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# Makefile.in generated by automake 1.11.1 from Makefile.am.
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# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
# 2003, 2004, 2005, 2006, 2007, 2008, 2009 Free Software Foundation,
# Inc.
# This Makefile.in is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
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# set flags
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# macros for program dependencies
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SQUIDUTILS = src/seqstat_main.c src/reformat_main.c src/shuffle_main.c src/revcomp_main.c src/getopt.c
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ps: ps-am
ps-am:
uninstall-am: uninstall-binPROGRAMS uninstall-dist_binSCRIPTS \
uninstall-includeHEADERS
@$(NORMAL_INSTALL)
$(MAKE) $(AM_MAKEFLAGS) uninstall-hook
.MAKE: all install-am install-data-am install-strip uninstall-am
.PHONY: CTAGS GTAGS all all-am am--refresh check check-am clean \
clean-binPROGRAMS clean-generic ctags dist dist-all dist-bzip2 \
dist-gzip dist-lzma dist-shar dist-tarZ dist-xz dist-zip \
distcheck distclean distclean-compile distclean-generic \
distclean-hdr distclean-tags distcleancheck distdir \
distuninstallcheck dvi dvi-am html html-am info info-am \
install install-am install-binPROGRAMS install-data \
install-data-am install-data-hook install-dist_binSCRIPTS \
install-dvi install-dvi-am install-exec install-exec-am \
install-html install-html-am install-includeHEADERS \
install-info install-info-am install-man install-pdf \
install-pdf-am install-ps install-ps-am install-strip \
installcheck installcheck-am installdirs maintainer-clean \
maintainer-clean-generic mostlyclean mostlyclean-compile \
mostlyclean-generic pdf pdf-am ps ps-am tags uninstall \
uninstall-am uninstall-binPROGRAMS uninstall-dist_binSCRIPTS \
uninstall-hook uninstall-includeHEADERS
# then create build rules
tRNAscan-SE: tRNAscan-SE.src Makefile
$(do_subst) < $(srcdir)/tRNAscan-SE.src > tRNAscan-SE
chmod +x tRNAscan-SE
tRNAscan-SE.conf: tRNAscan-SE.conf.src Makefile
$(do_subst) < $(srcdir)/tRNAscan-SE.conf.src > tRNAscan-SE.conf
chmod +x tRNAscan-SE.conf
bin/sstofa: src/sstofa.in Makefile
$(do_subst) < $(srcdir)/src/sstofa.in > bin/sstofa
chmod +x bin/sstofa
bin/fasta2gsi: src/fasta2gsi.in Makefile
$(do_subst) < $(srcdir)/src/fasta2gsi.in > bin/fasta2gsi
chmod +x bin/fasta2gsi
bin/EukHighConfidenceFilter: EukHighConfidenceFilter.in Makefile
$(do_subst) < $(srcdir)/EukHighConfidenceFilter.in > bin/EukHighConfidenceFilter
chmod +x bin/EukHighConfidenceFilter
# copy libraries. We don't have "libraries" in the libgmp.so.4 kind, but we do have data libraries, so we don't have to deal with lib_LTLIBRARIES.
install-data-hook:
chmod u+w $(exec_prefix)
test -d $(libdir) || mkdir $(libdir)
chmod u+w $(libdir)
test -d $(libdir)/tRNAscan-SE || mkdir $(libdir)/tRNAscan-SE
cp -rf $(srcdir)/lib/* $(libdir)/tRNAscan-SE
# remove lib/ files during uninstallation. A bit of a hack, since lib files are write-protected by default. Files
uninstall-hook:
chmod -R u+w $(libdir)/tRNAscan-SE
rm -rf $(libdir)/tRNAscan-SE
# Tell versions [3.59,3.63) of GNU make to not export all variables.
# Otherwise a system limit (for SysV at least) may be exceeded.
.NOEXPORT:
README
View file @ c9581aea
......@@ -5,7 +5,7 @@ Patricia Chan, Brian Lin, and Todd Lowe
School of Engineering, University of California, Santa Cruz, CA
--------------------------------------------------------------
Current release: 2.0 (December 2017)
Current release: 2.0.4 (September 2019)
tRNAscan-SE was written in the PERL (version 5) script language.
Input consists of DNA or RNA sequences in FASTA format. tRNA
......
aclocal.m4 deleted 100644 → 0
View file @ 2b9d4e11
This diff is collapsed.
configure deleted 100755 → 0
View file @ 2b9d4e11
This diff is collapsed.
debian/changelog
View file @ c9581aea
trnascan-se (2.0.3-2) UNRELEASED; urgency=medium
trnascan-se (2.0.5-1) unstable; urgency=medium
* Added a few autogenerated files to be excluded for
d/copyright.
* Standards-Version: 4.4.1 (routine-update)
* Remove trailing whitespace in debian/changelog (routine-update)
* debian/copyright: use spaces rather than tabs to start continuation
lines.
-- Steffen Moeller <moeller@debian.org> Sat, 03 Aug 2019 15:34:03 +0200
-- Steffen Moeller <moeller@debian.org> Sat, 18 Jan 2020 23:33:33 +0100
trnascan-se (2.0.3-1) unstable; urgency=medium
......
debian/control
View file @ c9581aea
......@@ -6,7 +6,7 @@ XS-Autobuild: no
Priority: optional
Build-Depends: debhelper-compat (= 12),
infernal
Standards-Version: 4.4.0
Standards-Version: 4.4.1
Vcs-Browser: https://salsa.debian.org/med-team/trnascan-se
Vcs-Git: https://salsa.debian.org/med-team/trnascan-se.git
Homepage: http://lowelab.ucsc.edu/tRNAscan-SE
......
depcomp deleted 100755 → 0
View file @ 2b9d4e11
#! /bin/sh
# depcomp - compile a program generating dependencies as side-effects
scriptversion=2009-04-28.21; # UTC
# Copyright (C) 1999, 2000, 2003, 2004, 2005, 2006, 2007, 2009 Free
# Software Foundation, Inc.
# 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, 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, see <http://www.gnu.org/licenses/>.
# As a special exception to the GNU General Public License, if you
# distribute this file as part of a program that contains a
# configuration script generated by Autoconf, you may include it under
# the same distribution terms that you use for the rest of that program.
# Originally written by Alexandre Oliva <oliva@dcc.unicamp.br>.
case $1 in
'')
echo "$0: No command. Try \`$0 --help' for more information." 1>&2
exit 1;
;;
-h | --h*)
cat <<\EOF
Usage: depcomp [--help] [--version] PROGRAM [ARGS]
Run PROGRAMS ARGS to compile a file, generating dependencies
as side-effects.
Environment variables:
depmode Dependency tracking mode.
source Source file read by `PROGRAMS ARGS'.
object Object file output by `PROGRAMS ARGS'.
DEPDIR directory where to store dependencies.
depfile Dependency file to output.
tmpdepfile Temporary file to use when outputing dependencies.
libtool Whether libtool is used (yes/no).
Report bugs to <bug-automake@gnu.org>.
EOF
exit $?
;;
-v | --v*)
echo "depcomp $scriptversion"
exit $?
;;
esac
if test -z "$depmode" || test -z "$source" || test -z "$object"; then
echo "depcomp: Variables source, object and depmode must be set" 1>&2
exit 1
fi
# Dependencies for sub/bar.o or sub/bar.obj go into sub/.deps/bar.Po.
depfile=${depfile-`echo "$object" |
sed 's|[^\\/]*$|'${DEPDIR-.deps}'/&|;s|\.\([^.]*\)$|.P\1|;s|Pobj$|Po|'`}
tmpdepfile=${tmpdepfile-`echo "$depfile" | sed 's/\.\([^.]*\)$/.T\1/'`}
rm -f "$tmpdepfile"
# Some modes work just like other modes, but use different flags. We
# parameterize here, but still list the modes in the big case below,
# to make depend.m4 easier to write. Note that we *cannot* use a case
# here, because this file can only contain one case statement.
if test "$depmode" = hp; then
# HP compiler uses -M and no extra arg.
gccflag=-M
depmode=gcc
fi
if test "$depmode" = dashXmstdout; then
# This is just like dashmstdout with a different argument.
dashmflag=-xM
depmode=dashmstdout
fi
cygpath_u="cygpath -u -f -"
if test "$depmode" = msvcmsys; then
# This is just like msvisualcpp but w/o cygpath translation.
# Just convert the backslash-escaped backslashes to single forward
# slashes to satisfy depend.m4
cygpath_u="sed s,\\\\\\\\,/,g"
depmode=msvisualcpp
fi
case "$depmode" in
gcc3)
## gcc 3 implements dependency tracking that does exactly what
## we want. Yay! Note: for some reason libtool 1.4 doesn't like
## it if -MD -MP comes after the -MF stuff. Hmm.
## Unfortunately, FreeBSD c89 acceptance of flags depends upon
## the command line argument order; so add the flags where they
## appear in depend2.am. Note that the slowdown incurred here
## affects only configure: in makefiles, %FASTDEP% shortcuts this.
for arg
do
case $arg in
-c) set fnord "$@" -MT "$object" -MD -MP -MF "$tmpdepfile" "$arg" ;;
*) set fnord "$@" "$arg" ;;
esac
shift # fnord
shift # $arg
done
"$@"
stat=$?
if test $stat -eq 0; then :
else
rm -f "$tmpdepfile"
exit $stat
fi
mv "$tmpdepfile" "$depfile"
;;
gcc)
## There are various ways to get dependency output from gcc. Here's
## why we pick this rather obscure method:
## - Don't want to use -MD because we'd like the dependencies to end
## up in a subdir. Having to rename by hand is ugly.
## (We might end up doing this anyway to support other compilers.)
## - The DEPENDENCIES_OUTPUT environment variable makes gcc act like
## -MM, not -M (despite what the docs say).
## - Using -M directly means running the compiler twice (even worse
## than renaming).
if test -z "$gccflag"; then
gccflag=-MD,
fi
"$@" -Wp,"$gccflag$tmpdepfile"
stat=$?
if test $stat -eq 0; then :
else
rm -f "$tmpdepfile"
exit $stat
fi
rm -f "$depfile"
echo "$object : \\" > "$depfile"
alpha=ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz
## The second -e expression handles DOS-style file names with drive letters.
sed -e 's/^[^:]*: / /' \
-e 's/^['$alpha']:\/[^:]*: / /' < "$tmpdepfile" >> "$depfile"
## This next piece of magic avoids the `deleted header file' problem.
## The problem is that when a header file which appears in a .P file
## is deleted, the dependency causes make to die (because there is
## typically no way to rebuild the header). We avoid this by adding
## dummy dependencies for each header file. Too bad gcc doesn't do
## this for us directly.
tr ' ' '
' < "$tmpdepfile" |
## Some versions of gcc put a space before the `:'. On the theory
## that the space means something, we add a space to the output as
## well.
## Some versions of the HPUX 10.20 sed can't process this invocation
## correctly. Breaking it into two sed invocations is a workaround.
sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile"
rm -f "$tmpdepfile"
;;
hp)
# This case exists only to let depend.m4 do its work. It works by
# looking at the text of this script. This case will never be run,
# since it is checked for above.
exit 1
;;
sgi)
if test "$libtool" = yes; then
"$@" "-Wp,-MDupdate,$tmpdepfile"
else
"$@" -MDupdate "$tmpdepfile"
fi
stat=$?
if test $stat -eq 0; then :
else
rm -f "$tmpdepfile"
exit $stat
fi
rm -f "$depfile"
if test -f "$tmpdepfile"; then # yes, the sourcefile depend on other files
echo "$object : \\" > "$depfile"
# Clip off the initial element (the dependent). Don't try to be
# clever and replace this with sed code, as IRIX sed won't handle
# lines with more than a fixed number of characters (4096 in
# IRIX 6.2 sed, 8192 in IRIX 6.5). We also remove comment lines;
# the IRIX cc adds comments like `#:fec' to the end of the
# dependency line.
tr ' ' '
' < "$tmpdepfile" \
| sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' | \
tr '
' ' ' >> "$depfile"
echo >> "$depfile"
# The second pass generates a dummy entry for each header file.
tr ' ' '
' < "$tmpdepfile" \
| sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' -e 's/$/:/' \
>> "$depfile"
else
# The sourcefile does not contain any dependencies, so just
# store a dummy comment line, to avoid errors with the Makefile
# "include basename.Plo" scheme.
echo "#dummy" > "$depfile"
fi
rm -f "$tmpdepfile"
;;
aix)
# The C for AIX Compiler uses -M and outputs the dependencies
# in a .u file. In older versions, this file always lives in the
# current directory. Also, the AIX compiler puts `$object:' at the
# start of each line; $object doesn't have directory information.
# Version 6 uses the directory in both cases.
dir=`echo "$object" | sed -e 's|/[^/]*$|/|'`
test "x$dir" = "x$object" && dir=
base=`echo "$object" | sed -e 's|^.*/||' -e 's/\.o$//' -e 's/\.lo$//'`
if test "$libtool" = yes; then
tmpdepfile1=$dir$base.u
tmpdepfile2=$base.u
tmpdepfile3=$dir.libs/$base.u
"$@" -Wc,-M
else
tmpdepfile1=$dir$base.u
tmpdepfile2=$dir$base.u
tmpdepfile3=$dir$base.u
"$@" -M
fi
stat=$?
if test $stat -eq 0; then :
else
rm -f "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3"
exit $stat
fi
for tmpdepfile in "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3"
do
test -f "$tmpdepfile" && break
done
if test -f "$tmpdepfile"; then
# Each line is of the form `foo.o: dependent.h'.
# Do two passes, one to just change these to
# `$object: dependent.h' and one to simply `dependent.h:'.
sed -e "s,^.*\.[a-z]*:,$object:," < "$tmpdepfile" > "$depfile"
# That's a tab and a space in the [].
sed -e 's,^.*\.[a-z]*:[ ]*,,' -e 's,$,:,' < "$tmpdepfile" >> "$depfile"
else
# The sourcefile does not contain any dependencies, so just
# store a dummy comment line, to avoid errors with the Makefile
# "include basename.Plo" scheme.
echo "#dummy" > "$depfile"
fi
rm -f "$tmpdepfile"
;;
icc)
# Intel's C compiler understands `-MD -MF file'. However on
# icc -MD -MF foo.d -c -o sub/foo.o sub/foo.c
# ICC 7.0 will fill foo.d with something like
# foo.o: sub/foo.c
# foo.o: sub/foo.h
# which is wrong. We want:
# sub/foo.o: sub/foo.c
# sub/foo.o: sub/foo.h
# sub/foo.c:
# sub/foo.h:
# ICC 7.1 will output
# foo.o: sub/foo.c sub/foo.h
# and will wrap long lines using \ :
# foo.o: sub/foo.c ... \
# sub/foo.h ... \
# ...
"$@" -MD -MF "$tmpdepfile"
stat=$?
if test $stat -eq 0; then :
else
rm -f "$tmpdepfile"
exit $stat
fi
rm -f "$depfile"
# Each line is of the form `foo.o: dependent.h',
# or `foo.o: dep1.h dep2.h \', or ` dep3.h dep4.h \'.
# Do two passes, one to just change these to
# `$object: dependent.h' and one to simply `dependent.h:'.
sed "s,^[^:]*:,$object :," < "$tmpdepfile" > "$depfile"
# Some versions of the HPUX 10.20 sed can't process this invocation
# correctly. Breaking it into two sed invocations is a workaround.
sed 's,^[^:]*: \(.*\)$,\1,;s/^\\$//;/^$/d;/:$/d' < "$tmpdepfile" |
sed -e 's/$/ :/' >> "$depfile"
rm -f "$tmpdepfile"
;;
hp2)
# The "hp" stanza above does not work with aCC (C++) and HP's ia64
# compilers, which have integrated preprocessors. The correct option
# to use with these is +Maked; it writes dependencies to a file named
# 'foo.d', which lands next to the object file, wherever that
# happens to be.
# Much of this is similar to the tru64 case; see comments there.
dir=`echo "$object" | sed -e 's|/[^/]*$|/|'`
test "x$dir" = "x$object" && dir=
base=`echo "$object" | sed -e 's|^.*/||' -e 's/\.o$//' -e 's/\.lo$//'`
if test "$libtool" = yes; then
tmpdepfile1=$dir$base.d
tmpdepfile2=$dir.libs/$base.d
"$@" -Wc,+Maked
else
tmpdepfile1=$dir$base.d
tmpdepfile2=$dir$base.d
"$@" +Maked
fi
stat=$?
if test $stat -eq 0; then :
else
rm -f "$tmpdepfile1" "$tmpdepfile2"
exit $stat
fi
for tmpdepfile in "$tmpdepfile1" "$tmpdepfile2"
do
test -f "$tmpdepfile" && break
done
if test -f "$tmpdepfile"; then
sed -e "s,^.*\.[a-z]*:,$object:," "$tmpdepfile" > "$depfile"
# Add `dependent.h:' lines.
sed -ne '2,${
s/^ *//
s/ \\*$//
s/$/:/
p
}' "$tmpdepfile" >> "$depfile"
else
echo "#dummy" > "$depfile"
fi
rm -f "$tmpdepfile" "$tmpdepfile2"
;;
tru64)
# The Tru64 compiler uses -MD to generate dependencies as a side
# effect. `cc -MD -o foo.o ...' puts the dependencies into `foo.o.d'.
# At least on Alpha/Redhat 6.1, Compaq CCC V6.2-504 seems to put
# dependencies in `foo.d' instead, so we check for that too.
# Subdirectories are respected.
dir=`echo "$object" | sed -e 's|/[^/]*$|/|'`
test "x$dir" = "x$object" && dir=
base=`echo "$object" | sed -e 's|^.*/||' -e 's/\.o$//' -e 's/\.lo$//'`
if test "$libtool" = yes; then
# With Tru64 cc, shared objects can also be used to make a
# static library. This mechanism is used in libtool 1.4 series to
# handle both shared and static libraries in a single compilation.
# With libtool 1.4, dependencies were output in $dir.libs/$base.lo.d.
#
# With libtool 1.5 this exception was removed, and libtool now
# generates 2 separate objects for the 2 libraries. These two
# compilations output dependencies in $dir.libs/$base.o.d and
# in $dir$base.o.d. We have to check for both files, because
# one of the two compilations can be disabled. We should prefer
# $dir$base.o.d over $dir.libs/$base.o.d because the latter is
# automatically cleaned when .libs/ is deleted, while ignoring
# the former would cause a distcleancheck panic.
tmpdepfile1=$dir.libs/$base.lo.d # libtool 1.4
tmpdepfile2=$dir$base.o.d # libtool 1.5
tmpdepfile3=$dir.libs/$base.o.d # libtool 1.5
tmpdepfile4=$dir.libs/$base.d # Compaq CCC V6.2-504
"$@" -Wc,-MD
else
tmpdepfile1=$dir$base.o.d
tmpdepfile2=$dir$base.d
tmpdepfile3=$dir$base.d
tmpdepfile4=$dir$base.d
"$@" -MD
fi
stat=$?
if test $stat -eq 0; then :
else
rm -f "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3" "$tmpdepfile4"
exit $stat
fi
for tmpdepfile in "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3" "$tmpdepfile4"
do
test -f "$tmpdepfile" && break
done
if test -f "$tmpdepfile"; then
sed -e "s,^.*\.[a-z]*:,$object:," < "$tmpdepfile" > "$depfile"
# That's a tab and a space in the [].
sed -e 's,^.*\.[a-z]*:[ ]*,,' -e 's,$,:,' < "$tmpdepfile" >> "$depfile"
else
echo "#dummy" > "$depfile"
fi
rm -f "$tmpdepfile"
;;
#nosideeffect)
# This comment above is used by automake to tell side-effect
# dependency tracking mechanisms from slower ones.
dashmstdout)
# Important note: in order to support this mode, a compiler *must*
# always write the preprocessed file to stdout, regardless of -o.
"$@" || exit $?
# Remove the call to Libtool.
if test "$libtool" = yes; then
while test "X$1" != 'X--mode=compile'; do
shift
done
shift
fi
# Remove `-o $object'.
IFS=" "
for arg
do
case $arg in
-o)
shift
;;
$object)
shift
;;
*)
set fnord "$@" "$arg"
shift # fnord
shift # $arg
;;
esac
done
test -z "$dashmflag" && dashmflag=-M
# Require at least two characters before searching for `:'
# in the target name. This is to cope with DOS-style filenames:
# a dependency such as `c:/foo/bar' could be seen as target `c' otherwise.
"$@" $dashmflag |
sed 's:^[ ]*[^: ][^:][^:]*\:[ ]*:'"$object"'\: :' > "$tmpdepfile"
rm -f "$depfile"
cat < "$tmpdepfile" > "$depfile"
tr ' ' '
' < "$tmpdepfile" | \
## Some versions of the HPUX 10.20 sed can't process this invocation
## correctly. Breaking it into two sed invocations is a workaround.
sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile"
rm -f "$tmpdepfile"
;;
dashXmstdout)
# This case only exists to satisfy depend.m4. It is never actually
# run, as this mode is specially recognized in the preamble.
exit 1
;;
makedepend)
"$@" || exit $?
# Remove any Libtool call
if test "$libtool" = yes; then
while test "X$1" != 'X--mode=compile'; do
shift
done
shift
fi
# X makedepend
shift
cleared=no eat=no
for arg
do
case $cleared in
no)
set ""; shift
cleared=yes ;;
esac
if test $eat = yes; then
eat=no
continue
fi
case "$arg" in
-D*|-I*)
set fnord "$@" "$arg"; shift ;;
# Strip any option that makedepend may not understand. Remove
# the object too, otherwise makedepend will parse it as a source file.
-arch)
eat=yes ;;
-*|$object)
;;
*)
set fnord "$@" "$arg"; shift ;;
esac
done
obj_suffix=`echo "$object" | sed 's/^.*\././'`
touch "$tmpdepfile"
${MAKEDEPEND-makedepend} -o"$obj_suffix" -f"$tmpdepfile" "$@"
rm -f "$depfile"
cat < "$tmpdepfile" > "$depfile"
sed '1,2d' "$tmpdepfile" | tr ' ' '
' | \
## Some versions of the HPUX 10.20 sed can't process this invocation
## correctly. Breaking it into two sed invocations is a workaround.
sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile"
rm -f "$tmpdepfile" "$tmpdepfile".bak
;;
cpp)
# Important note: in order to support this mode, a compiler *must*
# always write the preprocessed file to stdout.
"$@" || exit $?
# Remove the call to Libtool.
if test "$libtool" = yes; then
while test "X$1" != 'X--mode=compile'; do
shift
done
shift
fi
# Remove `-o $object'.
IFS=" "
for arg
do
case $arg in
-o)
shift
;;
$object)
shift
;;
*)
set fnord "$@" "$arg"
shift # fnord
shift # $arg
;;
esac
done
"$@" -E |
sed -n -e '/^# [0-9][0-9]* "\([^"]*\)".*/ s:: \1 \\:p' \
-e '/^#line [0-9][0-9]* "\([^"]*\)".*/ s:: \1 \\:p' |
sed '$ s: \\$::' > "$tmpdepfile"
rm -f "$depfile"
echo "$object : \\" > "$depfile"
cat < "$tmpdepfile" >> "$depfile"
sed < "$tmpdepfile" '/^$/d;s/^ //;s/ \\$//;s/$/ :/' >> "$depfile"
rm -f "$tmpdepfile"
;;
msvisualcpp)
# Important note: in order to support this mode, a compiler *must*
# always write the preprocessed file to stdout.
"$@" || exit $?
# Remove the call to Libtool.
if test "$libtool" = yes; then
while test "X$1" != 'X--mode=compile'; do
shift
done
shift
fi
IFS=" "
for arg
do
case "$arg" in
-o)
shift
;;
$object)
shift
;;
"-Gm"|"/Gm"|"-Gi"|"/Gi"|"-ZI"|"/ZI")
set fnord "$@"
shift
shift
;;
*)
set fnord "$@" "$arg"
shift
shift
;;
esac
done
"$@" -E 2>/dev/null |
sed -n '/^#line [0-9][0-9]* "\([^"]*\)"/ s::\1:p' | $cygpath_u | sort -u > "$tmpdepfile"
rm -f "$depfile"
echo "$object : \\" > "$depfile"
sed < "$tmpdepfile" -n -e 's% %\\ %g' -e '/^\(.*\)$/ s:: \1 \\:p' >> "$depfile"
echo " " >> "$depfile"
sed < "$tmpdepfile" -n -e 's% %\\ %g' -e '/^\(.*\)$/ s::\1\::p' >> "$depfile"
rm -f "$tmpdepfile"
;;
msvcmsys)
# This case exists only to let depend.m4 do its work. It works by
# looking at the text of this script. This case will never be run,
# since it is checked for above.
exit 1
;;
none)
exec "$@"
;;
*)
echo "Unknown depmode $depmode" 1>&2
exit 1
;;
esac
exit 0
# Local Variables:
# mode: shell-script
# sh-indentation: 2
# eval: (add-hook 'write-file-hooks 'time-stamp)
# time-stamp-start: "scriptversion="
# time-stamp-format: "%:y-%02m-%02d.%02H"
# time-stamp-time-zone: "UTC"
# time-stamp-end: "; # UTC"
# End:
install-sh deleted 100755 → 0
View file @ 2b9d4e11
#!/bin/sh
# install - install a program, script, or datafile
scriptversion=2009-04-28.21; # UTC
# This originates from X11R5 (mit/util/scripts/install.sh), which was
# later released in X11R6 (xc/config/util/install.sh) with the
# following copyright and license.
#
# Copyright (C) 1994 X Consortium
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to
# deal in the Software without restriction, including without limitation the
# rights to use, copy, modify, merge, publish, distribute, sublicense, and/or
# sell copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# X CONSORTIUM BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN
# AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNEC-
# TION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
#
# Except as contained in this notice, the name of the X Consortium shall not
# be used in advertising or otherwise to promote the sale, use or other deal-
# ings in this Software without prior written authorization from the X Consor-
# tium.
#
#
# FSF changes to this file are in the public domain.
#
# Calling this script install-sh is preferred over install.sh, to prevent
# `make' implicit rules from creating a file called install from it
# when there is no Makefile.
#
# This script is compatible with the BSD install script, but was written
# from scratch.
nl='
'
IFS=" "" $nl"
# set DOITPROG to echo to test this script
# Don't use :- since 4.3BSD and earlier shells don't like it.
doit=${DOITPROG-}
if test -z "$doit"; then
doit_exec=exec
else
doit_exec=$doit
fi
# Put in absolute file names if you don't have them in your path;
# or use environment vars.
chgrpprog=${CHGRPPROG-chgrp}
chmodprog=${CHMODPROG-chmod}
chownprog=${CHOWNPROG-chown}
cmpprog=${CMPPROG-cmp}
cpprog=${CPPROG-cp}
mkdirprog=${MKDIRPROG-mkdir}
mvprog=${MVPROG-mv}
rmprog=${RMPROG-rm}
stripprog=${STRIPPROG-strip}
posix_glob='?'
initialize_posix_glob='
test "$posix_glob" != "?" || {
if (set -f) 2>/dev/null; then
posix_glob=
else
posix_glob=:
fi
}
'
posix_mkdir=
# Desired mode of installed file.
mode=0755
chgrpcmd=
chmodcmd=$chmodprog
chowncmd=
mvcmd=$mvprog
rmcmd="$rmprog -f"
stripcmd=
src=
dst=
dir_arg=
dst_arg=
copy_on_change=false
no_target_directory=
usage="\
Usage: $0 [OPTION]... [-T] SRCFILE DSTFILE
or: $0 [OPTION]... SRCFILES... DIRECTORY
or: $0 [OPTION]... -t DIRECTORY SRCFILES...
or: $0 [OPTION]... -d DIRECTORIES...
In the 1st form, copy SRCFILE to DSTFILE.
In the 2nd and 3rd, copy all SRCFILES to DIRECTORY.
In the 4th, create DIRECTORIES.
Options:
--help display this help and exit.
--version display version info and exit.
-c (ignored)
-C install only if different (preserve the last data modification time)
-d create directories instead of installing files.
-g GROUP $chgrpprog installed files to GROUP.
-m MODE $chmodprog installed files to MODE.
-o USER $chownprog installed files to USER.
-s $stripprog installed files.
-t DIRECTORY install into DIRECTORY.
-T report an error if DSTFILE is a directory.
Environment variables override the default commands:
CHGRPPROG CHMODPROG CHOWNPROG CMPPROG CPPROG MKDIRPROG MVPROG
RMPROG STRIPPROG
"
while test $# -ne 0; do
case $1 in
-c) ;;
-C) copy_on_change=true;;
-d) dir_arg=true;;
-g) chgrpcmd="$chgrpprog $2"
shift;;
--help) echo "$usage"; exit $?;;
-m) mode=$2
case $mode in
*' '* | *' '* | *'
'* | *'*'* | *'?'* | *'['*)
echo "$0: invalid mode: $mode" >&2
exit 1;;
esac
shift;;
-o) chowncmd="$chownprog $2"
shift;;
-s) stripcmd=$stripprog;;
-t) dst_arg=$2
shift;;
-T) no_target_directory=true;;
--version) echo "$0 $scriptversion"; exit $?;;
--) shift
break;;
-*) echo "$0: invalid option: $1" >&2
exit 1;;
*) break;;
esac
shift
done
if test $# -ne 0 && test -z "$dir_arg$dst_arg"; then
# When -d is used, all remaining arguments are directories to create.
# When -t is used, the destination is already specified.
# Otherwise, the last argument is the destination. Remove it from $@.
for arg
do
if test -n "$dst_arg"; then
# $@ is not empty: it contains at least $arg.
set fnord "$@" "$dst_arg"
shift # fnord
fi
shift # arg
dst_arg=$arg
done
fi
if test $# -eq 0; then
if test -z "$dir_arg"; then
echo "$0: no input file specified." >&2
exit 1
fi
# It's OK to call `install-sh -d' without argument.
# This can happen when creating conditional directories.
exit 0
fi
if test -z "$dir_arg"; then
trap '(exit $?); exit' 1 2 13 15
# Set umask so as not to create temps with too-generous modes.
# However, 'strip' requires both read and write access to temps.
case $mode in
# Optimize common cases.
*644) cp_umask=133;;
*755) cp_umask=22;;
*[0-7])
if test -z "$stripcmd"; then
u_plus_rw=
else
u_plus_rw='% 200'
fi
cp_umask=`expr '(' 777 - $mode % 1000 ')' $u_plus_rw`;;
*)
if test -z "$stripcmd"; then
u_plus_rw=
else
u_plus_rw=,u+rw
fi
cp_umask=$mode$u_plus_rw;;
esac
fi
for src
do
# Protect names starting with `-'.
case $src in
-*) src=./$src;;
esac
if test -n "$dir_arg"; then
dst=$src
dstdir=$dst
test -d "$dstdir"
dstdir_status=$?
else
# Waiting for this to be detected by the "$cpprog $src $dsttmp" command
# might cause directories to be created, which would be especially bad
# if $src (and thus $dsttmp) contains '*'.
if test ! -f "$src" && test ! -d "$src"; then
echo "$0: $src does not exist." >&2
exit 1
fi
if test -z "$dst_arg"; then
echo "$0: no destination specified." >&2
exit 1
fi
dst=$dst_arg
# Protect names starting with `-'.
case $dst in
-*) dst=./$dst;;
esac
# If destination is a directory, append the input filename; won't work
# if double slashes aren't ignored.
if test -d "$dst"; then
if test -n "$no_target_directory"; then
echo "$0: $dst_arg: Is a directory" >&2
exit 1
fi
dstdir=$dst
dst=$dstdir/`basename "$src"`
dstdir_status=0
else
# Prefer dirname, but fall back on a substitute if dirname fails.
dstdir=`
(dirname "$dst") 2>/dev/null ||
expr X"$dst" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
X"$dst" : 'X\(//\)[^/]' \| \
X"$dst" : 'X\(//\)$' \| \
X"$dst" : 'X\(/\)' \| . 2>/dev/null ||
echo X"$dst" |
sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
s//\1/
q
}
/^X\(\/\/\)[^/].*/{
s//\1/
q
}
/^X\(\/\/\)$/{
s//\1/
q
}
/^X\(\/\).*/{
s//\1/
q
}
s/.*/./; q'
`
test -d "$dstdir"
dstdir_status=$?
fi
fi
obsolete_mkdir_used=false
if test $dstdir_status != 0; then
case $posix_mkdir in
'')
# Create intermediate dirs using mode 755 as modified by the umask.
# This is like FreeBSD 'install' as of 1997-10-28.
umask=`umask`
case $stripcmd.$umask in
# Optimize common cases.
*[2367][2367]) mkdir_umask=$umask;;
.*0[02][02] | .[02][02] | .[02]) mkdir_umask=22;;
*[0-7])
mkdir_umask=`expr $umask + 22 \
- $umask % 100 % 40 + $umask % 20 \
- $umask % 10 % 4 + $umask % 2
`;;
*) mkdir_umask=$umask,go-w;;
esac
# With -d, create the new directory with the user-specified mode.
# Otherwise, rely on $mkdir_umask.
if test -n "$dir_arg"; then
mkdir_mode=-m$mode
else
mkdir_mode=
fi
posix_mkdir=false
case $umask in
*[123567][0-7][0-7])
# POSIX mkdir -p sets u+wx bits regardless of umask, which
# is incompatible with FreeBSD 'install' when (umask & 300) != 0.
;;
*)
tmpdir=${TMPDIR-/tmp}/ins$RANDOM-$$
trap 'ret=$?; rmdir "$tmpdir/d" "$tmpdir" 2>/dev/null; exit $ret' 0
if (umask $mkdir_umask &&
exec $mkdirprog $mkdir_mode -p -- "$tmpdir/d") >/dev/null 2>&1
then
if test -z "$dir_arg" || {
# Check for POSIX incompatibilities with -m.
# HP-UX 11.23 and IRIX 6.5 mkdir -m -p sets group- or
# other-writeable bit of parent directory when it shouldn't.
# FreeBSD 6.1 mkdir -m -p sets mode of existing directory.
ls_ld_tmpdir=`ls -ld "$tmpdir"`
case $ls_ld_tmpdir in
d????-?r-*) different_mode=700;;
d????-?--*) different_mode=755;;
*) false;;
esac &&
$mkdirprog -m$different_mode -p -- "$tmpdir" && {
ls_ld_tmpdir_1=`ls -ld "$tmpdir"`
test "$ls_ld_tmpdir" = "$ls_ld_tmpdir_1"
}
}
then posix_mkdir=:
fi
rmdir "$tmpdir/d" "$tmpdir"
else
# Remove any dirs left behind by ancient mkdir implementations.
rmdir ./$mkdir_mode ./-p ./-- 2>/dev/null
fi
trap '' 0;;
esac;;
esac
if
$posix_mkdir && (
umask $mkdir_umask &&
$doit_exec $mkdirprog $mkdir_mode -p -- "$dstdir"
)
then :
else
# The umask is ridiculous, or mkdir does not conform to POSIX,
# or it failed possibly due to a race condition. Create the
# directory the slow way, step by step, checking for races as we go.
case $dstdir in
/*) prefix='/';;
-*) prefix='./';;
*) prefix='';;
esac
eval "$initialize_posix_glob"
oIFS=$IFS
IFS=/
$posix_glob set -f
set fnord $dstdir
shift
$posix_glob set +f
IFS=$oIFS
prefixes=
for d
do
test -z "$d" && continue
prefix=$prefix$d
if test -d "$prefix"; then
prefixes=
else
if $posix_mkdir; then
(umask=$mkdir_umask &&
$doit_exec $mkdirprog $mkdir_mode -p -- "$dstdir") && break
# Don't fail if two instances are running concurrently.
test -d "$prefix" || exit 1
else
case $prefix in
*\'*) qprefix=`echo "$prefix" | sed "s/'/'\\\\\\\\''/g"`;;
*) qprefix=$prefix;;
esac
prefixes="$prefixes '$qprefix'"
fi
fi
prefix=$prefix/
done
if test -n "$prefixes"; then
# Don't fail if two instances are running concurrently.
(umask $mkdir_umask &&
eval "\$doit_exec \$mkdirprog $prefixes") ||
test -d "$dstdir" || exit 1
obsolete_mkdir_used=true
fi
fi
fi
if test -n "$dir_arg"; then
{ test -z "$chowncmd" || $doit $chowncmd "$dst"; } &&
{ test -z "$chgrpcmd" || $doit $chgrpcmd "$dst"; } &&
{ test "$obsolete_mkdir_used$chowncmd$chgrpcmd" = false ||
test -z "$chmodcmd" || $doit $chmodcmd $mode "$dst"; } || exit 1
else
# Make a couple of temp file names in the proper directory.
dsttmp=$dstdir/_inst.$$_
rmtmp=$dstdir/_rm.$$_
# Trap to clean up those temp files at exit.
trap 'ret=$?; rm -f "$dsttmp" "$rmtmp" && exit $ret' 0
# Copy the file name to the temp name.
(umask $cp_umask && $doit_exec $cpprog "$src" "$dsttmp") &&
# and set any options; do chmod last to preserve setuid bits.
#
# If any of these fail, we abort the whole thing. If we want to
# ignore errors from any of these, just make sure not to ignore
# errors from the above "$doit $cpprog $src $dsttmp" command.
#
{ test -z "$chowncmd" || $doit $chowncmd "$dsttmp"; } &&
{ test -z "$chgrpcmd" || $doit $chgrpcmd "$dsttmp"; } &&
{ test -z "$stripcmd" || $doit $stripcmd "$dsttmp"; } &&
{ test -z "$chmodcmd" || $doit $chmodcmd $mode "$dsttmp"; } &&
# If -C, don't bother to copy if it wouldn't change the file.
if $copy_on_change &&
old=`LC_ALL=C ls -dlL "$dst" 2>/dev/null` &&
new=`LC_ALL=C ls -dlL "$dsttmp" 2>/dev/null` &&
eval "$initialize_posix_glob" &&
$posix_glob set -f &&
set X $old && old=:$2:$4:$5:$6 &&
set X $new && new=:$2:$4:$5:$6 &&
$posix_glob set +f &&
test "$old" = "$new" &&
$cmpprog "$dst" "$dsttmp" >/dev/null 2>&1
then
rm -f "$dsttmp"
else
# Rename the file to the real destination.
$doit $mvcmd -f "$dsttmp" "$dst" 2>/dev/null ||
# The rename failed, perhaps because mv can't rename something else
# to itself, or perhaps because mv is so ancient that it does not
# support -f.
{
# Now remove or move aside any old file at destination location.
# We try this two ways since rm can't unlink itself on some
# systems and the destination file might be busy for other
# reasons. In this case, the final cleanup might fail but the new
# file should still install successfully.
{
test ! -f "$dst" ||
$doit $rmcmd -f "$dst" 2>/dev/null ||
{ $doit $mvcmd -f "$dst" "$rmtmp" 2>/dev/null &&
{ $doit $rmcmd -f "$rmtmp" 2>/dev/null; :; }
} ||
{ echo "$0: cannot unlink or rename $dst" >&2
(exit 1); exit 1
}
} &&
# Now rename the file to the real destination.
$doit $mvcmd "$dsttmp" "$dst"
}
fi || exit 1
trap '' 0
fi
done
# Local variables:
# eval: (add-hook 'write-file-hooks 'time-stamp)
# time-stamp-start: "scriptversion="
# time-stamp-format: "%:y-%02m-%02d.%02H"
# time-stamp-time-zone: "UTC"
# time-stamp-end: "; # UTC"
# End:
lib/tRNAscanSE/CM.pm
View file @ c9581aea
......@@ -110,6 +110,13 @@ sub cm_cutoff
return $self->{cm_cutoff};
}
sub organelle_cm_cutoff
{
my $self = shift;
if (@_) { $self->{organelle_cm_cutoff} = shift; }
return $self->{organelle_cm_cutoff};
}
sub infernal_fp_cutoff
{
my $self = shift;
......@@ -1200,6 +1207,12 @@ sub decode_tRNA_properties
}
$trna->isotype($gc->get_tRNA_type($self, $trna->anticodon(), $cur_cm_file, $trna->model(), $self->cove_mode()));
if ($anticodon ne "TCA" and $trna->isotype() eq "SeC")
{
$trna->anticodon($gc->undef_anticodon());
$trna->isotype($gc->undef_isotype());
}
}
# Write current tRNA to temp file for re-analysis with other models
......@@ -1230,6 +1243,9 @@ sub fix_fMet
(substr($trna->ss(), length($trna->ss())-5) eq "<<<.."))
{
if (substr($trna->ss(), 0, 1) ne ".")
{
if (($trna->strand() eq "+" and $trna->start() > 1) or
($trna->strand() eq "-" and $trna->end() < $trna->src_seqlen()))
{
$trna->seq(substr($trna->upstream(), length($trna->upstream())-1) . $trna->seq());
$trna->upstream(substr($trna->upstream(), 0, length($trna->upstream())-1));
......@@ -1252,6 +1268,7 @@ sub fix_fMet
$rescore = 1;
}
}
elsif (substr($trna->ss(), 0, 4) eq ".>.>" and substr($trna->seq(), 0, 2) eq "CG")
{
my $pos71 = "";
......@@ -2418,14 +2435,14 @@ sub run_cmsearch
}
}
if ($opts->mito_mode())
{
$score_cutoff = $self->{organelle_cm_cutoff};
}
else
{
# if ($opts->mito_mode())
# {
# $score_cutoff = $self->{organelle_cm_cutoff};
# }
# else
# {
$score_cutoff = $self->{cm_cutoff};
}
# }
foreach my $cur_cm (sort keys %{$self->{main_cm_file_path}})
{
......@@ -3286,7 +3303,7 @@ sub analyze_mito
$cm_tRNA->start($cm_tRNA->start() + $prescan_tRNA->start() - 1);
$cm_tRNA->end($cm_tRNA->end() + $prescan_tRNA->start() - 1);
if ($cm_tRNA->score() < $self->{organelle_cm_cutoff})
if ($cm_tRNA->score() < $self->{cm_cutoff})
{
$log->broadcast("Low cmsearch score for ".$prescan_tRNA->tRNAscan_id().".$cms_hit_count: ".$cm_tRNA->score());
$trnaDesc .= "(CMSearch Hit#$cms_hit_count: ".$cm_tRNA->start()."-".$cm_tRNA->end().",".
......
lib/tRNAscanSE/Options.pm
View file @ c9581aea
......@@ -813,10 +813,20 @@ sub display_run_options
}
}
# if ($self->mito_mode())
# {
# if ($cm->organelle_cm_cutoff() != $global_constants->get("organelle_cm_cutoff"))
# {
# print $FHAND "tRNA covariance model search \n"." cutoff score: ".$cm->organelle_cm_cutoff()."\n";
# }
# }
# else
# {
if ($cm->cm_cutoff() != $global_constants->get("cm_cutoff"))
{
print $FHAND "tRNA covariance model search \n"." cutoff score: ".$cm->cm_cutoff()."\n";
}
# }
if ($self->{use_prev_ts_run})
{
......
lib/tRNAscanSE/Sequence.pm
View file @ c9581aea
......@@ -335,7 +335,10 @@ sub read_fasta
## Remove long runs of N's from consideration by pre-scanners
## By doing this, pre-scanner false-pos rate is normal, even
## when scanning unfinished genomes with long N insert "placeholders"
if ($opts->tscan_mode() or $opts->eufind_mode())
{
$self->{sequence} =~ s/NNNNNNNNNN/CCCCCCCCCC/g;
}
return 1;
}
......@@ -524,6 +527,7 @@ sub read_fasta_subseq_slow
sub read_more_fasta
{
my $self = shift;
my $opts = shift;
my $fh = $self->{FILE_H};
my ($seqlen, $filepos);
......@@ -579,7 +583,10 @@ sub read_more_fasta
## Remove long runs of N's from consideration by pre-scanners
## By doing this, pre-scanner false-pos rate is normal, even
## when scanning unfinished genomes with long N insert "placeholders"
if ($opts->tscan_mode() or $opts->eufind_mode())
{
$self->{sequence} =~ s/NNNNNNNNNN/CCCCCCCCCC/g;
}
return 1;
}
......@@ -656,7 +663,7 @@ sub get_tRNA_sequence
$self->seekpos(0);
if (!$self->read_fasta_subseq_slow($opts, $trna->seqname(), $src_seqid, $fwd_start, $query_len))
{
$log->warning("Could not find ".$trna->seqname()." in ".$opts->fastafile());
$log->warning("Could not find ".$trna->seqname()." in ".$opts->fasta_file());
$log->broadcast("Skipping to next tRNA hit...");
return 0;
}
......
missing deleted 100755 → 0
View file @ 2b9d4e11
#! /bin/sh
# Common stub for a few missing GNU programs while installing.
scriptversion=2009-04-28.21; # UTC
# Copyright (C) 1996, 1997, 1999, 2000, 2002, 2003, 2004, 2005, 2006,
# 2008, 2009 Free Software Foundation, Inc.
# Originally by Fran,cois Pinard <pinard@iro.umontreal.ca>, 1996.
# 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, 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, see <http://www.gnu.org/licenses/>.
# As a special exception to the GNU General Public License, if you
# distribute this file as part of a program that contains a
# configuration script generated by Autoconf, you may include it under
# the same distribution terms that you use for the rest of that program.
if test $# -eq 0; then
echo 1>&2 "Try \`$0 --help' for more information"
exit 1
fi
run=:
sed_output='s/.* --output[ =]\([^ ]*\).*/\1/p'
sed_minuso='s/.* -o \([^ ]*\).*/\1/p'
# In the cases where this matters, `missing' is being run in the
# srcdir already.
if test -f configure.ac; then
configure_ac=configure.ac
else
configure_ac=configure.in
fi
msg="missing on your system"
case $1 in
--run)
# Try to run requested program, and just exit if it succeeds.
run=
shift
"$@" && exit 0
# Exit code 63 means version mismatch. This often happens
# when the user try to use an ancient version of a tool on
# a file that requires a minimum version. In this case we
# we should proceed has if the program had been absent, or
# if --run hadn't been passed.
if test $? = 63; then
run=:
msg="probably too old"
fi
;;
-h|--h|--he|--hel|--help)
echo "\
$0 [OPTION]... PROGRAM [ARGUMENT]...
Handle \`PROGRAM [ARGUMENT]...' for when PROGRAM is missing, or return an
error status if there is no known handling for PROGRAM.
Options:
-h, --help display this help and exit
-v, --version output version information and exit
--run try to run the given command, and emulate it if it fails
Supported PROGRAM values:
aclocal touch file \`aclocal.m4'
autoconf touch file \`configure'
autoheader touch file \`config.h.in'
autom4te touch the output file, or create a stub one
automake touch all \`Makefile.in' files
bison create \`y.tab.[ch]', if possible, from existing .[ch]
flex create \`lex.yy.c', if possible, from existing .c
help2man touch the output file
lex create \`lex.yy.c', if possible, from existing .c
makeinfo touch the output file
tar try tar, gnutar, gtar, then tar without non-portable flags
yacc create \`y.tab.[ch]', if possible, from existing .[ch]
Version suffixes to PROGRAM as well as the prefixes \`gnu-', \`gnu', and
\`g' are ignored when checking the name.
Send bug reports to <bug-automake@gnu.org>."
exit $?
;;
-v|--v|--ve|--ver|--vers|--versi|--versio|--version)
echo "missing $scriptversion (GNU Automake)"
exit $?
;;
-*)
echo 1>&2 "$0: Unknown \`$1' option"
echo 1>&2 "Try \`$0 --help' for more information"
exit 1
;;
esac
# normalize program name to check for.
program=`echo "$1" | sed '
s/^gnu-//; t
s/^gnu//; t
s/^g//; t'`
# Now exit if we have it, but it failed. Also exit now if we
# don't have it and --version was passed (most likely to detect
# the program). This is about non-GNU programs, so use $1 not
# $program.
case $1 in
lex*|yacc*)
# Not GNU programs, they don't have --version.
;;
tar*)
if test -n "$run"; then
echo 1>&2 "ERROR: \`tar' requires --run"
exit 1
elif test "x$2" = "x--version" || test "x$2" = "x--help"; then
exit 1
fi
;;
*)
if test -z "$run" && ($1 --version) > /dev/null 2>&1; then
# We have it, but it failed.
exit 1
elif test "x$2" = "x--version" || test "x$2" = "x--help"; then
# Could not run --version or --help. This is probably someone
# running `$TOOL --version' or `$TOOL --help' to check whether
# $TOOL exists and not knowing $TOOL uses missing.
exit 1
fi
;;
esac
# If it does not exist, or fails to run (possibly an outdated version),
# try to emulate it.
case $program in
aclocal*)
echo 1>&2 "\
WARNING: \`$1' is $msg. You should only need it if
you modified \`acinclude.m4' or \`${configure_ac}'. You might want
to install the \`Automake' and \`Perl' packages. Grab them from
any GNU archive site."
touch aclocal.m4
;;
autoconf*)
echo 1>&2 "\
WARNING: \`$1' is $msg. You should only need it if
you modified \`${configure_ac}'. You might want to install the
\`Autoconf' and \`GNU m4' packages. Grab them from any GNU
archive site."
touch configure
;;
autoheader*)
echo 1>&2 "\
WARNING: \`$1' is $msg. You should only need it if
you modified \`acconfig.h' or \`${configure_ac}'. You might want
to install the \`Autoconf' and \`GNU m4' packages. Grab them
from any GNU archive site."
files=`sed -n 's/^[ ]*A[CM]_CONFIG_HEADER(\([^)]*\)).*/\1/p' ${configure_ac}`
test -z "$files" && files="config.h"
touch_files=
for f in $files; do
case $f in
*:*) touch_files="$touch_files "`echo "$f" |
sed -e 's/^[^:]*://' -e 's/:.*//'`;;
*) touch_files="$touch_files $f.in";;
esac
done
touch $touch_files
;;
automake*)
echo 1>&2 "\
WARNING: \`$1' is $msg. You should only need it if
you modified \`Makefile.am', \`acinclude.m4' or \`${configure_ac}'.
You might want to install the \`Automake' and \`Perl' packages.
Grab them from any GNU archive site."
find . -type f -name Makefile.am -print |
sed 's/\.am$/.in/' |
while read f; do touch "$f"; done
;;
autom4te*)
echo 1>&2 "\
WARNING: \`$1' is needed, but is $msg.
You might have modified some files without having the
proper tools for further handling them.
You can get \`$1' as part of \`Autoconf' from any GNU
archive site."
file=`echo "$*" | sed -n "$sed_output"`
test -z "$file" && file=`echo "$*" | sed -n "$sed_minuso"`
if test -f "$file"; then
touch $file
else
test -z "$file" || exec >$file
echo "#! /bin/sh"
echo "# Created by GNU Automake missing as a replacement of"
echo "# $ $@"
echo "exit 0"
chmod +x $file
exit 1
fi
;;
bison*|yacc*)
echo 1>&2 "\
WARNING: \`$1' $msg. You should only need it if
you modified a \`.y' file. You may need the \`Bison' package
in order for those modifications to take effect. You can get
\`Bison' from any GNU archive site."
rm -f y.tab.c y.tab.h
if test $# -ne 1; then
eval LASTARG="\${$#}"
case $LASTARG in
*.y)
SRCFILE=`echo "$LASTARG" | sed 's/y$/c/'`
if test -f "$SRCFILE"; then
cp "$SRCFILE" y.tab.c
fi
SRCFILE=`echo "$LASTARG" | sed 's/y$/h/'`
if test -f "$SRCFILE"; then
cp "$SRCFILE" y.tab.h
fi
;;
esac
fi
if test ! -f y.tab.h; then
echo >y.tab.h
fi
if test ! -f y.tab.c; then
echo 'main() { return 0; }' >y.tab.c
fi
;;
lex*|flex*)
echo 1>&2 "\
WARNING: \`$1' is $msg. You should only need it if
you modified a \`.l' file. You may need the \`Flex' package
in order for those modifications to take effect. You can get
\`Flex' from any GNU archive site."
rm -f lex.yy.c
if test $# -ne 1; then
eval LASTARG="\${$#}"
case $LASTARG in
*.l)
SRCFILE=`echo "$LASTARG" | sed 's/l$/c/'`
if test -f "$SRCFILE"; then
cp "$SRCFILE" lex.yy.c
fi
;;
esac
fi
if test ! -f lex.yy.c; then
echo 'main() { return 0; }' >lex.yy.c
fi
;;
help2man*)
echo 1>&2 "\
WARNING: \`$1' is $msg. You should only need it if
you modified a dependency of a manual page. You may need the
\`Help2man' package in order for those modifications to take
effect. You can get \`Help2man' from any GNU archive site."
file=`echo "$*" | sed -n "$sed_output"`
test -z "$file" && file=`echo "$*" | sed -n "$sed_minuso"`
if test -f "$file"; then
touch $file
else
test -z "$file" || exec >$file
echo ".ab help2man is required to generate this page"
exit $?
fi
;;
makeinfo*)
echo 1>&2 "\
WARNING: \`$1' is $msg. You should only need it if
you modified a \`.texi' or \`.texinfo' file, or any other file
indirectly affecting the aspect of the manual. The spurious
call might also be the consequence of using a buggy \`make' (AIX,
DU, IRIX). You might want to install the \`Texinfo' package or
the \`GNU make' package. Grab either from any GNU archive site."
# The file to touch is that specified with -o ...
file=`echo "$*" | sed -n "$sed_output"`
test -z "$file" && file=`echo "$*" | sed -n "$sed_minuso"`
if test -z "$file"; then
# ... or it is the one specified with @setfilename ...
infile=`echo "$*" | sed 's/.* \([^ ]*\) *$/\1/'`
file=`sed -n '
/^@setfilename/{
s/.* \([^ ]*\) *$/\1/
p
q
}' $infile`
# ... or it is derived from the source name (dir/f.texi becomes f.info)
test -z "$file" && file=`echo "$infile" | sed 's,.*/,,;s,.[^.]*$,,'`.info
fi
# If the file does not exist, the user really needs makeinfo;
# let's fail without touching anything.
test -f $file || exit 1
touch $file
;;
tar*)
shift
# We have already tried tar in the generic part.
# Look for gnutar/gtar before invocation to avoid ugly error
# messages.
if (gnutar --version > /dev/null 2>&1); then
gnutar "$@" && exit 0
fi
if (gtar --version > /dev/null 2>&1); then
gtar "$@" && exit 0
fi
firstarg="$1"
if shift; then
case $firstarg in
*o*)
firstarg=`echo "$firstarg" | sed s/o//`
tar "$firstarg" "$@" && exit 0
;;
esac
case $firstarg in
*h*)
firstarg=`echo "$firstarg" | sed s/h//`
tar "$firstarg" "$@" && exit 0
;;
esac
fi
echo 1>&2 "\
WARNING: I can't seem to be able to run \`tar' with the given arguments.
You may want to install GNU tar or Free paxutils, or check the
command line arguments."
exit 1
;;
*)
echo 1>&2 "\
WARNING: \`$1' is needed, and is $msg.
You might have modified some files without having the
proper tools for further handling them. Check the \`README' file,
it often tells you about the needed prerequisites for installing
this package. You may also peek at any GNU archive site, in case
some other package would contain this missing \`$1' program."
exit 1
;;
esac
exit 0
# Local variables:
# eval: (add-hook 'write-file-hooks 'time-stamp)
# time-stamp-start: "scriptversion="
# time-stamp-format: "%:y-%02m-%02d.%02H"
# time-stamp-time-zone: "UTC"
# time-stamp-end: "; # UTC"
# End:
tRNAscan-SE.src
View file @ c9581aea
......@@ -4,7 +4,7 @@
# tRNAscan-SE: a program for improved detection of transfer RNA
# genes in genomic sequence
#
# Version 2.0.3
# Version 2.0.5
#
# Copyright (C) 2019 Patricia Chan and Todd Lowe
#
......@@ -39,8 +39,8 @@ use tRNAscanSE::IntResultFile;
use tRNAscanSE::MultiResultFile;
use tRNAscanSE::SS;
our $version = "2.0.3";
our $release_date = "April 2019";
our $version = "2.0.5";
our $release_date = "October 2019";
our $program_id = "tRNAscan-SE-".$version;
# modified by 'make'
......@@ -260,7 +260,7 @@ sub first_pass_prescan
if ($seq_file->seq_buf_overrun())
{
$start_index = $seq_file->buffer_end_index() + 1;
if ($seq_file->read_more_fasta())
if ($seq_file->read_more_fasta($opts))
{
$sequence_scanned = 0;
}
......@@ -1520,7 +1520,7 @@ sub set_options
# do max scan
if ($opt_max != 0)
{
if ($opt_eufind || $opt_tscan || $opt_cove || $opt_legacy || $opt_mid)
if ($opt_eufind || $opt_tscan || $opt_cove || $opt_legacy || ($opt_mid and $opt_mito != 0))
{
die "FATAL: Conflicting search options have been selected. --max, -t, -e, -C, and -L cannot be used simultaneously.\n";
}
......@@ -1531,6 +1531,10 @@ sub set_options
{
$opts->infernal_fp(0);
}
elsif ($opt_mito)
{
$opt_mid = 0;
}
}
# set hmm filter flag for infernal
......