er=0;
myself=`dirname "$0"`/`basename "$0"`; export myself
-version="v6.717b (2009/12/03)"; export version
+version="v6.857b (2011/05/30)"; export version
LANG=C; export LANG
os=`uname`
progname=`basename "$0"`
os="darwin"
elif [ `echo $os | grep -i sunos` ]; then
os="sunos"
+elif [ `echo $os | grep -i linux` ]; then
+ os="linux"
else
os="unix"
fi
if [ "$MAFFT_BINARIES" ]; then
prefix="$MAFFT_BINARIES"
else
- prefix=/usr/lib/mafft
+ prefix=/usr/libexec/mafft
fi
export prefix
defaultiterate=2
defaultdistance="sixtuples"
fi
+outputfile=""
+namelength=15
+anysymbol=0
+parallelizationstrategy="BAATARI2"
kappa=$defaultkappa
sbstmodel=$defaultsbstmodel
fmodel=$defaultfmodel
laraparams="/dev/null"
foldalignopt=" "
treealg=" -X "
+scoreoutarg=" "
+numthreads=0
+randomseed=0
+addfile="/dev/null"
+addarg0=" "
+outnum=" "
if [ $# -gt 0 ]; then
while [ $# -gt 1 ];
do
if [ "$1" = "--auto" ]; then
auto=1
+ elif [ "$1" = "--anysymbol" ]; then
+ anysymbol=1
+ elif [ "$1" = "--preservecase" ]; then
+ anysymbol=1
elif [ "$1" = "--clustalout" ]; then
outputformat="clustal"
+ elif [ "$1" = "--phylipout" ]; then
+ outputformat="phylip"
elif [ "$1" = "--reorder" ]; then
outorder="aligned"
partorderopt=" "
elif [ "$1" = "--algq" ]; then
algopt=" -Q "
algoptit=" -QB "
+ elif [ "$1" = "--namelength" ]; then
+ shift
+ namelength=`expr "$1" - 0`
elif [ "$1" = "--groupsize" ]; then
shift
groupsize=`expr "$1" - 0`
coreext=" -c "
elif [ "$1" = "--core" ]; then
coreout=1
+ elif [ "$1" = "--out" ]; then
+ shift
+ outputfile="$1"
+ elif [ "$1" = "--thread" ]; then
+ shift
+ numthreads=`expr "$1" - 0`
+ elif [ "$1" = "--randomseed" ]; then
+ shift
+ randomseed=`expr "$1" - 0`
+ elif [ "$1" = "--bestfirst" ]; then
+ parallelizationstrategy="BESTFIRST"
+ elif [ "$1" = "--adhoc0" ]; then
+ parallelizationstrategy="BAATARI0"
+ elif [ "$1" = "--adhoc1" ]; then
+ parallelizationstrategy="BAATARI1"
+ elif [ "$1" = "--adhoc2" ]; then
+ parallelizationstrategy="BAATARI2"
+ elif [ "$1" = "--simplehillclimbing" ]; then
+ parallelizationstrategy="BAATARI2"
+ elif [ "$1" = "--scoreout" ]; then
+ scoreoutarg="-S -B"
+ elif [ "$1" = "--outnum" ]; then
+ scoreoutarg="-n"
+ elif [ "$1" = "--addprofile" ]; then
+ shift
+ addarg0="-I"
+ addfile="$1"
+ elif [ "$1" = "--add" ]; then
+ shift
+ addarg0="-K -I"
+ addfile="$1"
elif [ "$1" = "--maxiterate" ]; then
shift
iterate=`expr "$1" - 0`
fi
if [ $# -eq 1 ]; then
if [ -r "$1" -o "$1" = - ]; then
- cat "$1" | tr "\r" "\n" > $TMPFILE/infile
+
+ if [ -r "$addfile" ]; then
+ printf '';
+ else
+ echo "$0": Cannot open "$addfile". 1>&2
+ exit 1;
+ fi
+
+ cat "$1" | tr "\r" "\n" > $TMPFILE/infile
+ echo "" >> $TMPFILE/infile
+ cat "$addfile" | tr "\r" "\n" | grep -v "^$" >> $TMPFILE/infile
+ cat "$addfile" | tr "\r" "\n" | grep -v "^$" > $TMPFILE/_addfile
cat "$aamatrix" | tr "\r" "\n" | grep -v "^$" > $TMPFILE/_aamtx
cat "$treeinfile" | tr "\r" "\n" | grep -v "^$" > $TMPFILE/_guidetree
cat "$seedtablefile" | tr "\r" "\n" | grep -v "^$" > $TMPFILE/_seedtablefile
while [ $# -gt 1 ];
do
shift
- cat "$1" | tr "\r" "\n" > $TMPFILE/seed$#
+ if [ -r "$1" ]; then
+ cat "$1" | tr "\r" "\n" > $TMPFILE/seed$#
+ else
+ echo "$0": Cannot open "$1". 1>&2
+ exit 1;
+ fi
seednseq=$seednseq" "`grep -c '^[>|=]' $TMPFILE/seed$#`
seedfilesintmp=$seedfilesintmp" "seed$#
done
# ls $TMPFILE
# echo $seedfilesintmp
# echo $seednseq
+
+
else
echo "$0": Cannot open "$1". 1>&2
er=1
fi
+ if [ $os != "linux" ]; then
+ numthreads=0
+ fi
+
+ if [ $numthreads -eq 0 -a $parallelizationstrategy = "BESTFIRST" ]; then
+ echo 'Impossible' 1>&2;
+ exit 1;
+ fi
+
if [ $auto -eq 1 ]; then
"$prefix/countlen" < $TMPFILE/infile > $TMPFILE/size
nseq=`awk '{print $1}' $TMPFILE/size`
fi
fi
- if [ $iterate -gt 16 ]; then #??
- iterate=16
+ if [ $parallelizationstrategy = "BESTFIRST" -o $parallelizationstrategy = "BAATARI0" ]; then
+ iteratelimit=254
+ else
+ iteratelimit=16
+ fi
+ if [ $iterate -gt $iteratelimit ]; then #??
+ iterate=$iteratelimit
fi
if [ $rnaalifold -eq 1 ]; then
# echo " Input format: fasta" 1>&2
# echo "" 1>&2
# echo " Usage: `basename $0` [options] inputfile > outputfile" 1>&2
- echo " http://align.bmr.kyushu-u.ac.jp/mafft/software/" 1>&2
+ echo " http://mafft.cbrc.jp/alignment/software/" 1>&2
echo " NAR 30:3059-3066 (2002), Briefings in Bioinformatics 9:286-298 (2008)" 1>&2
# echo "------------------------------------------------------------------------------" 1>&2
# echo " % mafft in > out" 1>&2
# echo "" 1>&2
echo "High speed:" 1>&2
echo " % mafft in > out" 1>&2
- echo " % mafft --retree 1 in > out (fastest)" 1>&2
+ echo " % mafft --retree 1 in > out (fast)" 1>&2
echo "" 1>&2
echo "High accuracy (for <~200 sequences x <~2,000 aa/nt):" 1>&2
echo " % mafft --maxiterate 1000 --localpair in > out (% linsi in > out is also ok)" 1>&2
echo "--clustalout : Output: clustal format, default: fasta" 1>&2
echo "--reorder : Outorder: aligned, default: input order" 1>&2
echo "--quiet : Do not report progress" 1>&2
+ echo "--thread # : Number of threads. (# must be <= number of physical cores - 1)" 1>&2
# echo "" 1>&2
# echo " % mafft --maxiterate 1000 --localpair in > out (L-INS-i)" 1>&2
# echo " most accurate in many cases, assumes only one alignable domain" 1>&2
cycle=3
fi
- if [ $nseq -gt 1000 -a $iterate -gt 1 ]; then
+ if [ $nseq -gt 4000 -a $iterate -gt 1 ]; then
echo "Too many sequences to perform iterative refinement!" 1>&2
echo "Please use a progressive method." 1>&2
exit 1
if [ $cycle -lt 2 ]; then
cycle=2 # nazeda
fi
+ if [ $iterate -lt 2 ]; then
+ echo "############################################################################" 1>&2
+ echo "# Warning:" 1>&2
+ echo "# Progressive alignment method is incompatible with the --seed option." 1>&2
+ echo "# Automatically switched to the iterative refinement method." 1>&2
+ echo "# " 1>&2
+ echo "# Also consider using the '--add' option, which is compatible with" 1>&2
+ echo "# the progressive method and FASTER than the '--seed' option." 1>&2
+ echo "# Usage is:" 1>&2
+ echo "# % mafft --add newSequences existingAlignment > output" 1>&2
+ echo "############################################################################" 1>&2
+ iterate=2
+ fi
localparam="-l "$weighti
elif [ $distance = "parttree" ]; then
localparam=" "
echo 'Use either one of seedtable and seed. Not both.' 1>&2
exit 1
fi
+# if [ $seedtable != "x" -a $anysymbol -gt 0 ]; then
+# echo 'The combination of --seedtable and --anysymbol is not supported.' 1>&2
+# exit 1
+# fi
if [ $treein -eq 1 ]; then
# if [ $iterate -gt 0 ]; then
cycle=1
fi
+ if [ "$addarg0" != " " ]; then
+ "$prefix/countlen" < $TMPFILE/_addfile > $TMPFILE/addsize
+ nadd=`awk '{print $1}' $TMPFILE/addsize`
+ if [ $nadd -eq "0" ]; then
+ echo Check $addfile 1>&2
+ exit 1;
+ fi
+ addarg="$addarg0 $nadd"
+ cycle=1
+ iterate=0
+ if [ $seed != "x" -o $seedtable != "x" ]; then
+ echo 'Impossible' 1>&2;
+ echo 'Use either ONE of --seed, --seedtable, --addprofile and --add.' 1>&2
+ exit 1;
+ fi
+ fi
+
if [ $mccaskill -eq 1 -o $rnaalifold -eq 1 -o $contrafold -eq 1 ]; then
if [ $distance = "sixtuples" ]; then
echo 'Not supported.' 1>&2
fi
if [ $outputformat = "clustal" -a $outorder = "aligned" ]; then
- outputopt=" -c $strategy -r order "
+ outputopt=" -c $strategy -r $TMPFILE/order "
elif [ $outputformat = "clustal" -a $outorder = "input" ]; then
outputopt=" -c $strategy "
+ elif [ $outputformat = "phylip" -a $outorder = "aligned" ]; then
+ outputopt=" -y -r $TMPFILE/order "
+ elif [ $outputformat = "phylip" -a $outorder = "input" ]; then
+ outputopt=" -y "
elif [ $outputformat = "pir" -a $outorder = "aligned" ]; then
- outputopt=" -f -r order "
+ outputopt=" -f -r $TMPFILE/order "
else
outputopt="null"
fi
(
cd $TMPFILE;
+
if [ $quiet -gt 0 ]; then
+
+ if [ $anysymbol -eq 1 ]; then
+ mv infile orig
+ "$prefix/replaceu" -i orig > infile 2>/dev/null || exit 1
+ fi
+
if [ $seed != "x" ]; then
mv infile infile2
+ if [ $anysymbol -eq 1 ]; then
+ mv orig orig2
+ cat /dev/null > orig
+ fi
cat /dev/null > infile
cat /dev/null > hat3.seed
seedoffset=0
do
shift
# echo "num="$#
- "$prefix/multi2hat3s" -t $nseq -o $seedoffset -i seed$# >> infile 2>/dev/null || exit 1
+
+ if [ $anysymbol -eq 1 ]; then
+ cat seed$# >> orig
+ "$prefix/replaceu" -i seed$# -o $seedoffset > clean 2>/dev/null || exit 1
+ mv clean seed$#
+ fi
+ "$prefix/multi2hat3s" -t $nseq -o $seedoffset -i seed$# >> infile 2>/dev/null || exit 1
cat hat3 >> hat3.seed
# echo "$1"
seedoffset=`expr $seedoffset + $1`
# echo "seedoffset="$seedoffset
done;
# echo "seedoffset="$seedoffset
- cat infile2 >> infile
+ if [ $anysymbol -eq 1 ]; then
+ "$prefix/replaceu" -i orig2 -o $seedoffset >> infile 2>/dev/null || exit 1 # yarinaoshi
+ cat orig2 >> orig
+ else
+ cat infile2 >> infile
+ fi
elif [ $seedtable != "x" ]; then
cat _seedtablefile > hat3.seed
else
cat /dev/null > hat3.seed
fi
# cat hat3.seed
+
+
if [ $mccaskill -eq 1 ]; then
- "$prefix/mccaskillwrap" -d "$prefix" -i infile > hat4 2>/dev/null || exit 1
+ "$prefix/mccaskillwrap" -C $numthreads -d "$prefix" -i infile > hat4 2>/dev/null || exit 1
elif [ $contrafold -eq 1 ]; then
"$prefix/contrafoldwrap" -d "$prefix" -i infile > hat4 2>/dev/null || exit 1
fi
"$prefix/dndfast7" $swopt < infile > /dev/null 2>&1 || exit 1
cat hat3.seed hat3 > hatx
mv hatx hat3
- "$prefix/tbfast" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt $treealg < infile > /dev/null 2>&1 || exit 1
+ "$prefix/tbfast" $outnum $addarg -C $numthreads $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>&1 || exit 1
elif [ $distance = "blast" ]; then
"$prefix/dndblast" < infile > /dev/null 2>&1 || exit 1
cat hat3.seed hat3 > hatx
mv hatx hat3
- "$prefix/tbfast" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt $treealg < infile > /dev/null 2>&1 || exit 1
+ "$prefix/tbfast" $outnum $addarg -C $numthreads $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>&1 || exit 1
elif [ $distance = "foldalignlocal" ]; then
- "$prefix/pairlocalalign" $seqtype $foldalignopt $model -g $lexp -f $lgop -h $laof -H -d "$prefix" < infile > /dev/null 2>&1 || exit 1
+ "$prefix/pairlocalalign" -C $numthreads $seqtype $foldalignopt $model -g $lexp -f $lgop -h $laof -H -d "$prefix" < infile > /dev/null 2>&1 || exit 1
cat hat3.seed hat3 > hatx
mv hatx hat3
- "$prefix/tbfast" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt $treealg < infile > /dev/null 2>&1 || exit 1
+ "$prefix/tbfast" $outnum $addarg -C $numthreads $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>&1 || exit 1
elif [ $distance = "foldalignglobal" ]; then
- "$prefix/pairlocalalign" $seqtype $foldalignopt $model -g $pgexp -f $pggop -h $pgaof -H -o -global -d "$prefix" < infile > /dev/null 2>&1 || exit 1
+ "$prefix/pairlocalalign" -C $numthreads $seqtype $foldalignopt $model -g $pgexp -f $pggop -h $pgaof -H -o -global -d "$prefix" < infile > /dev/null 2>&1 || exit 1
cat hat3.seed hat3 > hatx
mv hatx hat3
- "$prefix/tbfast" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt $treealg < infile > /dev/null 2>&1 || exit 1
+ "$prefix/tbfast" $outnum $addarg -C $numthreads $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>&1 || exit 1
elif [ $distance = "slara" ]; then
- "$prefix/pairlocalalign" -p $laraparams $seqtype $model -f $lgop -T -d "$prefix" < infile > /dev/null 2>&1 || exit 1
+ "$prefix/pairlocalalign" -C $numthreads -p $laraparams $seqtype $model -f $lgop -T -d "$prefix" < infile > /dev/null 2>&1 || exit 1
cat hat3.seed hat3 > hatx
mv hatx hat3
- "$prefix/tbfast" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt $treealg < infile > /dev/null 2>&1 || exit 1
+ "$prefix/tbfast" $outnum $addarg -C $numthreads $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>&1 || exit 1
elif [ $distance = "lara" ]; then
- "$prefix/pairlocalalign" -p $laraparams $seqtype $model -f $lgop -B -d "$prefix" < infile > /dev/null 2>&1 || exit 1
+ "$prefix/pairlocalalign" -C $numthreads -p $laraparams $seqtype $model -f $lgop -B -d "$prefix" < infile > /dev/null 2>&1 || exit 1
cat hat3.seed hat3 > hatx
mv hatx hat3
- "$prefix/tbfast" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt $treealg < infile > /dev/null 2>&1 || exit 1
+ "$prefix/tbfast" $outnum $addarg -C $numthreads $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>&1 || exit 1
elif [ $distance = "scarna" ]; then
- "$prefix/pairlocalalign" $seqtype $model -f $pggop -s -d "$prefix" < infile > /dev/null 2>&1 || exit 1
+ "$prefix/pairlocalalign" -C $numthreads $seqtype $model -f $pggop -s -d "$prefix" < infile > /dev/null 2>&1 || exit 1
cat hat3.seed hat3 > hatx
mv hatx hat3
- "$prefix/tbfast" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt $treealg < infile > /dev/null 2>&1 || exit 1
+ "$prefix/tbfast" $outnum $addarg -C $numthreads $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>&1 || exit 1
elif [ $distance = "global" ]; then
- "$prefix/pairlocalalign" $seqtype $model -g $pgexp -f $pggop -h $pgaof -F < infile > /dev/null 2>&1 || exit 1
+ "$prefix/pairlocalalign" -C $numthreads $seqtype $model -g $pgexp -f $pggop -h $pgaof -F < infile > /dev/null 2>&1 || exit 1
cat hat3.seed hat3 > hatx
mv hatx hat3
- "$prefix/tbfast" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt $treealg < infile > /dev/null 2>&1 || exit 1
+ "$prefix/tbfast" $outnum $addarg -C $numthreads $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>&1 || exit 1
elif [ $distance = "local" ]; then
- "$prefix/pairlocalalign" $seqtype $model -g $lexp -f $lgop -h $laof -L < infile > /dev/null 2>&1 || exit 1
+ "$prefix/pairlocalalign" -C $numthreads $seqtype $model -g $lexp -f $lgop -h $laof -L < infile > /dev/null 2>&1 || exit 1
cat hat3.seed hat3 > hatx
mv hatx hat3
- "$prefix/tbfast" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt $treealg < infile > /dev/null 2>&1 || exit 1
+ "$prefix/tbfast" $outnum $addarg -C $numthreads $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>&1 || exit 1
elif [ $distance = "globalgenaf" ]; then
- "$prefix/pairlocalalign" $seqtype $model -g $pgexp -f $pggop -h $pgaof -O $GGOP -E $GEXP -K < infile > /dev/null 2>&1 || exit 1
+ "$prefix/pairlocalalign" -C $numthreads $seqtype $model -g $pgexp -f $pggop -h $pgaof -O $GGOP -E $GEXP -K < infile > /dev/null 2>&1 || exit 1
cat hat3.seed hat3 > hatx
mv hatx hat3
- "$prefix/tbfast" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt $treealg < infile > /dev/null 2>&1 || exit 1
+ "$prefix/tbfast" $outnum $addarg -C $numthreads $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>&1 || exit 1
elif [ $distance = "localgenaf" ]; then
- "$prefix/pairlocalalign" $seqtype $model -g $lexp -f $lgop -h $laof -O $LGOP -E $LEXP -N < infile > /dev/null 2>&1 || exit 1
+ "$prefix/pairlocalalign" -C $numthreads $seqtype $model -g $lexp -f $lgop -h $laof -O $LGOP -E $LEXP -N < infile > /dev/null 2>&1 || exit 1
cat hat3.seed hat3 > hatx
mv hatx hat3
- "$prefix/tbfast" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt $treealg < infile > /dev/null 2>&1 || exit 1
+ "$prefix/tbfast" $outnum $addarg -C $numthreads $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>&1 || exit 1
elif [ $distance = "distonly" ]; then
- "$prefix/pairlocalalign" $seqtype $model -g $pgexp -f $pggop -h $pgaof -t < infile > /dev/null 2>&1 || exit 1
- "$prefix/tbfast" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt $treealg < infile > /dev/null 2>&1 || exit 1
+ "$prefix/pairlocalalign" -C $numthreads $seqtype $model -g $pgexp -f $pggop -h $pgaof -t < infile > /dev/null 2>&1 || exit 1
+ "$prefix/tbfast" $outnum $addarg -C $numthreads $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>&1 || exit 1
elif [ $distance = "parttree" ]; then
"$prefix/splittbfast" -Q $splitopt $partorderopt $parttreeoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft -p $partsize -s $groupsize $treealg -i infile > pre 2>/dev/null || exit 1
mv hat3.seed hat3
else
- "$prefix/disttbfast" $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $algopt $treealg < infile > pre 2>/dev/null || exit 1
+ "$prefix/disttbfast" -O $outnum $addarg -C $numthreads $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $algopt $treealg $scoreoutarg < infile > pre 2>/dev/null || exit 1
mv hat3.seed hat3
fi
while [ $cycle -gt 1 ]
mv pre infile
"$prefix/splittbfast" -Z -Q $splitopt $partorderopt $parttreeoutopt $memopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft -p $partsize -s $groupsize $treealg -i infile > pre 2>/dev/null || exit 1
else
- "$prefix/tbfast" $rnaopt $weightopt $treeoutopt $distoutopt $memopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt -J $treealg < pre > /dev/null 2>&1 || exit 1
+ "$prefix/tbfast" -O $outnum -C $numthreads $rnaopt $weightopt $treeoutopt $distoutopt $memopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt -J $treealg $scoreoutarg < pre > /dev/null 2>&1 || exit 1
fi
cycle=`expr $cycle - 1`
done
if [ $iterate -gt 0 ]; then
if [ $distance = "sixtuples" ]; then
- "$prefix/dndpre" < pre > /dev/null 2>&1 || exit 1
+ "$prefix/dndpre" -C $numthreads < pre > /dev/null 2>&1 || exit 1
fi
- "$prefix/dvtditr" $rnaoptit $memopt $scorecalcopt $localparam -z 50 $seqtype $model -f "-"$gop -h "-"$aof -I $iterate $weightopt $treeinopt $algoptit $treealg < pre > /dev/null 2>&1 || exit 1
+ "$prefix/dvtditr" -C $numthreads -t $randomseed $rnaoptit $memopt $scorecalcopt $localparam -z 50 $seqtype $model -f "-"$gop -h "-"$aof -I $iterate $weightopt $treeinopt $algoptit $treealg -p $parallelizationstrategy $scoreoutarg < pre > /dev/null 2>&1 || exit 1
fi
else
+
+ if [ $anysymbol -eq 1 ]; then
+ mv infile orig
+ "$prefix/replaceu" -i orig > infile || exit 1
+ fi
+
if [ $seed != "x" ]; then
mv infile infile2
+ if [ $anysymbol -eq 1 ]; then
+ mv orig orig2
+ cat /dev/null > orig
+ fi
cat /dev/null > infile
cat /dev/null > hat3.seed
seedoffset=0
do
shift
# echo "num="$#
- "$prefix/multi2hat3s" -t $nseq -o $seedoffset -i seed$# >> infile || exit 1
+
+ if [ $anysymbol -eq 1 ]; then
+ cat seed$# >> orig
+ "$prefix/replaceu" -i seed$# -o $seedoffset > clean || exit 1
+ mv clean seed$#
+ fi
+ "$prefix/multi2hat3s" -t $nseq -o $seedoffset -i seed$# >> infile || exit 1
cat hat3 >> hat3.seed
# echo "$1"
seedoffset=`expr $seedoffset + $1`
# echo "seedoffset="$seedoffset
done;
# echo "seedoffset="$seedoffset
- cat infile2 >> infile
+ if [ $anysymbol -eq 1 ]; then
+ "$prefix/replaceu" -i orig2 -o $seedoffset >> infile || exit 1 # yarinaoshi
+ cat orig2 >> orig
+ else
+ cat infile2 >> infile
+ fi
elif [ $seedtable != "x" ]; then
cat _seedtablefile > hat3.seed
else
cat /dev/null > hat3.seed
fi
# cat hat3.seed
+
if [ $mccaskill -eq 1 ]; then
- "$prefix/mccaskillwrap" -d "$prefix" -i infile > hat4 || exit 1
+ "$prefix/mccaskillwrap" -C $numthreads -d "$prefix" -i infile > hat4 || exit 1
elif [ $contrafold -eq 1 ]; then
"$prefix/contrafoldwrap" -d "$prefix" -i infile > hat4 || exit 1
fi
"$prefix/dndfast7" $swopt < infile > /dev/null || exit 1
cat hat3.seed hat3 > hatx
mv hatx hat3
- "$prefix/tbfast" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt $treealg < infile > /dev/null || exit 1
+ "$prefix/tbfast" $outnum $addarg -C $numthreads $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null || exit 1
elif [ $distance = "blast" ]; then
"$prefix/dndblast" < infile > /dev/null || exit 1
cat hat3.seed hat3 > hatx
mv hatx hat3
- "$prefix/tbfast" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt $treealg < infile > /dev/null || exit 1
+ "$prefix/tbfast" $outnum $addarg -C $numthreads $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null || exit 1
elif [ $distance = "foldalignlocal" ]; then
- "$prefix/pairlocalalign" $seqtype $foldalignopt $model -g $lexp -f $lgop -h $laof -H -d "$prefix" < infile > /dev/null || exit 1
+ "$prefix/pairlocalalign" -C $numthreads $seqtype $foldalignopt $model -g $lexp -f $lgop -h $laof -H -d "$prefix" < infile > /dev/null || exit 1
cat hat3.seed hat3 > hatx
mv hatx hat3
- "$prefix/tbfast" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt $treealg < infile > /dev/null 2>&1 || exit 1
+ "$prefix/tbfast" $outnum $addarg -C $numthreads $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>&1 || exit 1
elif [ $distance = "foldalignglobal" ]; then
- "$prefix/pairlocalalign" $seqtype $foldalignopt $model -g $pgexp -f $pggop -h $pgaof -H -o -global -d "$prefix" < infile > /dev/null || exit 1
+ "$prefix/pairlocalalign" -C $numthreads $seqtype $foldalignopt $model -g $pgexp -f $pggop -h $pgaof -H -o -global -d "$prefix" < infile > /dev/null || exit 1
cat hat3.seed hat3 > hatx
mv hatx hat3
- "$prefix/tbfast" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt $treealg < infile > /dev/null 2>&1 || exit 1
+ "$prefix/tbfast" $outnum $addarg -C $numthreads $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>&1 || exit 1
elif [ $distance = "slara" ]; then
- "$prefix/pairlocalalign" -p $laraparams $seqtype $model -f $lgop -T -d "$prefix" < infile > /dev/null || exit 1
+ "$prefix/pairlocalalign" -C $numthreads -p $laraparams $seqtype $model -f $lgop -T -d "$prefix" < infile > /dev/null || exit 1
cat hat3.seed hat3 > hatx
mv hatx hat3
- "$prefix/tbfast" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt $treealg < infile > /dev/null 2>&1 || exit 1
+ "$prefix/tbfast" $outnum $addarg -C $numthreads $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>&1 || exit 1
elif [ $distance = "lara" ]; then
- "$prefix/pairlocalalign" -p $laraparams $seqtype $model -f $lgop -B -d "$prefix" < infile > /dev/null || exit 1
+ "$prefix/pairlocalalign" -C $numthreads -p $laraparams $seqtype $model -f $lgop -B -d "$prefix" < infile > /dev/null || exit 1
cat hat3.seed hat3 > hatx
mv hatx hat3
- "$prefix/tbfast" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt $treealg < infile > /dev/null 2>&1 || exit 1
+ "$prefix/tbfast" $outnum $addarg -C $numthreads $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>&1 || exit 1
elif [ $distance = "scarna" ]; then
- "$prefix/pairlocalalign" $seqtype $model -f $pggop -s -d "$prefix" < infile > /dev/null || exit 1
+ "$prefix/pairlocalalign" -C $numthreads $seqtype $model -f $pggop -s -d "$prefix" < infile > /dev/null || exit 1
cat hat3.seed hat3 > hatx
mv hatx hat3
- "$prefix/tbfast" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt $treealg < infile > /dev/null 2>&1 || exit 1
+ "$prefix/tbfast" $outnum $addarg -C $numthreads $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>&1 || exit 1
elif [ $distance = "global" ]; then
- "$prefix/pairlocalalign" $seqtype $model -g $pgexp -f $pggop -h $pgaof -F < infile > /dev/null || exit 1
+ "$prefix/pairlocalalign" -C $numthreads $seqtype $model -g $pgexp -f $pggop -h $pgaof -F < infile > /dev/null || exit 1
cat hat3.seed hat3 > hatx
mv hatx hat3
- "$prefix/tbfast" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt $treealg < infile > /dev/null || exit 1
+ "$prefix/tbfast" $outnum $addarg -C $numthreads $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null || exit 1
elif [ $distance = "local" ]; then
- "$prefix/pairlocalalign" $seqtype $model -g $lexp -f $lgop -h $laof -L < infile > /dev/null || exit 1
+ "$prefix/pairlocalalign" -C $numthreads $seqtype $model -g $lexp -f $lgop -h $laof -L < infile > /dev/null || exit 1
cat hat3.seed hat3 > hatx
mv hatx hat3
- "$prefix/tbfast" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt $treealg < infile > /dev/null || exit 1
+ "$prefix/tbfast" $outnum $addarg -C $numthreads $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null || exit 1
elif [ $distance = "globalgenaf" ]; then
- "$prefix/pairlocalalign" $seqtype $model -g $pgexp -f $pggop -h $pgaof -O $GGOP -E $GEXP -K < infile > /dev/null || exit 1
+ "$prefix/pairlocalalign" -C $numthreads $seqtype $model -g $pgexp -f $pggop -h $pgaof -O $GGOP -E $GEXP -K < infile > /dev/null || exit 1
cat hat3.seed hat3 > hatx
mv hatx hat3
- "$prefix/tbfast" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt $treealg < infile > /dev/null || exit 1
+ "$prefix/tbfast" $outnum $addarg -C $numthreads $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null || exit 1
elif [ $distance = "localgenaf" ]; then
- "$prefix/pairlocalalign" $seqtype $model -g $lexp -f $lgop -h $laof -O $LGOP -E $LEXP -N < infile > /dev/null || exit 1
+ "$prefix/pairlocalalign" -C $numthreads $seqtype $model -g $lexp -f $lgop -h $laof -O $LGOP -E $LEXP -N < infile > /dev/null || exit 1
cat hat3.seed hat3 > hatx
mv hatx hat3
- "$prefix/tbfast" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt $treealg < infile > /dev/null || exit 1
+ "$prefix/tbfast" $outnum $addarg -C $numthreads $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null || exit 1
elif [ $distance = "distonly" ]; then
- "$prefix/pairlocalalign" $seqtype $model -g $pgexp -f $pggop -h $pgaof -t < infile > /dev/null || exit 1
- "$prefix/tbfast" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt $treealg < infile > /dev/null || exit 1
+ "$prefix/pairlocalalign" -C $numthreads $seqtype $model -g $pgexp -f $pggop -h $pgaof -t < infile > /dev/null || exit 1
+ "$prefix/tbfast" $outnum $addarg -C $numthreads $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null || exit 1
elif [ $distance = "parttree" ]; then
"$prefix/splittbfast" -Q $splitopt $partorderopt $parttreeoutopt $memopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft -p $partsize -s $groupsize $treealg -i infile > pre || exit 1
mv hat3.seed hat3
else
- "$prefix/disttbfast" $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $algopt $treealg < infile > pre || exit 1
+ "$prefix/disttbfast" -O $outnum $addarg -C $numthreads $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $algopt $treealg $scoreoutarg < infile > pre || exit 1
mv hat3.seed hat3
fi
mv pre infile
"$prefix/splittbfast" -Z -Q $splitopt $partorderopt $parttreeoutopt $memopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft -p $partsize -s $groupsize $treealg -i infile > pre || exit 1
else
- "$prefix/tbfast" $rnaopt $weightopt $treeoutopt $distoutopt $memopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt -J $treealg < pre > /dev/null || exit 1
+ "$prefix/tbfast" -O $outnum -C $numthreads $rnaopt $weightopt $treeoutopt $distoutopt $memopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt -J $treealg $scoreoutarg < pre > /dev/null || exit 1
fi
cycle=`expr $cycle - 1`
done
if [ $iterate -gt 0 ]; then
if [ $distance = "sixtuples" ]; then
- "$prefix/dndpre" < pre > /dev/null 2>&1 || exit 1
+ "$prefix/dndpre" -C $numthreads < pre > /dev/null 2>&1 || exit 1
fi
- "$prefix/dvtditr" $rnaoptit $memopt $scorecalcopt $localparam -z 50 $seqtype $model -f "-"$gop -h "-"$aof -I $iterate $weightopt $treeinopt $algoptit $treealg < pre > /dev/null || exit 1
+ "$prefix/dvtditr" -C $numthreads -t $randomseed $rnaoptit $memopt $scorecalcopt $localparam -z 50 $seqtype $model -f "-"$gop -h "-"$aof -I $iterate $weightopt $treeinopt $algoptit $treealg -p $parallelizationstrategy $scoreoutarg < pre > /dev/null || exit 1
fi
fi
-
-
if [ $coreout -eq 1 ]; then
"$prefix/setcore" -w $corewin -i $corethr $coreext < pre > pre2
mv pre2 pre
+ elif [ $anysymbol -eq 1 ]; then
+ "$prefix/restoreu" -a pre -i orig > restored || exit 1
+ mv restored pre
fi
+
+ if [ $quiet -eq 0 ]; then
+ echo '' 1>&2
+ if [ $mccaskill -eq 1 ]; then
+ echo "RNA base pairing probaility was calculated by the McCaskill algorithm (1)" 1>&2
+ echo "implemented in Vienna RNA package (2) and MXSCARNA (3), and then" 1>&2
+ echo "incorporated in the iterative alignment process (4)." 1>&2
+ echo "(1) McCaskill, 1990, Biopolymers 29:1105-1119" 1>&2
+ echo "(2) Hofacker et al., 2002, J. Mol. Biol. 319:3724-3732" 1>&2
+ echo "(3) Tabei et al., 2008, BMC Bioinformatics 9:33" 1>&2
+ echo "(4) Katoh and Toh, 2008, BMC Bioinformatics 9:212" 1>&2
+ echo "" 1>&2
+ elif [ $contrafold -eq 1 ]; then
+ echo "RNA base pairing probaility was calculated by the CONTRAfold algorithm (1)" 1>&2
+ echo "and then incorporated in the iterative alignment process (4)." 1>&2
+ echo "(1) Do et al., 2006, Bioinformatics 22:e90-98" 1>&2
+ echo "(2) Katoh and Toh, 2008, BMC Bioinformatics 9:212" 1>&2
+ echo "" 1>&2
+ fi
+ if [ $distance = "fasta" -o $partdist = "fasta" ]; then
+ echo "Pairwise alignments were computed by FASTA" 1>&2
+ echo "(Pearson & Lipman, 1988, PNAS 85:2444-2448)" 1>&2
+ fi
+ if [ $distance = "blast" ]; then
+ echo "Pairwise alignments were computed by BLAST" 1>&2
+ echo "(Altschul et al., 1997, NAR 25:3389-3402)" 1>&2
+ fi
+ if [ $distance = "scarna" ]; then
+ echo "Pairwise alignments were computed by MXSCARNA" 1>&2
+ echo "(Tabei et al., 2008, BMC Bioinformatics 9:33)." 1>&2
+ fi
+ if [ $distance = "lara" -o $distance = "slara" ]; then
+ echo "Pairwise alignments were computed by LaRA" 1>&2
+ echo "(Bauer et al., 2007, BMC Bioinformatics 8:271)." 1>&2
+ fi
+ if [ $distance = "foldalignlocal" ]; then
+ echo "Pairwise alignments were computed by FOLDALIGN (local)" 1>&2
+ echo "(Havgaard et al., 2007, PLoS Computational Biology 3:e193)." 1>&2
+ fi
+ if [ $distance = "foldalignglobal" ]; then
+ echo "Pairwise alignments were computed by FOLDALIGN (global)" 1>&2
+ echo "(Havgaard et al., 2007, PLoS Computational Biology 3:e193)." 1>&2
+ fi
+ printf "\n" 1>&2
+ echo 'Strategy:' 1>&2
+ printf ' '$strategy 1>&2
+ echo ' ('$performance')' 1>&2
+ echo ' '$explanation 1>&2
+ echo '' 1>&2
+ echo "If unsure which option to use, try 'mafft --auto input > output'." 1>&2
+# echo "If long gaps are expected, try 'mafft --ep 0.0 --auto input > output'." 1>&2
+ echo "If the possibility of long gaps can be excluded, add '--ep 0.123'." 1>&2
+ echo "For more information, see 'mafft --help', 'mafft --man' and the mafft page." 1>&2
+ echo '' 1>&2
+ fi
+ )
+
+ if [ "$outputfile" = "" ]; then
if [ "$outputopt" = "null" ]; then
- cat < pre || exit 1
+ cat < $TMPFILE/pre || exit 1
else
- "$prefix/f2cl" $outputopt < pre || exit 1
+ "$prefix/f2cl" -n $namelength $outputopt < $TMPFILE/pre || exit 1
fi
- )
+ else
+ if [ "$outputopt" = "null" ]; then
+ cat < $TMPFILE/pre > "$outputfile" || exit 1
+ else
+ "$prefix/f2cl" -n $namelength $outputopt < $TMPFILE/pre > "$outputfile" || exit 1
+ fi
+ fi
if [ $treeout -eq 1 ]; then
cp $TMPFILE/infile.tree "$infilename.tree"
cp $TMPFILE/hat2 "$infilename.hat2"
fi
- if [ $quiet -eq 0 ]; then
- echo '' 1>&2
- if [ $mccaskill -eq 1 ]; then
- echo "RNA base pairing probaility was calculated by the McCaskill algorithm (1)" 1>&2
- echo "implemented in Vienna RNA package (2) and MXSCARNA (3), and then" 1>&2
- echo "incorporated in the iterative alignment process (4)." 1>&2
- echo "(1) McCaskill, 1990, Biopolymers 29:1105-1119" 1>&2
- echo "(2) Hofacker et al., 2002, J. Mol. Biol. 319:3724-3732" 1>&2
- echo "(3) Tabei et al., 2008, BMC Bioinformatics 9:33" 1>&2
- echo "(4) Katoh and Toh, 2008, BMC Bioinformatics 9:212" 1>&2
- echo "" 1>&2
- elif [ $contrafold -eq 1 ]; then
- echo "RNA base pairing probaility was calculated by the CONTRAfold algorithm (1)" 1>&2
- echo "and then incorporated in the iterative alignment process (4)." 1>&2
- echo "(1) Do et al., 2006, Bioinformatics 22:e90-98" 1>&2
- echo "(2) Katoh and Toh, 2008, BMC Bioinformatics 9:212" 1>&2
- echo "" 1>&2
- fi
- if [ $distance = "fasta" -o $partdist = "fasta" ]; then
- echo "Pairwise alignments were computed by FASTA" 1>&2
- echo "(Pearson & Lipman, 1988, PNAS 85:2444-2448)" 1>&2
- fi
- if [ $distance = "blast" ]; then
- echo "Pairwise alignments were computed by BLAST" 1>&2
- echo "(Altschul et al., 1997, NAR 25:3389-3402)" 1>&2
- fi
- if [ $distance = "scarna" ]; then
- echo "Pairwise alignments were computed by MXSCARNA" 1>&2
- echo "(Tabei et al., 2008, BMC Bioinformatics 9:33)." 1>&2
- fi
- if [ $distance = "lara" -o $distance = "slara" ]; then
- echo "Pairwise alignments were computed by LaRA" 1>&2
- echo "(Bauer et al., 2007, BMC Bioinformatics 8:271)." 1>&2
- fi
- if [ $distance = "foldalignlocal" ]; then
- echo "Pairwise alignments were computed by FOLDALIGN (local)" 1>&2
- echo "(Havgaard et al., 2007, PLoS Computational Biology 3:e193)." 1>&2
- fi
- if [ $distance = "foldalignglobal" ]; then
- echo "Pairwise alignments were computed by FOLDALIGN (global)" 1>&2
- echo "(Havgaard et al., 2007, PLoS Computational Biology 3:e193)." 1>&2
- fi
- printf "\n" 1>&2
- echo 'Strategy:' 1>&2
- printf ' '$strategy 1>&2
- echo ' ('$performance')' 1>&2
- echo ' '$explanation 1>&2
- echo '' 1>&2
- echo "If unsure which option to use, try 'mafft --auto input > output'." 1>&2
-# echo "If long gaps are expected, try 'mafft --ep 0.0 --auto input > output'." 1>&2
- echo "If the possibility of long gaps can be excluded, add '--ep 0.123'." 1>&2
- echo "For more information, see 'mafft --help', 'mafft --man' and the mafft page." 1>&2
- echo '' 1>&2
- fi
exit 0;
fi
prog="$tmpawk"
fi
-echo "prog="$prog 1>&2
+#echo "prog="$prog 1>&2
umask 077
-export defaultaof
-export defaultgop
-export defaultfft
-export defaultcycle
-export defaultiterate
(
$prog '
BEGIN {
prefix = ENVIRON["prefix"];
version = ENVIRON["version"];
myself = ENVIRON["myself"];
- defaultgop = ENVIRON["defaultgop"]
- defaultaof = ENVIRON["defaultaof"]
- defaultfft = ENVIRON["defaultfft"]
- defaultcycle = ENVIRON["defaultcycle"]
- defaultiterate = ENVIRON["defaultiterate"]
while( 1 )
{
options = ""
printf( "\n" ) > "/dev/tty";
printf( " MAFFT %s\n", version ) > "/dev/tty";
printf( "\n" ) > "/dev/tty";
- printf( " Copyright (c) 2009 Kazutaka Katoh\n" ) > "/dev/tty";
+ printf( " Copyright (c) 2011 Kazutaka Katoh\n" ) > "/dev/tty";
printf( " NAR 30:3059-3066, NAR 33:511-518\n" ) > "/dev/tty";
- printf( " http://align.bmr.kyushu-u.ac.jp/mafft/software/\n" ) > "/dev/tty";
+ printf( " http://mafft.cbrc.jp/alignment/software/\n" ) > "/dev/tty";
printf( "---------------------------------------------------------------------\n" ) > "/dev/tty";
printf( "\n" ) > "/dev/tty";
close( "/dev/tty" )
if( res == 0 || NF == 0 )
continue;
- infile0 = sprintf( "%s", $1 );
- infile = sprintf( "%s", $1 );
+ infile = sprintf( "%s", $0 );
res = getline < infile;
close( infile );
if( res == -1 )
+ {
printf( "%s: No such file.\n\n", infile ) > "/dev/tty";
+ printf( "Filename extension (eg., .txt) must be typed, if any.\n\n" ) > "/dev/tty";
+ }
else if( res == 0 )
printf( "%s: Empty.\n", infile ) > "/dev/tty";
else
continue;
else
{
- outfile = sprintf( "%s", $1 );
+ outfile = sprintf( "%s", $0 );
printf( "OK. outfile = %s\n\n", outfile ) > "/dev/tty";
break;
}
}
-
while( 1 )
{
- retree = defaultcycle
+ outargs = "";
printf( "\n" ) > "/dev/tty";
- printf( "Number of tree-rebuilding?\n" ) > "/dev/tty";
- printf( "@ [%d] ", retree ) > "/dev/tty";
+ printf( "Output format?\n" ) > "/dev/tty";
+ printf( " 1. Clustal format / Sorted\n" ) > "/dev/tty";
+ printf( " 2. Clustal format / Input order\n" ) > "/dev/tty";
+ printf( " 3. Fasta format / Sorted\n" ) > "/dev/tty";
+ printf( " 4. Fasta format / Input order\n" ) > "/dev/tty";
+ printf( " 5. Phylip format / Sorted\n" ) > "/dev/tty";
+ printf( " 6. Phylip format / Input order\n" ) > "/dev/tty";
+ printf( "@ " ) > "/dev/tty";
res = getline < "/dev/tty";
close( "/dev/tty" );
- if( res == 0 )
+# printf( "res=%d, NF=%d\n", res, NF );
+
+ resnum = 0 + $1;
+# printf( "resnum=%d\n", resnum );
+
+ if( resnum < 1 || 6 < resnum )
continue;
- else if( NF == 0 )
- ;
- else
- retree = 0 + $1;
- if( retree < 1 || 10 < retree )
- ;
else
{
- printf( "OK. %d\n\n", retree ) > "/dev/tty";
+ if( resnum == 1 )
+ outargs = "--clustalout --reorder";
+ else if( resnum == 2 )
+ outargs = "--clustalout --inputorder";
+ else if( resnum == 3 )
+ outargs = "--reorder";
+ else if( resnum == 4 )
+ outargs = "--inputorder";
+ else if( resnum == 5 )
+ outargs = "--phylipout --reorder";
+ else if( resnum == 6 )
+ outargs = "--phylipout --inputorder";
+ else
+ continue;
+ printf( "OK. arguments = %s\n\n", outargs ) > "/dev/tty";
break;
}
}
while( 1 )
{
- niterate = defaultiterate;
+ arguments = "";
printf( "\n" ) > "/dev/tty";
- printf( "Maximum number of iterations?\n" ) > "/dev/tty";
- printf( "@ [%d] ", niterate ) > "/dev/tty";
+ printf( "Strategy?\n" ) > "/dev/tty";
+ printf( " 1. --auto\n" ) > "/dev/tty";
+ printf( " 2. FFT-NS-1 (fast)\n" ) > "/dev/tty";
+ printf( " 3. FFT-NS-2 (default)\n" ) > "/dev/tty";
+ printf( " 4. G-INS-i (accurate)\n" ) > "/dev/tty";
+ printf( " 5. L-INS-i (accurate)\n" ) > "/dev/tty";
+ printf( " 6. E-INS-i (accurate)\n" ) > "/dev/tty";
+ printf( "@ " ) > "/dev/tty";
res = getline < "/dev/tty";
close( "/dev/tty" );
- if( res == 0 )
+# printf( "res=%d, NF=%d\n", res, NF );
+
+ resnum = 0 + $1;
+# printf( "resnum=%d\n", resnum );
+
+ if( resnum < 1 || 6 < resnum )
continue;
- else if( NF == 0 )
- ;
- else
- niterate = 0 + $1;
- if( niterate < 0 || 1000 < niterate )
- ;
else
{
- printf( "OK. %d\n\n", niterate ) > "/dev/tty";
+ if( resnum == 1 )
+ arguments = "--auto";
+ else if( resnum == 2 )
+ arguments = "--retree 1";
+ else if( resnum == 3 )
+ arguments = "--retree 2";
+ else if( resnum == 4 )
+ arguments = "--globalpair --maxiterate 16";
+ else if( resnum == 5 )
+ arguments = "--localpair --maxiterate 16";
+ else if( resnum == 6 )
+ arguments = "--genafpair --maxiterate 16";
+ else
+ arguments = sprintf( "%s", $0 );
+ printf( "OK. arguments = %s %s\n\n", arguments, outargs ) > "/dev/tty";
break;
}
}
- while( 1 )
- {
- fft = defaultfft;
- printf( "\n" ) > "/dev/tty";
- printf( "Use fft?\n" ) > "/dev/tty";
- printf( "@ [%s] ", fft?"Yes":"No" ) > "/dev/tty";
- res = getline < "/dev/tty";
- close( "/dev/tty" );
- if( res == 0 )
- continue;
- else if( NF == 0 )
- {
- break;
- }
- else if( NF == 0 || $0 ~ /^[Yy]/ )
- {
- fft = 1;
- break;
- }
- else if( NF == 0 || $0 ~ /^[Nn]/ )
- {
- fft = 0;
- break;
- }
- }
- if( fft )
- {
- printf( "OK. FFT is enabled.\n\n" ) > "/dev/tty";
- fftparam = " ";
- }
- else
- {
- printf( "OK. FFT is disabled.\n\n" ) > "/dev/tty";
- fftparam = " --nofft ";
- }
while( 1 )
{
- scoringmatrix = 3;
printf( "\n" ) > "/dev/tty";
- printf( "Scoring matrix? (ignored when DNA sequence is input.)\n" ) > "/dev/tty";
- printf( " 1. BLOSUM 30\n" ) > "/dev/tty";
- printf( " 2. BLOSUM 45\n" ) > "/dev/tty";
- printf( " 3. BLOSUM 62\n" ) > "/dev/tty";
- printf( " 4. BLOSUM 80\n" ) > "/dev/tty";
- printf( " 5. JTT 200\n" ) > "/dev/tty";
- printf( " 6. JTT 100\n" ) > "/dev/tty";
- printf( "@ [%d] ", scoringmatrix ) > "/dev/tty";
+ printf( "Additional arguments? (--ep #, --op #, --kappa #, etc)\n" ) > "/dev/tty";
+ printf( "@ " ) > "/dev/tty";
res = getline < "/dev/tty";
close( "/dev/tty" );
- if( res == 0 )
- continue;
- else if( NF == 0 )
- ;
- else
- scoringmatrix = 0 + $1;
- if( scoringmatrix < 1 || 6 < scoringmatrix )
- ;
- else
+ if( res == 0 || NF == 0 )
{
break;
}
- }
- if( scoringmatrix == 1 )
- scoringparam = " --bl 30 ";
- else if( scoringmatrix == 2 )
- scoringparam = " --bl 45 ";
- else if( scoringmatrix == 3 )
- scoringparam = " --bl 62 ";
- else if( scoringmatrix == 4 )
- scoringparam = " --bl 80 ";
- else if( scoringmatrix == 5 )
- scoringparam = " --jtt 200 ";
- else if( scoringmatrix == 6 )
- scoringparam = " --jtt 100 ";
- printf( "OK. %s\n\n",scoringparam ) > "/dev/tty";
-
- while( 1 )
- {
- penalty = 0.0 + defaultgop;
- offset = 0.0 + defaultaof;
- printf( "\n" ) > "/dev/tty";
- printf( "Parameters (gap opening penalty, offset)?\n", penalty, offset ) > "/dev/tty";
- printf( "@ [%5.3f, %5.3f] ", penalty, offset ) > "/dev/tty";
- res = getline < "/dev/tty";
- close( "/dev/tty" );
- if( res == 0 )
- continue;
- else if( NF == 2 )
- {
- penalty = 0.0 + $1;
- offset = 0.0 + $2;
- }
- else if( NF == 0 )
- ;
- else
- continue;
- if( penalty < 0.0 || 10.0 < penalty )
- ;
- else if( offset < 0.0 || 10.0 < offset )
- ;
else
{
- printf( "OK. %5.3f %5.3f\n\n", penalty, offset ) > "/dev/tty";
+ addargs = sprintf( "%s", $0 );
+ printf( "OK. arguments = %s %s %s\n\n", addargs, arguments, outargs ) > "/dev/tty";
break;
}
}
-
- command = sprintf( "\"%s\" %s --retree %d --maxiterate %d %s --op %f --ep %f %s > %s", myself, fftparam, retree, niterate, scoringparam, penalty, offset, infile, outfile );
+
+ arguments = sprintf( "%s %s %s", addargs, arguments, outargs );
+
+ print ""
+ command = sprintf( "\"%s\" %s \"%s\" > \"%s\"", myself, arguments, infile, outfile );
gsub( /\\/, "/", command );
- printf( "%s\n\n", command ) > "/dev/tty";
+ printf( "command=\n%s\n", command ) > "/dev/tty";
while( 1 )
{
go = 0;
- printf( "\n" ) > "/dev/tty";
printf( "OK?\n" ) > "/dev/tty";
printf( "@ [Y] " ) > "/dev/tty";
res = getline < "/dev/tty";
printf( "\n" ) > "/dev/tty";
}
system( command );
+ command = sprintf( "less \"%s\"", outfile );
+ system( command );
printf( "Press Enter to exit." ) > "/dev/tty";
res = getline < "/dev/tty";
}
git://source.jalview.org / jabaws.git / blobdiff