+++ /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