+++ /dev/null
-#! /bin/sh
-
-
-er=0;
-myself=`dirname "$0"`/`basename "$0"`; export myself
-version="v6.857b (2011/05/30)"; export version
-LANG=C; export LANG
-os=`uname`
-progname=`basename "$0"`
-if [ `echo $os | grep -i cygwin` ]; then
- os="cygwin"
-elif [ `echo $os | grep -i darwin` ]; then
- os="darwin"
-elif [ `echo $os | grep -i sunos` ]; then
- os="sunos"
-elif [ `echo $os | grep -i linux` ]; then
- os="linux"
-else
- os="unix"
-fi
-export os
-
-if [ "$MAFFT_BINARIES" ]; then
- prefix="$MAFFT_BINARIES"
-else
- prefix=/usr/libexec/mafft
-fi
-export prefix
-
-if [ $# -gt 0 ]; then
- if [ "$1" = "--man" ]; then
- man "$prefix/mafft.1"
- exit 0;
- fi
-fi
-
-if [ ! -x "$prefix/tbfast" ]; then
- echo "" 1>&2
- echo "correctly installed?" 1>&2
- echo "mafft binaries have to be installed in \$MAFFT_BINARIES" 1>&2
- echo "or the $prefix directory". 1>&2
- echo "" 1>&2
- exit 1
- er=1
-fi
-
-defaultiterate=0
-defaultcycle=2
-defaultgop="1.53"
-#defaultaof="0.123"
-defaultaof="0.000"
-defaultlaof="0.100"
-defaultlgop="-2.00"
-defaultfft=1
-defaultrough=0
-defaultdistance="sixtuples"
-#defaultdistance="local"
-defaultweighti="2.7"
-defaultweightr="0.0"
-defaultweightm="1.0"
-defaultmccaskill=0
-defaultcontrafold=0
-defaultalgopt=" "
-defaultalgoptit=" "
-defaultsbstmodel=" -b 62 "
-defaultfmodel=" "
-defaultkappa=" "
-if [ $progname = "xinsi" -o $progname = "mafft-xinsi" ]; then
- defaultfft=1
- defaultcycle=1
- defaultiterate=1000
- defaultdistance="scarna"
- defaultweighti="3.2"
- defaultweightr="8.0"
- defaultweightm="2.0"
- defaultmccaskill=1
- defaultcontrafold=0
- defaultalgopt=" -A "
- defaultalgoptit=" -AB " ## chui
- defaultaof="0.0"
- defaultsbstmodel=" -b 62 "
- defaultkappa=" "
- defaultfmodel=" -a "
-elif [ $progname = "qinsi" -o $progname = "mafft-qinsi" ]; then
- defaultfft=1
- defaultcycle=1
- defaultiterate=1000
- defaultdistance="global"
- defaultweighti="3.2"
- defaultweightr="8.0"
- defaultweightm="2.0"
- defaultmccaskill=1
- defaultcontrafold=0
- defaultalgopt=" -A "
- defaultalgoptit=" -AB " ## chui
- defaultaof="0.0"
- defaultsbstmodel=" -b 62 "
- defaultkappa=" "
- defaultfmodel=" -a "
-elif [ $progname = "linsi" -o $progname = "mafft-linsi" ]; then
- defaultfft=0
- defaultcycle=1
- defaultiterate=1000
- defaultdistance="local"
-elif [ $progname = "ginsi" -o $progname = "mafft-ginsi" ]; then
- defaultfft=1
- defaultcycle=1
- defaultiterate=1000
- defaultdistance="global"
-elif [ $progname = "einsi" -o $progname = "mafft-einsi" ]; then
- defaultfft=0
- defaultcycle=1
- defaultiterate=1000
- defaultdistance="localgenaf"
-elif [ $progname = "fftns" -o $progname = "mafft-fftns" ]; then
- defaultfft=1
- defaultcycle=2
- defaultdistance="sixtuples"
-elif [ $progname = "fftnsi" -o $progname = "mafft-fftnsi" ]; then
- defaultfft=1
- defaultcycle=2
- defaultiterate=2
- defaultdistance="sixtuples"
-elif [ $progname = "nwns" -o $progname = "mafft-nwns" ]; then
- defaultfft=0
- defaultcycle=2
- defaultdistance="sixtuples"
-elif [ $progname = "nwnsi" -o $progname = "mafft-nwnsi" ]; then
- defaultfft=0
- defaultcycle=2
- defaultiterate=2
- defaultdistance="sixtuples"
-fi
-outputfile=""
-namelength=15
-anysymbol=0
-parallelizationstrategy="BAATARI2"
-kappa=$defaultkappa
-sbstmodel=$defaultsbstmodel
-fmodel=$defaultfmodel
-gop=$defaultgop
-aof=$defaultaof
-cycle=$defaultcycle
-iterate=$defaultiterate
-fft=$defaultfft
-rough=$defaultrough
-distance=$defaultdistance
-forcefft=0
-memopt=" "
-weightopt=" "
-GGOP="-6.00"
-LGOP="-6.00"
-LEXP="-0.000"
-GEXP="-0.000"
-lgop=$defaultlgop
-lexp="-0.100"
-laof=$defaultlaof
-pggop="-2.00"
-pgexp="-0.10"
-pgaof="0.10"
-rgop="-1.530"
-rgep="-0.000"
-seqtype=" "
-weighti=$defaultweighti
-weightr=$defaultweightr
-weightm=$defaultweightm
-rnaalifold=0
-mccaskill=$defaultmccaskill
-contrafold=$defaultcontrafold
-quiet=0
-debug=0
-sw=0
-algopt=$defaultalgopt
-algoptit=$defaultalgoptit
-scorecalcopt=" "
-coreout=0
-corethr="0.5"
-corewin="100"
-coreext=" "
-outputformat="pir"
-outorder="input"
-seed="x"
-seedtable="x"
-auto=0
-groupsize=-1
-partsize=50
-partdist="sixtuples"
-partorderopt=" -x "
-treeout=0
-distout=0
-treein=0
-topin=0
-treeinopt=" "
-seedfiles="/dev/null"
-seedtablefile="/dev/null"
-aamatrix="/dev/null"
-treeinfile="/dev/null"
-rnascoremtx=" "
-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" = "--inputorder" ]; then
- outorder="input"
- partorderopt=" -x "
- elif [ "$1" = "--unweight" ]; then
- weightopt=" -u "
- 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`
- elif [ "$1" = "--partsize" ]; then
- shift
- partsize=`expr "$1" - 0`
- elif [ "$1" = "--parttree" ]; then
- distance="parttree"
- partdist="sixtuples"
- elif [ "$1" = "--dpparttree" ]; then
- distance="parttree"
- partdist="localalign"
- elif [ "$1" = "--fastaparttree" ]; then
- distance="parttree"
- partdist="fasta"
- elif [ "$1" = "--treeout" ]; then
- treeout=1
- elif [ "$1" = "--distout" ]; then
- distout=1
- elif [ "$1" = "--fastswpair" ]; then
- distance="fasta"
- sw=1
- elif [ "$1" = "--fastapair" ]; then
- distance="fasta"
- sw=0
- elif [ "$1" = "--averagelinkage" ]; then
- treealg=" -E "
- elif [ "$1" = "--minimumlinkage" ]; then
- treealg=" -q "
- elif [ "$1" = "--noscore" ]; then
- scorecalcopt=" -Z "
- elif [ "$1" = "--6merpair" ]; then
- distance="sixtuples"
- elif [ "$1" = "--blastpair" ]; then
- distance="blast"
- elif [ "$1" = "--globalpair" ]; then
- distance="global"
- elif [ "$1" = "--localpair" ]; then
- distance="local"
- elif [ "$1" = "--scarnapair" ]; then
- distance="scarna"
- elif [ "$1" = "--larapair" ]; then
- distance="lara"
- elif [ "$1" = "--slarapair" ]; then
- distance="slara"
- elif [ "$1" = "--foldalignpair" ]; then
- distance="foldalignlocal"
- elif [ "$1" = "--foldalignlocalpair" ]; then
- distance="foldalignlocal"
- elif [ "$1" = "--foldalignglobalpair" ]; then
- distance="foldalignglobal"
- elif [ "$1" = "--globalgenafpair" ]; then
- distance="globalgenaf"
- elif [ "$1" = "--localgenafpair" ]; then
- distance="localgenaf"
- elif [ "$1" = "--genafpair" ]; then
- distance="localgenaf"
- elif [ "$1" = "--memsave" ]; then
- memopt=" -M -B " # -B (bunkatsunashi no riyu ga omoidasenai)
- elif [ "$1" = "--nomemsave" ]; then
- memopt=" -N "
- elif [ "$1" = "--nuc" ]; then
- seqtype=" -D "
- elif [ "$1" = "--amino" ]; then
- seqtype=" -P "
- elif [ "$1" = "--fft" ]; then
- fft=1
- forcefft=1
- elif [ "$1" = "--nofft" ]; then
- fft=0
- elif [ "$1" = "--quiet" ]; then
- quiet=1
- elif [ "$1" = "--debug" ]; then
- debug=1
- elif [ "$1" = "--coreext" ]; then
- 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`
- elif [ "$1" = "--retree" ]; then
- shift
- cycle=`expr "$1" - 0`
- elif [ "$1" = "--aamatrix" ]; then
- shift
- sbstmodel=" -b -1 "
- aamatrix="$1"
- elif [ "$1" = "--treein" ]; then
- shift
- treeinopt=" -U "
- treein=1
- treeinfile="$1"
- elif [ "$1" = "--topin" ]; then
- shift
- treeinopt=" -V "
- treein=1
- treeinfile="$1"
- echo "The --topin option has been disabled." 1>&2
- echo "There was a bug in version < 6.530." 1>&2
- echo "This bug has not yet been fixed." 1>&2
- exit 1
- elif [ "$1" = "--kappa" ]; then
- shift
- kappa=" -k $1 "
- elif [ "$1" = "--fmodel" ]; then
- fmodel=" -a "
- elif [ "$1" = "--jtt" ]; then
- shift
- sbstmodel=" -j $1"
- elif [ "$1" = "--kimura" ]; then
- shift
- sbstmodel=" -j $1"
- elif [ "$1" = "--tm" ]; then
- shift
- sbstmodel=" -m $1"
- elif [ "$1" = "--bl" ]; then
- shift
- sbstmodel=" -b $1"
- elif [ "$1" = "--weighti" ]; then
- shift
- weighti="$1"
- elif [ "$1" = "--weightr" ]; then
- shift
- weightr="$1"
- elif [ "$1" = "--weightm" ]; then
- shift
- weightm="$1"
- elif [ "$1" = "--rnaalifold" ]; then
- rnaalifold=1
- elif [ "$1" = "--mccaskill" ]; then
- mccaskill=1
- contrafold=0
- elif [ "$1" = "--contrafold" ]; then
- mccaskill=0
- contrafold=1
- elif [ "$1" = "--ribosum" ]; then
- rnascoremtx=" -s "
- elif [ "$1" = "--op" ]; then
- shift
- gop="$1"
- elif [ "$1" = "--ep" ]; then
- shift
- aof="$1"
- elif [ "$1" = "--rop" ]; then
- shift
- rgop="$1"
- elif [ "$1" = "--rep" ]; then
- shift
- rgep="$1"
- elif [ "$1" = "--lop" ]; then
- shift
- lgop="$1"
- elif [ "$1" = "--LOP" ]; then
- shift
- LGOP="$1"
- elif [ "$1" = "--lep" ]; then
- shift
- laof="$1"
- elif [ "$1" = "--lexp" ]; then
- shift
- lexp="$1"
- elif [ "$1" = "--LEXP" ]; then
- shift
- LEXP="$1"
- elif [ "$1" = "--GEXP" ]; then
- shift
- GEXP="$1"
- elif [ "$1" = "--GOP" ]; then
- shift
- GGOP="$1"
- elif [ "$1" = "--gop" ]; then
- shift
- pggop="$1"
- elif [ "$1" = "--gep" ]; then
- shift
- pgaof="$1"
- elif [ "$1" = "--gexp" ]; then
- shift
- pgexp="$1"
- elif [ "$1" = "--laraparams" ]; then
- shift
- laraparams="$1"
- elif [ "$1" = "--corethr" ]; then
- shift
- corethr="$1"
- elif [ "$1" = "--corewin" ]; then
- shift
- corewin="$1"
- elif [ "$1" = "--seedtable" ]; then
- shift
- seedtable="y"
- seedtablefile="$1"
- elif [ "$1" = "--seed" ]; then
- shift
- seed="m"
- seedfiles="$seedfiles $1"
- elif [ $progname = "fftns" -o $progname = "nwns" ]; then
- if [ "$1" -gt 0 ]; then
- cycle=`expr "$1" - 0`
- fi
- else
- echo "Unknown option: $1" 1>&2
- er=1;
- fi
- shift
- done;
-
-
-
-# TMPFILE=/tmp/$progname.$$
- TMPFILE=`mktemp -dt $progname.XXXXXXXXXX`
- if [ $? -ne 0 ]; then
- echo "mktemp seems to be obsolete. Re-trying without -t" 1>&2
- TMPFILE=`mktemp -d /tmp/$progname.XXXXXXXXXX`
- fi
- umask 077
-# mkdir $TMPFILE || er=1
- if [ $debug -eq 1 ]; then
- trap "tar cfvz debuginfo.tgz $TMPFILE; rm -rf $TMPFILE " 0
- else
- trap "rm -rf $TMPFILE " 0
- fi
- if [ $# -eq 1 ]; then
- if [ -r "$1" -o "$1" = - ]; then
-
- if [ -r "$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 "^$" > $TMPFILE/_seedtablefile
- cat "$laraparams" | tr "\r" "\n" | grep -v "^$" > $TMPFILE/_lara.params
-# echo $seedfiles
- infilename="$1"
- seedfilesintmp="/dev/null"
- seednseq="0"
- set $seedfiles > /dev/null
- while [ $# -gt 1 ];
- do
- shift
- 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 "$1". 1>&2
- er=1
-# exit 1;
- fi
- else
- echo '$#'"=$#" 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`
- nlen=`awk '{print $3}' $TMPFILE/size`
- if [ $nlen -lt 2000 -a $nseq -lt 100 ]; then
- distance="local"
- iterate=1000
- elif [ $nlen -lt 10000 -a $nseq -lt 500 ]; then
- distance="sixtuples"
- iterate=2
- else
- distance="sixtuples"
- iterate=0
- fi
- if [ $quiet -eq 0 ]; then
- echo "nseq = " $nseq 1>&2
- echo "nlen = " $nlen 1>&2
- echo "distance = " $distance 1>&2
- echo "iterate = " $iterate 1>&2
- fi
- fi
-
- 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
- rnaopt=" -e $rgep -o $rgop -c $weightm -r $weightr -R $rnascoremtx "
-# rnaoptit=" -o $rgop -BT -c $weightm -r $weightr -R "
- rnaoptit=" -o $rgop -F -c $weightm -r $weightr -R "
- elif [ $mccaskill -eq 1 -o $contrafold -eq 1 ]; then
- rnaopt=" -o $rgop -c $weightm -r $weightr "
-# rnaoptit=" -e $rgep -o $rgop -BT -c $weightm -r $weightr $rnascoremtx "
- rnaoptit=" -e $rgep -o $rgop -F -c $weightm -r $weightr $rnascoremtx "
- else
- rnaopt=" "
- rnaoptit=" -F "
- fi
-
- model="$sbstmodel $kappa $fmodel"
-
- if [ $er -eq 1 ]; then
- echo "------------------------------------------------------------------------------" 1>&2
- echo " MAFFT" $version 1>&2
-# echo "" 1>&2
-# echo " Input format: fasta" 1>&2
-# echo "" 1>&2
-# echo " Usage: `basename $0` [options] inputfile > outputfile" 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 "" 1>&2
- echo "High speed:" 1>&2
- echo " % mafft in > out" 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 " % mafft --maxiterate 1000 --genafpair in > out (% einsi in > out)" 1>&2
- echo " % mafft --maxiterate 1000 --globalpair in > out (% ginsi in > out)" 1>&2
- echo "" 1>&2
- echo "If unsure which option to use:" 1>&2
- echo " % mafft --auto in > out" 1>&2
- echo "" 1>&2
-# echo "Other options:" 1>&2
- echo "--op # : Gap opening penalty, default: 1.53" 1>&2
- echo "--ep # : Offset (works like gap extension penalty), default: 0.0" 1>&2
- echo "--maxiterate # : Maximum number of iterative refinement, default: 0" 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
-# echo "" 1>&2
-# echo " % mafft --maxiterate 1000 --genafpair in > out (E-INS-i)" 1>&2
-# echo " works well if many unalignable residues exist between alignable domains" 1>&2
-# echo "" 1>&2
-# echo " % mafft --maxiterate 1000 --globalpair in > out (G-INS-i)" 1>&2
-# echo " suitable for globally alignable sequences " 1>&2
-# echo "" 1>&2
-# echo " % mafft --maxiterate 1000 in > out (FFT-NS-i)" 1>&2
-# echo " accurate and slow, iterative refinement method " 1>&2
-# echo "" 1>&2
-# echo "If the input sequences are long (~1,000,000nt)," 1>&2
-# echo " % mafft --retree 1 --memsave --fft in > out (FFT-NS-1-memsave, new in v5.8)" 1>&2
-# echo "" 1>&2
-# echo "If many (~5,000) sequences are to be aligned," 1>&2
-# echo "" 1>&2
-# echo " % mafft --retree 1 [--memsave] --nofft in > out (NW-NS-1, new in v5.8)" 1>&2
-# echo "" 1>&2
-# echo " --localpair : All pairwise local alignment information is included" 1>&2
-# echo " to the objective function, default: off" 1>&2
-# echo " --globalpair : All pairwise global alignment information is included" 1>&2
-# echo " to the objective function, default: off" 1>&2
-# echo " --op # : Gap opening penalty, default: $defaultgop " 1>&2
-# echo " --ep # : Offset (works like gap extension penalty), default: $defaultaof " 1>&2
-# echo " --bl #, --jtt # : Scoring matrix, default: BLOSUM62" 1>&2
-# echo " Alternatives are BLOSUM (--bl) 30, 45, 62, 80, " 1>&2
-# echo " or JTT (--jtt) # PAM. " 1>&2
-# echo " --nuc or --amino : Sequence type, default: auto" 1>&2
-# echo " --retree # : The number of tree building in progressive method " 1>&2
-# echo " (see the paper for detail), default: $defaultcycle " 1>&2
-# echo " --maxiterate # : Maximum number of iterative refinement, default: $defaultiterate " 1>&2
-# if [ $defaultfft -eq 1 ]; then
-# echo " --fft or --nofft: FFT is enabled or disabled, default: enabled" 1>&2
-# else
-# echo " --fft or --nofft: FFT is enabled or disabled, default: disabled" 1>&2
-# fi
-# echo " --memsave: Memory saving mode" 1>&2
-# echo " (for long genomic sequences), default: off" 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 "-----------------------------------------------------------------------------" 1>&2
- exit 1;
- fi
- if [ $sw -eq 1 ]; then
- swopt=" -A "
- else
- swopt=" "
- fi
-
- if [ $distance = "fasta" -o $partdist = "fasta" ]; then
- if [ ! "$FASTA_4_MAFFT" ]; then
- FASTA_4_MAFFT=`which fasta34`
- fi
-
- if [ ! -x "$FASTA_4_MAFFT" ]; then
- echo "" 1>&2
- echo "== Install FASTA ========================================================" 1>&2
- echo "This option requires the fasta34 program (FASTA version x.xx or higher)" 1>&2
- echo "installed in your PATH. If you have the fasta34 program but have renamed" 1>&2
- echo "(like /usr/local/bin/myfasta), set the FASTA_4_MAFFT environment variable" 1>&2
- echo "to point your fasta34 (like setenv FASTA_4_MAFFT /usr/local/bin/myfasta)." 1>&2
- echo "=========================================================================" 1>&2
- echo "" 1>&2
- exit 1
- fi
- fi
- if [ $distance = "lara" -o $distance = "slara" ]; then
- if [ ! -x "$prefix/mafft_lara" ]; then
- echo "" 1>&2
- echo "== Install LaRA =========================================================" 1>&2
- echo "This option requires LaRA (Bauer et al. http://www.planet-lisa.net/)." 1>&2
- echo "The executable have to be renamed to 'mafft_lara' and installed into " 1>&2
- echo "the $prefix directory. " 1>&2
- echo "A configuration file of LaRA also have to be given" 1>&2
- echo "mafft-xinsi --larapair --laraparams parameter_file" 1>&2
- echo "mafft-xinsi --slarapair --laraparams parameter_file" 1>&2
- echo "=========================================================================" 1>&2
- echo "" 1>&2
- exit 1
- fi
- if [ ! -s "$laraparams" ]; then
- echo "" 1>&2
- echo "== Configure LaRA =======================================================" 1>&2
- echo "A configuration file of LaRA have to be given" 1>&2
- echo "mafft-xinsi --larapair --laraparams parameter_file" 1>&2
- echo "mafft-xinsi --slarapair --laraparams parameter_file" 1>&2
- echo "=========================================================================" 1>&2
- echo "" 1>&2
- exit 1
- fi
- fi
- if [ $distance = "foldalignlocal" -o $distance = "foldalignglobal" ]; then
- if [ ! -x "$prefix/foldalign210" ]; then
- echo "" 1>&2
- echo "== Install FOLDALIGN ====================================================" 1>&2
- echo "This option requires FOLDALIGN (Havgaard et al. http://foldalign.ku.dk/)." 1>&2
- echo "The executable have to be renamed to 'foldalign210' and installed into " 1>&2
- echo "the $prefix directory. " 1>&2
- echo "=========================================================================" 1>&2
- echo "" 1>&2
- exit 1
- fi
- fi
- if [ $distance = "scarna" ]; then
- if [ ! -x "$prefix/mxscarnamod" ]; then
- echo "" 1>&2
- echo "== Install MXSCARNA ======================================================" 1>&2
- echo "MXSCARNA (Tabei et al. BMC Bioinformatics 2008 9:33) is required." 1>&2
- echo "Please 'make' at the 'extensions' directory of the MAFFT source package," 1>&2
- echo "which contains the modified version of MXSCARNA." 1>&2
- echo "http://align.bmr.kyushu-u.ac.jp/mafft/software/source.html " 1>&2
- echo "==========================================================================" 1>&2
- echo "" 1>&2
- exit 1
- fi
- fi
- if [ $mccaskill -eq 1 ]; then
- if [ ! -x "$prefix/mxscarnamod" ]; then
- echo "" 1>&2
- echo "== Install MXSCARNA ======================================================" 1>&2
- echo "MXSCARNA (Tabei et al. BMC Bioinformatics 2008 9:33) is required." 1>&2
- echo "Please 'make' at the 'extensions' directory of the MAFFT source package," 1>&2
- echo "which contains the modified version of MXSCARNA." 1>&2
- echo "http://align.bmr.kyushu-u.ac.jp/mafft/software/source.html " 1>&2
- echo "==========================================================================" 1>&2
- echo "" 1>&2
- exit 1
- fi
- fi
- if [ $contrafold -eq 1 ]; then
- if [ ! -x "$prefix/contrafold" ]; then
- echo "" 1>&2
- echo "== Install CONTRAfold ===================================================" 1>&2
- echo "This option requires CONTRAfold" 1>&2
- echo "(Do et al. http://contra.stanford.edu/contrafold/)." 1>&2
- echo "The executable 'contrafold' have to be installed into " 1>&2
- echo "the $prefix directory. " 1>&2
- echo "=========================================================================" 1>&2
- echo "" 1>&2
- exit 1
- fi
- fi
-
-#old
-# if [ $treeout -eq 1 ]; then
-# parttreeoutopt="-t"
-# if [ $cycle -eq 0 ]; then
-# treeoutopt="-t -T"
-# groupsize=1
-# iterate=0
-# if [ $distance = "global" -o $distance = "local" -o $distance = "localgenaf" -o $distance = "globalgenaf" ]; then
-# distance="distonly"
-# fi
-# else
-# treeoutopt="-t"
-# fi
-# else
-# parttreeoutopt=" "
-# if [ $cycle -eq 0 ]; then
-# treeoutopt="-t -T"
-# iterate=0
-# if [ $distance = "global" -o $distance = "local" -o $distance = "localgenaf" -o $distance = "globalgenaf" ]; then
-# distance="distonly"
-# fi
-# else
-# treeoutopt=" "
-# fi
-# fi
-
-#new
- if [ $cycle -eq 0 ]; then
- treeoutopt="-t -T"
- iterate=0
- if [ $distance = "global" -o $distance = "local" -o $distance = "localgenaf" -o $distance = "globalgenaf" ]; then
- distance="distonly"
- fi
- if [ $treeout -eq 1 ]; then
- parttreeoutopt="-t"
- groupsize=1
- else
- parttreeoutopt=" "
- fi
- if [ $distout -eq 1 ]; then
- distoutopt="-y -T"
- fi
- else
- if [ $treeout -eq 1 ]; then
- parttreeoutopt="-t"
- treeoutopt="-t"
- else
- parttreeoutopt=" "
- treeoutopt=" "
- fi
- if [ $distout -eq 1 ]; then
- distoutopt="-y"
- fi
- fi
-#
-
- formatcheck=`grep -c '^[[:blank:]]\+>' $TMPFILE/infile | head -1 `
- if [ $formatcheck -gt 0 ]; then
- echo "The first character of a description line must be " 1>&2
- echo "the greater-than (>) symbol, not a blank." 1>&2
- echo "Please check the format around the following line(s):" 1>&2
- grep -n '^[[:blank:]]\+>' $TMPFILE/infile 1>&2
- exit 1
- fi
-
- nseq=`grep -c '^[>|=]' $TMPFILE/infile | head -1 `
- if [ $nseq -eq 2 ]; then
- cycle=1
- fi
- if [ $cycle -gt 3 ]; then
- cycle=3
- fi
-
- 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
- fi
-
-
- if [ $distance = "sixtuples" -a \( $seed = "x" -a $seedtable = "x" \) ]; then
- localparam=" "
- elif [ $distance = "sixtuples" -a \( $seed != "x" -o $seedtable != "x" \) ]; then
- 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=" "
- if [ $groupsize -gt -1 ]; then
- cycle=1
- fi
- else
- localparam=" -l "$weighti
- if [ $cycle -gt 1 ]; then # 09/01/08
- cycle=1
- fi
- fi
-
- if [ $distance = "localgenaf" -o $distance = "globalgenaf" ]; then
- aof="0.000"
- fi
-
- if [ "$memopt" = " -M -B " -a "$distance" != "sixtuples" ]; then
- echo "Impossible" 1>&2
- exit 1
- fi
-#exit
-
- if [ $distance = "parttree" ]; then
- if [ $seed != "x" -o $seedtable != "x" ]; then
- echo "Impossible" 1>&2
- exit 1
- fi
- if [ $iterate -gt 1 ]; then
- echo "Impossible" 1>&2
- exit 1
- fi
- if [ $outorder = "aligned" ]; then
- outorder="input"
- fi
- outorder="input" # partorder ga kiku
- if [ $partdist = "localalign" ]; then
- splitopt=" -L " # -L -l -> fast
- elif [ $partdist = "fasta" ]; then
- splitopt=" -S "
- else
- splitopt=" "
- fi
- fi
-
-
-# if [ $nseq -gt 5000 ]; then
-# fft=0
-# fi
- if [ $forcefft -eq 1 ]; then
- param_fft=" -G "
- fft=1
- elif [ $fft -eq 1 ]; then
- param_fft=" -F "
- else
- param_fft=" "
- fi
-
- if [ $seed != "x" -a $seedtable != "x" ]; then
- 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 [ $iterate -gt 0 ]; then
-# echo 'Not supported yet.' 1>&2
-# exit 1
-# fi
- cycle=1
- fi
-
- if [ "$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
- echo 'Please add --globalpair, --localpair, --scarnapair,' 1>&2
- echo '--larapair, --slarapair, --foldalignlocalpair or --foldalignglobalpair' 1>&2
- exit 1
- fi
- fi
-
- if [ $mccaskill -eq 1 -o $rnaalifold -eq 1 -o $contrafold -eq 1 ]; then
- if [ $distance = "scarna" -o $distance = "lara" -o $distance = "slara" -o $distance = "foldalignlocal" -o $distance = "foldalignglobal" ]; then
- strategy="X-I"
- elif [ $distance = "global" -o $distance = "local" -o $distance = "localgenaf" -o "globalgenaf" ]; then
- strategy="Q-I"
- fi
- elif [ $distance = "fasta" -a $sw -eq 0 ]; then
- strategy="F-I"
- elif [ $distance = "fasta" -a $sw -eq 1 ]; then
- strategy="H-I"
- elif [ $distance = "blast" ]; then
- strategy="B-I"
- elif [ $distance = "global" -o $distance = "distonly" ]; then
- strategy="G-I"
- elif [ $distance = "local" ]; then
- strategy="L-I"
- elif [ $distance = "localgenaf" ]; then
- strategy="E-I"
- elif [ $distance = "globalgenaf" ]; then
- strategy="K-I"
- elif [ $fft -eq 1 ]; then
- strategy="FFT-"
- else
- strategy="NW-"
- fi
- strategy=$strategy"NS-"
- if [ $iterate -gt 0 ]; then
- strategy=$strategy"i"
- elif [ $distance = "parttree" ]; then
- if [ $partdist = "fasta" ]; then
- strategy=$strategy"FastaPartTree-"$cycle
- elif [ $partdist = "localalign" ]; then
- strategy=$strategy"DPPartTree-"$cycle
- else
- strategy=$strategy"PartTree-"$cycle
- fi
- else
- strategy=$strategy$cycle
- fi
-
- explanation='?'
- performance='Not tested.'
- if [ $strategy = "F-INS-i" ]; then
- explanation='Iterative refinement method (<'$iterate') with LOCAL pairwise alignment information'
- performance='Most accurate, but very slow'
- elif [ $strategy = "L-INS-i" ]; then
- explanation='Iterative refinement method (<'$iterate') with LOCAL pairwise alignment information'
- performance='Probably most accurate, very slow'
- elif [ $strategy = "E-INS-i" ]; then
- explanation='Iterative refinement method (<'$iterate') with LOCAL pairwise alignment with generalized affine gap costs (Altschul 1998)'
- performance='Suitable for sequences with long unalignable regions, very slow'
- elif [ $strategy = "G-INS-i" ]; then
- explanation='Iterative refinement method (<'$iterate') with GLOBAL pairwise alignment information'
- performance='Suitable for sequences of similar lengths, very slow'
- elif [ $strategy = "X-INS-i" ]; then
- explanation='RNA secondary structure information is taken into account.'
- performance='For short RNA sequences only, extremely slow'
- elif [ $strategy = "F-INS-1" ]; then
- explanation='Progressive method incorporating LOCAL pairwise alignment information'
- elif [ $strategy = "L-INS-1" ]; then
- explanation='Progressive method incorporating LOCAL pairwise alignment information'
- elif [ $strategy = "G-INS-1" ]; then
- explanation='Progressive method incorporating GLOBAL pairwise alignment information'
- elif [ $strategy = "FFT-NS-i" -o $strategy = "NW-NS-i" ]; then
- explanation='Iterative refinement method (max. '$iterate' iterations)'
- if [ $iterate -gt 2 ]; then
- performance='Accurate but slow'
- else
- performance='Standard'
- fi
- elif [ $strategy = "FFT-NS-2" -o $strategy = "NW-NS-2" ]; then
- explanation='Progressive method (guide trees were built '$cycle' times.)'
- performance='Fast but rough'
- elif [ $strategy = "FFT-NS-1" -o $strategy = "NW-NS-1" ]; then
- explanation='Progressive method (rough guide tree was used.)'
- performance='Very fast but very rough'
- fi
-
- if [ $outputformat = "clustal" -a $outorder = "aligned" ]; then
- 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 $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 [ $anysymbol -eq 1 ]; then
- mv orig orig2
- cat /dev/null > orig
- fi
- cat /dev/null > infile
- cat /dev/null > hat3.seed
- seedoffset=0
-# echo "seednseq="$seednseq
-# echo "seedoffset="$seedoffset
- set $seednseq > /dev/null
-# echo $#
- while [ $# -gt 1 ]
- do
- shift
-# echo "num="$#
-
- 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 "$1"
-# echo "seedoffset="$seedoffset
- done;
-# echo "seedoffset="$seedoffset
- 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" -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
- if [ $distance = "fasta" ]; then
- "$prefix/dndfast7" $swopt < infile > /dev/null 2>&1 || exit 1
- cat hat3.seed hat3 > hatx
- mv hatx hat3
- "$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" $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" -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" $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" -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" $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" -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" $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" -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" $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" -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" $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" -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" $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" -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" $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" -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" $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" -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" $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" -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" -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 ]
- do
- if [ $distance = "parttree" ]; then
- mv pre infile
- "$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" -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" -C $numthreads < pre > /dev/null 2>&1 || exit 1
- fi
- "$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 [ $anysymbol -eq 1 ]; then
- mv orig orig2
- cat /dev/null > orig
- fi
- cat /dev/null > infile
- cat /dev/null > hat3.seed
- seedoffset=0
-# echo "seednseq="$seednseq
-# echo "seedoffset="$seedoffset
- set $seednseq > /dev/null
-# echo $#
- while [ $# -gt 1 ]
- do
- shift
-# echo "num="$#
-
- 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 "$1"
-# echo "seedoffset="$seedoffset
- done;
-# echo "seedoffset="$seedoffset
- 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" -C $numthreads -d "$prefix" -i infile > hat4 || exit 1
- elif [ $contrafold -eq 1 ]; then
- "$prefix/contrafoldwrap" -d "$prefix" -i infile > hat4 || exit 1
- fi
- if [ $distance = "fasta" ]; then
- "$prefix/dndfast7" $swopt < infile > /dev/null || exit 1
- cat hat3.seed hat3 > hatx
- mv hatx hat3
- "$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" $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" -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" $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" -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" $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" -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" $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" -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" $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" -C $numthreads $seqtype $model -f $pggop -s -d "$prefix" < infile > /dev/null || exit 1
- cat hat3.seed hat3 > hatx
- mv hatx hat3
- "$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" -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" $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" -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" $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" -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" $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" -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" $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" -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" -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
-
- while [ $cycle -gt 1 ]
- do
- if [ $distance = "parttree" ]; then
- mv pre infile
- "$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" -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" -C $numthreads < pre > /dev/null 2>&1 || exit 1
- fi
- "$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 < $TMPFILE/pre || exit 1
- else
- "$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"
- fi
-
- if [ $distout -eq 1 ]; then
- cp $TMPFILE/hat2 "$infilename.hat2"
- fi
-
- exit 0;
-fi
-
-prog="awk"
-
-tmpawk=`which nawk 2>/dev/null | awk '{print $1}'`
-if [ -x "$tmpawk" ]; then
- prog="$tmpawk"
-fi
-
-tmpawk=`which gawk 2>/dev/null | awk '{print $1}'`
-if [ -x "$tmpawk" ]; then
- prog="$tmpawk"
-fi
-
-#echo "prog="$prog 1>&2
-
-umask 077
-(
-$prog '
-BEGIN {
- prefix = ENVIRON["prefix"];
- version = ENVIRON["version"];
- myself = ENVIRON["myself"];
- while( 1 )
- {
- options = ""
- printf( "\n" ) > "/dev/tty";
- printf( "---------------------------------------------------------------------\n" ) > "/dev/tty";
- printf( "\n" ) > "/dev/tty";
- printf( " MAFFT %s\n", version ) > "/dev/tty";
- printf( "\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://mafft.cbrc.jp/alignment/software/\n" ) > "/dev/tty";
- printf( "---------------------------------------------------------------------\n" ) > "/dev/tty";
- printf( "\n" ) > "/dev/tty";
-
- while( 1 )
- {
- printf( "\n" ) > "/dev/tty";
- printf( "Input file? (fasta format)\n@ " ) > "/dev/tty";
- res = getline < "/dev/tty";
- close( "/dev/tty" )
- if( res == 0 || NF == 0 )
- continue;
- 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
- {
- printf( "OK. infile = %s\n\n", infile ) > "/dev/tty";
- break;
- }
- }
- nseq = 0;
-
- while( 1 )
- {
- printf( "\n" ) > "/dev/tty";
- printf( "Output file?\n" ) > "/dev/tty";
- printf( "@ " ) > "/dev/tty";
- res = getline < "/dev/tty";
- close( "/dev/tty" );
- if( res == 0 || NF == 0 )
- continue;
- else
- {
- outfile = sprintf( "%s", $0 );
- printf( "OK. outfile = %s\n\n", outfile ) > "/dev/tty";
- break;
- }
- }
-
- while( 1 )
- {
- outargs = "";
- printf( "\n" ) > "/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" );
-# printf( "res=%d, NF=%d\n", res, NF );
-
- resnum = 0 + $1;
-# printf( "resnum=%d\n", resnum );
-
- if( resnum < 1 || 6 < resnum )
- continue;
- else
- {
- 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 )
- {
- arguments = "";
- printf( "\n" ) > "/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" );
-# printf( "res=%d, NF=%d\n", res, NF );
-
- resnum = 0 + $1;
-# printf( "resnum=%d\n", resnum );
-
- if( resnum < 1 || 6 < resnum )
- continue;
- else
- {
- 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 )
- {
- printf( "\n" ) > "/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 || NF == 0 )
- {
- break;
- }
- else
- {
- addargs = sprintf( "%s", $0 );
- printf( "OK. arguments = %s %s %s\n\n", addargs, arguments, outargs ) > "/dev/tty";
- break;
- }
- }
-
- arguments = sprintf( "%s %s %s", addargs, arguments, outargs );
-
- print ""
- command = sprintf( "\"%s\" %s \"%s\" > \"%s\"", myself, arguments, infile, outfile );
- gsub( /\\/, "/", command );
-
-
- printf( "command=\n%s\n", command ) > "/dev/tty";
-
-
- while( 1 )
- {
- go = 0;
- printf( "OK?\n" ) > "/dev/tty";
- printf( "@ [Y] " ) > "/dev/tty";
- res = getline < "/dev/tty";
- close( "/dev/tty" );
- if( res == 0 )
- continue;
- else if( NF == 0 || $0 ~ /^[Yy]/ )
- {
- go=1;
- break;
- }
- else
- break;
- }
- if( go ) break;
- printf( "\n" ) > "/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";
-}
-'
-)
-exit 0;
git://source.jalview.org / jabaws.git / blobdiff