--- /dev/null
+#! /bin/sh
+er=0;
+myself=`dirname $0`/`basename $0`; export myself
+version="version 6.00 (2005/05/01)"; 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"
+else
+ os="unix"
+fi
+export os
+
+if [ $MAFFT_BINARIES ]; then
+ prefix=$MAFFT_BINARIES
+else
+ prefix=_PREFIX
+fi
+export prefix
+if [ ! -x $prefix/tbfast ]; then
+ echo ""
+ echo "correctly installed?" 2>&1
+ echo "mafft binaries have to be installed in" $prefix.
+ echo ""
+ exit 1
+ er=1
+fi
+
+defaultiterate=0
+defaultcycle=2
+defaultmodel=" -b 62 "
+defaultgop="1.53"
+defaultaof="0.123"
+defaultfft=1
+defaultrough=0
+defaultdistance="sixtuples"
+if [ $progname = "linsi" ]; then
+ defaultfft=0
+ defaultcycle=1
+ defaultiterate=1000
+ defaultdistance="local"
+elif [ $progname = "ginsi" ]; then
+ defaultfft=1
+ defaultcycle=1
+ defaultiterate=1000
+ defaultdistance="global"
+elif [ $progname = "einsi" ]; then
+ defaultfft=0
+ defaultcycle=1
+ defaultiterate=1000
+ defaultdistance="genaf"
+elif [ $progname = "fftns" ]; then
+ defaultfft=1
+ defaultcycle=2
+elif [ $progname = "fftnsi" ]; then
+ defaultfft=1
+ defaultcycle=2
+ defaultiterate=2
+elif [ $progname = "nwns" ]; then
+ defaultfft=0
+ defaultcycle=2
+elif [ $progname = "nwnsi" ]; then
+ defaultfft=0
+ defaultcycle=2
+ defaultiterate=2
+fi
+model=$defaultmodel
+gop=$defaultgop
+aof=$defaultaof
+cycle=$defaultcycle
+iterate=$defaultiterate
+fft=$defaultfft
+rough=$defaultrough
+distance=$defaultdistance
+LGOP="-6.00"
+LEXP="-0.000"
+lgop="-2.00"
+lexp="-0.100"
+laof="0.100"
+seqtype=" "
+param_it=" -x "
+weighti="2.7"
+quiet=0
+sw=0
+scorecalcopt=" "
+coreout=0
+corethr="0.5"
+corewin="100"
+coreext=" "
+outputformat="pir"
+outorder="input"
+if [ $# -gt 0 ]; then
+ while [ $# -gt 1 ];
+ do
+ if [ $1 = "--clustalout" ]; then
+ outputformat="clustal"
+ elif [ $1 = "--reorder" ]; then
+ outorder="aligned"
+ elif [ $1 = "--rough" ]; then
+ rough=1
+ elif [ $1 = "--noscore" ]; then
+ scorecalcopt=" -Z "
+ elif [ $1 = "--fastswpair" ]; then
+ distance="fasta"
+ sw=1
+ elif [ $1 = "--fastapair" ]; then
+ distance="fasta"
+ sw=0
+ elif [ $1 = "--suboptpair" ]; then
+ distance="subopt"
+ elif [ $1 = "--blastpair" ]; then
+ distance="blast"
+ elif [ $1 = "--globalpair" ]; then
+ distance="global"
+ elif [ $1 = "--localpair" ]; then
+ distance="local"
+ elif [ $1 = "--genafpair" ]; then
+ distance="genaf"
+ elif [ $1 = "--nuc" ]; then
+ seqtype=" -D "
+ elif [ $1 = "--amino" ]; then
+ seqtype=" -P "
+ elif [ $1 = "--fft" ]; then
+ fft=1
+ elif [ $1 = "--nofft" ]; then
+ fft=0
+ elif [ $1 = "--quiet" ]; then
+ quiet=1
+ elif [ $1 = "--nj" ]; then
+ param_it=" -n "
+ elif [ $1 = "--coreext" ]; then
+ coreext=" -c "
+ elif [ $1 = "--core" ]; then
+ coreout=1
+ elif [ $1 = "--maxiterate" ]; then
+ shift
+ iterate=`expr $1 - 0`
+ elif [ $1 = "--retree" ]; then
+ shift
+ cycle=`expr $1 - 0` || er=1
+ elif [ $1 = "--jtt" ]; then
+ shift
+ model=" -j "$1
+ elif [ $1 = "--tm" ]; then
+ shift
+ model=" -m "$1
+ elif [ $1 = "--bl" ]; then
+ shift
+ model=" -b "$1
+ elif [ $1 = "--weighti" ]; then
+ shift
+ weighti=$1
+ elif [ $1 = "--op" ]; then
+ shift
+ gop=$1
+ elif [ $1 = "--ep" ]; then
+ shift
+ aof=$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 = "--corethr" ]; then
+ shift
+ corethr=$1
+ elif [ $1 = "--corewin" ]; then
+ shift
+ corewin=$1
+ elif [ $1 -gt 0 -a $progname = "fftns" -o $1 -gt 0 -a $progname = "nwns" ]; then
+ cycle=`expr $1 - 0`
+ else
+ echo "Unknown option: " $1 2>&1
+ er=1;
+ fi
+ shift
+ done;
+ if [ $fft -eq 1 ]; then
+ param_fft=" -F "
+ else
+ param_fft=" "
+ fi
+ if [ $sw -eq 1 ]; then
+ swopt=" -A "
+ else
+ swopt=" "
+ fi
+
+ if [ $distance = "fasta" ]; then
+ if [ ! $FASTA_4_MAFFT ]; then
+ FASTA_4_MAFFT=`which fasta34`
+ fi
+
+ if [ ! -x $FASTA_4_MAFFT ]; then
+ echo ""
+ echo "== Install FASTA ========================================================"
+ echo "This option requires the fasta34 program (FASTA version x.xx or higher)"
+ echo "installed in your PATH. If you have the fasta34 program but have renamed"
+ echo "(like /usr/local/bin/myfasta), set the FASTA_4_MAFFT environment variable"
+ echo "to point your fasta34 (like setenv FASTA_4_MAFFT /usr/local/bin/myfasta)."
+ echo "========================================================================="
+ echo ""
+ exit
+ fi
+ fi
+ if [ $distance = "sixtuples" ]; then
+ localparam=" "
+ else
+ cycle=1
+ localparam=" -l "$weighti
+ fi
+
+ if [ $distance = "fasta" -a $sw -eq 0 ]; then
+ strategy="F-I"
+ elif [ $distance = "fasta" -a $sw -eq 1 ]; then
+ strategy="H-I"
+ elif [ $distance = "subopt" ]; then
+ strategy="S-I"
+ elif [ $distance = "blast" ]; then
+ strategy="B-I"
+ elif [ $distance = "global" ]; then
+ strategy="G-I"
+ elif [ $distance = "local" ]; then
+ strategy="L-I"
+ elif [ $distance = "genaf" ]; then
+ strategy="E-I"
+ elif [ $fft -eq 1 ]; then
+ strategy="FFT-"
+ else
+ strategy="NW-"
+ fi
+ strategy=$strategy"NS-"
+ if [ $iterate -gt 0 ]; then
+ strategy=$strategy"i"
+ elif [ $rough -eq 1 ]; then
+ strategy=$strategy"ROUGH"
+ else
+ strategy=$strategy$cycle
+ fi
+
+ explanation='?'
+ performance='Not tested.'
+ if [ $strategy = "F-INS-i" ]; then
+ explanation='Iterative refinement method incorporating LOCAL pairwise alignment information'
+ performance='Most accurate, but very slow'
+ elif [ $strategy = "L-INS-i" ]; then
+ explanation='Iterative refinement method incorporating LOCAL pairwise alignment information'
+ performance='Probably most accurate, very slow'
+ elif [ $strategy = "E-INS-i" ]; then
+ explanation='Iterative refinement method incorporating LOCAL pairwise alignment with generalized affine gap costs (Altshul 1998)'
+ performance='Suitable for sequences with long unalignable regions, very slow'
+ elif [ $strategy = "G-INS-i" ]; then
+ explanation='Iterative refinement method incorporating GLOBAL pairwise alignment information'
+ performance='Suitable for sequences of similar lengths, very 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 $outorder = "aligned" ]; then
+ outputcommand="$prefix/f2cl -c $strategy -r order "
+ elif [ $outputformat = "clustal" -a $outorder = "input" ]; then
+ outputcommand="$prefix/f2cl -c $strategy "
+ elif [ $outputformat = "pir" -a $outorder = "aligned" ]; then
+ outputcommand="$prefix/f2cl -f -r order "
+ else
+ outputcommand=" cat "
+ fi
+
+ TMPFILE=/tmp/`basename $0`.`whoami`.$$.`date +%y%m%d%H%M%S`
+ TMPFILE=/tmp/$progname.$$
+ umask 077
+ mkdir $TMPFILE || er=1
+ trap "rm -r $TMPFILE " 0
+ if [ $# -eq 1 ]; then
+ if [ -s "$1" -o "$1" = - ]; then
+ cat "$1" | tr "\r" "\n" > $TMPFILE/infile
+ else
+ echo "Cannot open $1." 2>&1
+ er=1
+ fi
+ else
+ echo '$#'"=$#" 2>&1
+ er=1
+ fi
+
+
+ if [ $er -eq 1 ]; then
+ echo "" 2>&1
+ echo "MAFFT" $version 2>&1
+ echo "" 2>&1
+ echo " References: " 2>&1
+ echo " Katoh et al., 2002, NAR 30: 3059-3066" 2>&1
+ echo " Katoh et al., 2005, NAR 33: 511-518" 2>&1
+ echo " http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft" 2>&1
+ echo "" 2>&1
+# echo "Usage: `basename $0` [options] inputfile > outputfile" 2>&1
+ echo " Options: " 2>&1
+ echo " --globalpair : All pairwise global alignment information is included." 2>&1
+ echo " default: off" 2>&1
+ echo " --localpair : All pairwise local alignment information is included." 2>&1
+ echo " default: off" 2>&1
+ echo " --op # : Gap opening penalty (>0). default: $defaultgop " 2>&1
+ echo " --ep # : Offset (>0, works like gap extension penalty). " 2>&1
+ echo " default: $defaultaof " 2>&1
+ echo " --bl #, --jtt # : Scoring matrix. default: BLOSUM62" 2>&1
+ echo " Alternatives are BLOSUM (--bl) 30, 45, 62, 80, " 2>&1
+ echo " or JTT (--jtt) # PAM. " 2>&1
+ echo " --nuc or --amino : Sequence type. default: auto" 2>&1
+ echo " --retree # : The number of tree building in progressive method " 2>&1
+ echo " (see the paper for detail). default: $defaultcycle " 2>&1
+ echo " --maxiterate # : Maximum number of iterative refinement. default: $defaultiterate " 2>&1
+ echo " --nj : Tree dependent iterative refinement is performed" 2>&1
+ echo " on an NJ tree. default: UPG tree" 2>&1
+ if [ $defaultfft -eq 1 ]; then
+ echo " --fft or --nofft: FFT is enabled or disabled. default: enabled" 2>&1
+ else
+ echo " --fft or --nofft: FFT is enabled or disabled. default: disabled" 2>&1
+ fi
+# if [ $defaultrough -eq 1 ]; then
+# echo " --rough : Rough alignment, for >1,000 sequences. default: enabled" 2>&1
+# else
+# echo " --rough : Rough alignment, for >1,000 sequences. default: disabled" 2>&1
+# i
+ echo " --clustalout: Output: clustal format (not tested). default: fasta" 2>&1
+ echo " --reorder: Outorder: aligned (not tested). default: input order" 2>&1
+ echo " --quiet : Do not report progress." 2>&1
+ echo "" 2>&1
+ echo " Input format: fasta format" 2>&1
+ echo "" 2>&1
+ echo " Typical usages:" 2>&1
+ echo " % mafft --maxiterate 1000 --localpair input > output" 2>&1
+ echo " L-INS-i (most accurate and very slow, iterative refinement" 2>&1
+ echo " method incorporating LOCAL alignment information)" 2>&1
+ echo "" 2>&1
+ echo " % mafft --maxiterate 1000 --globalpair input > output" 2>&1
+ echo " G-INS-i (slightly less accurate than L-INS-i and very slow," 2>&1
+ echo " iterative refinement method incorporating GLOBAL alignment" 2>&1
+ echo " information, suitable for sequences of similar lengths) " 2>&1
+ echo "" 2>&1
+ echo " % mafft --maxiterate 1000 input > output" 2>&1
+ echo " FFT-NS-i (accurate and slow, iterative refinement method)" 2>&1
+ echo "" 2>&1
+ echo " % mafft --retree 2 input > output (DEFAULT; same as mafft input > output)" 2>&1
+ echo " FFT-NS-2 (rough and fast, default, progressive method)" 2>&1
+ echo "" 2>&1
+ echo " % mafft --retree 1 input > output" 2>&1
+ echo " FFT-NS-1 (very rough and very fast, progressive method with" 2>&1
+ echo " a rough guide tree)" 2>&1
+ echo "" 2>&1
+ exit 1;
+ fi
+
+ (
+ cd $TMPFILE;
+ if [ $rough -gt 0 ]; then
+ $prefix/splitseq infile 500
+ for spfile in sp-[0-9]*[0-9]
+ do
+ echo $spfile > /dev/tty
+ nseq=`grep -c '^[>|=]' $spfile`
+ echo $nseq > /dev/tty
+ if [ $nseq -eq 1 ]; then
+ cp $spfile $spfile.aln
+ else
+ $prefix/sextet5 $seqtype < $spfile > /dev/null 2>&1 || exit 1
+ $prefix/tbfast $seqtype $model -f "-"$gop -h "-"$aof $param_fft -Ax < $spfile > /dev/null 2>&1 || exit 1
+ cat pre > $spfile.aln
+ fi
+ done
+ ngroup=0
+ for alfile in sp-[0-9]*[0-9].aln
+ do
+ ngroup=`expr $ngroup + 1`
+ echo $alfile > /dev/tty
+ if [ $ngroup -eq 1 ]; then
+ cp $alfile alall
+ else
+ $prefix/galn -A alall $alfile > altmp
+ mv altmp alall
+ fi
+ done
+ cat alall
+ else
+ if [ $quiet -gt 0 ]; then
+ if [ $distance = "subopt" ]; then
+ $prefix/pairlocalalign $seqtype -b 62 -g $lexp -f $lgop -h $laof -O $LGOP -E $LEXP -S < infile > /dev/null 2>&1 || exit 1
+ $prefix/tbfast $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam -Ax < infile > /dev/null 2>&1 || exit 1
+ elif [ $distance = "fasta" ]; then
+ $prefix/dndfast7 $swopt < infile > /dev/null 2>&1 || exit 1
+ $prefix/tbfast $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam -Ax < infile > /dev/null 2>&1 || exit 1
+ elif [ $distance = "blast" ]; then
+ $prefix/dndblast < infile > /dev/null 2>&1 || exit 1
+ $prefix/tbfast $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam -Ax < infile > /dev/null 2>&1 || exit 1
+ elif [ $distance = "global" ]; then
+ $prefix/pairlocalalign $seqtype $model -f "-"$gop -h "-"$aof -F < infile > /dev/null 2>&1 || exit 1
+ $prefix/tbfast $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam -Ax < infile > /dev/null 2>&1 || exit 1
+ elif [ $distance = "local" ]; then
+ $prefix/pairlocalalign $seqtype -b 62 -g $lexp -f $lgop -h $laof -L < infile > /dev/null 2>&1 || exit 1
+ $prefix/tbfast $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam -Ax < infile > /dev/null 2>&1 || exit 1
+ elif [ $distance = "genaf" ]; then
+ $prefix/pairlocalalign $seqtype -b 62 -g $lexp -f $lgop -h $laof -O $LGOP -E $LEXP -N < infile > /dev/null 2>&1 || exit 1
+ $prefix/tbfast $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam -Ax < infile > /dev/null 2>&1 || exit 1
+ else
+ $prefix/disttbfast $seqtype $model -f "-"$gop -h "-"$aof $param_fft -Ax < infile > pre 2>/dev/null || exit 1
+ fi
+ while [ $cycle -gt 1 ]
+ do
+ $prefix/tbfast $seqtype $model -f "-"$gop -h "-"$aof $param_fft -JAx < pre > /dev/null 2>&1 || exit 1
+ cycle=`expr $cycle - 1`
+ done
+ if [ $iterate -gt 0 ]; then
+ if [ $distance == "sixtuples" ]; then
+ $prefix/dndpre < pre > /dev/null 2>&1 || exit 1
+ fi
+ $prefix/dvtditr $scorecalcopt $localparam -F -z 50 $seqtype $model -f "-"$gop -h "-"$aof -A -c -I $iterate $param_it < pre > /dev/null 2>&1 || exit 1
+ fi
+ else
+ if [ $distance = "subopt" ]; then
+ $prefix/pairlocalalign $seqtype -b 62 -g $lexp -f $lgop -h $laof -O $LGOP -E $LEXP -S < infile > /dev/null || exit 1
+ $prefix/tbfast $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam -Ax < infile > /dev/null || exit 1
+ elif [ $distance = "fasta" ]; then
+ $prefix/dndfast7 $swopt < infile > /dev/null || exit 1
+ $prefix/tbfast $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam -Ax < infile > /dev/null || exit 1
+ elif [ $distance = "blast" ]; then
+ $prefix/dndblast < infile > /dev/null || exit 1
+ $prefix/tbfast $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam -Ax < infile > /dev/null || exit 1
+ elif [ $distance = "global" ]; then
+ $prefix/pairlocalalign $seqtype $model -f "-"$gop -h "-"$aof -F < infile > /dev/null || exit 1
+ $prefix/tbfast $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam -Ax < infile > /dev/null || exit 1
+ elif [ $distance = "local" ]; then
+ $prefix/pairlocalalign $seqtype -b 62 -g $lexp -f $lgop -h $laof -L < infile > /dev/null || exit 1
+ $prefix/tbfast $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam -Ax < infile > /dev/null || exit 1
+ elif [ $distance = "genaf" ]; then
+ $prefix/pairlocalalign $seqtype -b 62 -g $lexp -f $lgop -h $laof -O $LGOP -E $LEXP -N < infile > /dev/null || exit 1
+ $prefix/tbfast $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam -Ax < infile > /dev/null || exit 1
+ else
+ $prefix/disttbfast $seqtype $model -f "-"$gop -h "-"$aof $param_fft -Ax < infile > pre || exit 1
+ fi
+ while [ $cycle -gt 1 ]
+ do
+ $prefix/tbfast $seqtype $model -f "-"$gop -h "-"$aof $param_fft -JAx < pre > /dev/null || exit 1
+ cycle=`expr $cycle - 1`
+ done
+ if [ $iterate -gt 0 ]; then
+ if [ $distance = "sixtuples" ]; then
+ $prefix/dndpre < pre > /dev/null 2>&1 || exit 1
+ fi
+ $prefix/dvtditr $scorecalcopt $localparam -F -z 50 $seqtype $model -f "-"$gop -h "-"$aof -A -c -I $iterate $param_it < pre > /dev/null || exit 1
+ fi
+ fi
+# cat < pre || exit 1
+ if [ $coreout -eq 0 ]; then
+ $outputcommand < pre || exit 1
+ else
+ $prefix/setcore -w $corewin -i $corethr $coreext < pre > pre2
+ $outputcommand < pre2 || exit 1
+ fi
+ fi
+ )
+ echo '' >/dev/tty
+ if [ $distance = "fasta" ]; then
+ echo "Pairwise alignments were computed by FASTA" >/dev/tty
+ echo "(Pearson & Lipman, 1988, PNAS 85:2444-2448)" >/dev/tty
+ fi
+ if [ $distance = "blast" ]; then
+ echo "Pairwise alignments were computed by BLAST">/dev/tty
+ echo "(Altschul et al., 1997, NAR 25:3389-3402)">/dev/tty
+ fi
+ printf "\n" >/dev/tty
+ echo 'Strategy:' >/dev/tty
+ printf ' '$strategy >/dev/tty
+ echo ' ('$performance')' >/dev/tty
+ echo ' '$explanation >/dev/tty
+ echo '' >/dev/tty
+ echo "Type '$0 --help' for other options." >/dev/tty
+ echo '' >/dev/tty
+ exit 0;
+fi
+
+prog="awk"
+
+if [ $os != "darwin" ]; then
+ echo "checking nawk"
+ tmpawk=`which nawk 2>/dev/null | awk '{print $1}'`
+ if [ -x $tmpawk ]; then
+ prog=$tmpawk
+ fi
+
+ echo "checking gawk"
+ tmpawk=`which gawk 2>/dev/null | awk '{print $1}'`
+ if [ -x $tmpawk ]; then
+ prog=$tmpawk
+ fi
+fi
+
+echo "prog="$prog
+
+umask 077
+export defaultaof
+export defaultgop
+export defaultfft
+export defaultcycle
+export defaultiterate
+(
+$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( "---------------------------------------------------------------------\n" ) > "/dev/tty";
+ printf( "\n" ) > "/dev/tty";
+ printf( " MAFFT %s\n", version ) > "/dev/tty";
+ printf( "\n" ) > "/dev/tty";
+ printf( " K. Katoh, K. Misawa, K. Kuma and T. Miyata (2002)\n" ) > "/dev/tty";
+ printf( " Nucleic Acids Research 30: 3059-3066.\n" ) > "/dev/tty";
+ printf( " http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft\n" ) > "/dev/tty";
+ printf( "---------------------------------------------------------------------\n" ) > "/dev/tty";
+ printf( "\n" );
+
+ 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;
+ infile0 = sprintf( "%s", $1 );
+ infile = sprintf( "%s", $1 );
+
+ res = getline < infile;
+ close( infile );
+ if( res == -1 )
+ printf( "%s: No such file.\n\n", infile );
+ else if( res == 0 )
+ printf( "%s: Empty.\n", infile );
+ else
+ {
+ printf( "OK. infile = %s\n\n", infile );
+ 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", $1 );
+ printf( "OK. outfile = %s\n\n", outfile );
+ break;
+ }
+ }
+
+
+ while( 1 )
+ {
+ retree = defaultcycle
+ printf( "\n" );
+ printf( "Number of tree-rebuilding?\n" ) > "/dev/tty";
+ printf( "@ [%d] ", retree ) > "/dev/tty";
+ res = getline < "/dev/tty";
+ close( "/dev/tty" );
+ if( res == 0 )
+ continue;
+ else if( NF == 0 )
+ ;
+ else
+ retree = 0 + $1;
+ if( retree < 1 || 10 < retree )
+ ;
+ else
+ {
+ printf( "OK. %d\n\n", retree );
+ break;
+ }
+ }
+
+ while( 1 )
+ {
+ niterate = defaultiterate;
+ printf( "\n" );
+ printf( "Maximum number of iterations?\n" ) > "/dev/tty";
+ printf( "@ [%d] ", niterate ) > "/dev/tty";
+ res = getline < "/dev/tty";
+ close( "/dev/tty" );
+ if( res == 0 )
+ continue;
+ else if( NF == 0 )
+ ;
+ else
+ niterate = 0 + $1;
+ if( niterate < 0 || 1000 < niterate )
+ ;
+ else
+ {
+ printf( "OK. %d\n\n", niterate );
+ break;
+ }
+ }
+
+ while( 1 )
+ {
+ fft = defaultfft;
+ printf( "\n" );
+ 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" );
+ fftparam = " --fft ";
+ }
+ else
+ {
+ printf( "OK. FFT is disabled.\n\n" );
+ fftparam = " --nofft ";
+ }
+
+ while( 1 )
+ {
+ scoringmatrix = 3;
+ printf( "\n" );
+ 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";
+ 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
+ {
+ 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 );
+
+ while( 1 )
+ {
+ penalty = 0.0 + defaultgop;
+ offset = 0.0 + defaultaof;
+ printf( "\n" );
+ 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 );
+ 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 );
+ printf( "%s\n\n", command );
+
+
+ while( 1 )
+ {
+ go = 0;
+ printf( "\n" );
+ printf( "OK?\n" );
+ 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" );
+ printf( "\n" );
+ }
+ system( command );
+}
+'
+)
+exit 0;
git://source.jalview.org / jabaws.git / blobdiff