein configure 1.1.09
		generated by GNU Autoconf 2.69

		Copyright (C) 2012 Free Software Foundation, Inc.
		@@ -1359,7 +1359,7 @@ cat >config.log <<_ACEOF
		This file contains any messages produced by compilers while
		running configure, to aid debugging if configure makes a mistake.

		It was created by predictprotein $as_me 1.1.08, which was
		It was created by predictprotein $as_me 1.1.09, which was
		generated by GNU Autoconf 2.69. Invocation command line was

		$ $0 $@
		@@ -2223,7 +2223,7 @@ fi

		# Define the identity of the package.
		PACKAGE='predictprotein'
		VERSION='1.1.08'
		VERSION='1.1.09'


		cat >>confdefs.h <<_ACEOF
		@@ -2876,7 +2876,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF \|\| ac_write_fail=1
		# report actual input values of CONFIG_FILES etc. instead of their
		# values after options handling.
		ac_log="
		This file was extended by predictprotein $as_me 1.1.08, which was
		This file was extended by predictprotein $as_me 1.1.09, which was
		generated by GNU Autoconf 2.69. Invocation command line was

		CONFIG_FILES = $CONFIG_FILES
		@@ -2929,7 +2929,7 @@ _ACEOF
		cat >>$CONFIG_STATUS <<_ACEOF \|\| ac_write_fail=1
		ac_cs_config="`$as_echo "$ac_configure_args" \| sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
		ac_cs_version="\\
		predictprotein config.status 1.1.08
		predictprotein config.status 1.1.09
		configured by $0, generated by GNU Autoconf 2.69,
		with options \\"\$ac_cs_config\\"

configure.ac

+1 −1

Original line number	Diff line number	Diff line
		AC_INIT([predictprotein], [1.1.08], [https://rostlab.org/bugzilla3/enter_bug.cgi?product=predictprotein])
		AC_INIT([predictprotein], [1.1.09], [https://rostlab.org/bugzilla3/enter_bug.cgi?product=predictprotein])
		AC_CONFIG_SRCDIR([predictprotein])
		AM_INIT_AUTOMAKE
		AC_CONFIG_FILES([Makefile] [perl/Build.PL] [examples/Makefile] [helper_apps/Makefile] [resources/Makefile])

predictprotein

+2 −2

Original line number	Diff line number	Diff line
		@@ -75,8 +75,8 @@ our %meth_ext_hash = (
		phdNotHtm => 'phd',
		phdPred => 'phd',
		phdRdb => 'phd',
		predbind => 'predbind',
		profAscii => 'prof',
		prona => 'prona',
		reprof => 'reprof',
		profbval => 'profbval',
		profb4snap => 'profbval',
		@@ -652,7 +652,7 @@ These methods are run by the target 'optional'.
		protein-RNA, somena somena somena(1)
		protein-DNA
		interaction sites
		DNA- , RNA- and predbind predbind predbind(1)
		DNA- , RNA- and prona prona prona2019(1)
		Protein-binding
		protein and binding
		sites