-#! /bin/sh
-
+#! /bin/bash
er=0;
myself=`dirname "$0"`/`basename "$0"`; export myself
-version="v6.857b (2011/05/30)"; export version
+version="v7.310 (2017/Mar/17)"; 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 mingw` ]; then
+ os="mingw"
elif [ `echo $os | grep -i darwin` ]; then
os="darwin"
elif [ `echo $os | grep -i sunos` ]; then
fi
fi
-if [ ! -x "$prefix/tbfast" ]; then
+if [ -x "$prefix/version" ]; then
+ versionbin=`"$prefix/version"` # for cygwin 2.7
+ else
+ versionbin="0.000"
+fi
+
+if ! expr "$version" : v"$versionbin" > /dev/null ; then
+ echo "" 1>&2
+ echo "v$versionbin != $version" 1>&2
+ echo "" 1>&2
+ echo "There is a problem in the configuration of your shell." 1>&2
+ echo "Check the MAFFT_BINARIES environmental variable by" 1>&2
+ echo "$ echo \$MAFFT_BINARIES" 1>&2
+ echo "" 1>&2
+ echo "This variable must be *unset*, unless you have installed MAFFT" 1>&2
+ echo "with a special configuration. To unset this variable, type" 1>&2
+ echo "$ unset MAFFT_BINARIES" 1>&2
+ echo "or" 1>&2
+ echo "% unsetenv MAFFT_BINARIES" 1>&2
+ echo "Then retry" 1>&2
+ echo "$ mafft input > output" 1>&2
+ echo "" 1>&2
+ echo "To keep this change permanently, edit setting files" 1>&2
+ echo "(.bash_profile, .profile, .cshrc, etc) in your home directory" 1>&2
+ echo "to delete the MAFFT_BINARIES line." 1>&2
+ echo "On MacOSX, also edit or remove the .MacOSX/environment.plist file" 1>&2
+ echo "and then re-login (MacOSX 10.6) or reboot (MacOSX 10.7)." 1>&2
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 "Please send a problem report to kazutaka.katoh@aist.go.jp," 1>&2
+ echo "if this problem remains." 1>&2
echo "" 1>&2
exit 1
er=1
defaultlgop="-2.00"
defaultfft=1
defaultrough=0
-defaultdistance="sixtuples"
+defaultdistance="ktuples"
#defaultdistance="local"
defaultweighti="2.7"
defaultweightr="0.0"
defaultweightm="1.0"
+defaultdafs=0
defaultmccaskill=0
defaultcontrafold=0
defaultalgopt=" "
defaultweightm="2.0"
defaultmccaskill=1
defaultcontrafold=0
+ defaultdafs=0
defaultalgopt=" -A "
defaultalgoptit=" -AB " ## chui
defaultaof="0.0"
defaultsbstmodel=" -b 62 "
defaultkappa=" "
- defaultfmodel=" -a "
+ defaultfmodel=" " # 2013/06/18
elif [ $progname = "qinsi" -o $progname = "mafft-qinsi" ]; then
defaultfft=1
defaultcycle=1
defaultweightm="2.0"
defaultmccaskill=1
defaultcontrafold=0
+ defaultdafs=0
defaultalgopt=" -A "
defaultalgoptit=" -AB " ## chui
defaultaof="0.0"
defaultsbstmodel=" -b 62 "
defaultkappa=" "
- defaultfmodel=" -a "
+ defaultfmodel=" " # 2013/06/18
elif [ $progname = "linsi" -o $progname = "mafft-linsi" ]; then
defaultfft=0
defaultcycle=1
elif [ $progname = "fftns" -o $progname = "mafft-fftns" ]; then
defaultfft=1
defaultcycle=2
- defaultdistance="sixtuples"
+ defaultdistance="ktuples"
elif [ $progname = "fftnsi" -o $progname = "mafft-fftnsi" ]; then
defaultfft=1
defaultcycle=2
defaultiterate=2
- defaultdistance="sixtuples"
+ defaultdistance="ktuples"
elif [ $progname = "nwns" -o $progname = "mafft-nwns" ]; then
defaultfft=0
defaultcycle=2
- defaultdistance="sixtuples"
+ defaultdistance="ktuples"
elif [ $progname = "nwnsi" -o $progname = "mafft-nwnsi" ]; then
defaultfft=0
defaultcycle=2
defaultiterate=2
- defaultdistance="sixtuples"
+ defaultdistance="ktuples"
fi
outputfile=""
-namelength=15
+namelength=-1
anysymbol=0
parallelizationstrategy="BAATARI2"
kappa=$defaultkappa
sbstmodel=$defaultsbstmodel
fmodel=$defaultfmodel
+nmodel=" "
gop=$defaultgop
+gopdist=$defaultgop
aof=$defaultaof
cycle=$defaultcycle
iterate=$defaultiterate
weightr=$defaultweightr
weightm=$defaultweightm
rnaalifold=0
+dafs=$defaultdafs
mccaskill=$defaultmccaskill
contrafold=$defaultcontrafold
-quiet=0
+progressfile="/dev/stderr"
debug=0
sw=0
algopt=$defaultalgopt
algoptit=$defaultalgoptit
+#algspecified=0
+pairspecified=0
scorecalcopt=" "
coreout=0
corethr="0.5"
corewin="100"
coreext=" "
outputformat="pir"
+f2clext="-N"
outorder="input"
seed="x"
seedtable="x"
auto=0
groupsize=-1
partsize=50
-partdist="sixtuples"
+partdist="ktuples"
partorderopt=" -x "
treeout=0
distout=0
treeinopt=" "
seedfiles="/dev/null"
seedtablefile="/dev/null"
+pdblist="/dev/null"
+ownlist="/dev/null"
+strdir="$PWD"
aamatrix="/dev/null"
treeinfile="/dev/null"
rnascoremtx=" "
laraparams="/dev/null"
foldalignopt=" "
-treealg=" -X "
+treealg=" -X 0.1 "
+sueff="1.0"
scoreoutarg=" "
numthreads=0
+numthreadsit=-1
+numthreadstb=-1
randomseed=0
addfile="/dev/null"
addarg0=" "
+addarg=" "
+addsinglearg=" "
+add2ndhalfarg=" "
+mapoutfile="/dev/null"
+fragment=0
+legacygapopt=" "
+mergetable="/dev/null"
+mergearg=" "
+seedoffset=0
outnum=" "
+last_e=5000
+last_m=3
+last_subopt=" "
+last_once=" "
+adjustdirection=0
+tuplesize=6
+termgapopt=" -O "
+#termgapopt=" " # gap/gap ga kakenai node
+similarityoffset="0.0"
+unalignlevel="0.0"
+unalignspecified=0
+spfactor="100.0"
+shiftpenaltyspecified=0
+opdistspecified=0
+allowshift=0
+enrich=0
+enrichseq=0
+enrichstr=0
+seektarget=""
+fixthreshold="0.0"
+bunkatsuopt=" "
+npickup=0
+minimumweight="0.00001" # 2016/Mar
+usenaivepairscore=" "
+oldgenafparam=0
+sprigorous=0
+pileuporshuffle="l"
+initialramusage="20GB"
+focusarg=" "
if [ $# -gt 0 ]; then
+ if [ "$1" = "--version" ]; then
+ echo "$version" 1>&2
+ exit 0;
+ elif [ "$1" = "--help" -o "$1" = "--info" ]; then
+ shift
+ er=1;
+ fi
while [ $# -gt 1 ];
do
if [ "$1" = "--auto" ]; then
partorderopt=" -x "
elif [ "$1" = "--unweight" ]; then
weightopt=" -u "
+ elif [ "$1" = "--termgappenalty" ]; then
+ termgapopt=" "
+ elif [ "$1" = "--alga" ]; then
+ algopt=" "
+ algoptit=" "
+# algspecified=1
elif [ "$1" = "--algq" ]; then
algopt=" -Q "
- algoptit=" -QB "
+ algoptit=" "
+ echo "" 1>&2
+ echo "--algq is no longer supported!" 1>&2
+ echo "" 1>&2
+ exit 1;
+# algspecified=1
elif [ "$1" = "--namelength" ]; then
shift
namelength=`expr "$1" - 0`
+ if ! expr "$1" : "[0-9]" > /dev/null ; then
+ echo "Specify the length of name in clustal format output!" 1>&2
+ exit
+ fi
elif [ "$1" = "--groupsize" ]; then
shift
groupsize=`expr "$1" - 0`
+ if ! expr "$1" : "[0-9]" > /dev/null ; then
+ echo "Specify groupsize!" 1>&2
+ exit
+ fi
elif [ "$1" = "--partsize" ]; then
shift
partsize=`expr "$1" - 0`
+ if ! expr "$1" : "[0-9]" > /dev/null ; then
+ echo "Specify partsize!" 1>&2
+ exit
+ fi
elif [ "$1" = "--parttree" ]; then
distance="parttree"
- partdist="sixtuples"
+ partdist="ktuples"
elif [ "$1" = "--dpparttree" ]; then
distance="parttree"
partdist="localalign"
distout=1
elif [ "$1" = "--fastswpair" ]; then
distance="fasta"
+ pairspecified=1
sw=1
elif [ "$1" = "--fastapair" ]; then
distance="fasta"
+ pairspecified=1
sw=0
elif [ "$1" = "--averagelinkage" ]; then
- treealg=" -E "
+ treealg=" -X 1.0 "
+ sueff="1.0"
elif [ "$1" = "--minimumlinkage" ]; then
- treealg=" -q "
+ treealg=" -X 0.0 "
+ sueff="0.0"
+ elif [ "$1" = "--mixedlinkage" ]; then
+ shift
+ sueff="$1"
+ treealg=" -X $1"
elif [ "$1" = "--noscore" ]; then
scorecalcopt=" -Z "
+ elif [ "$1" = "--6mermultipair" ]; then
+ distance="ktuplesmulti"
+ tuplesize=6
+ pairspecified=1
+ elif [ "$1" = "--10mermultipair" ]; then
+ distance="ktuplesmulti"
+ tuplesize=10
+ pairspecified=1
elif [ "$1" = "--6merpair" ]; then
- distance="sixtuples"
+ distance="ktuples"
+ tuplesize=6
+ pairspecified=1
+ elif [ "$1" = "--10merpair" ]; then
+ distance="ktuples"
+ tuplesize=10
+ pairspecified=1
elif [ "$1" = "--blastpair" ]; then
distance="blast"
+ pairspecified=1
+ elif [ "$1" = "--lastmultipair" ]; then
+ distance="lastmulti"
+ pairspecified=1
elif [ "$1" = "--globalpair" ]; then
distance="global"
+ pairspecified=1
+ elif [ "$1" = "--shortlongpair" ]; then
+ distance="local"
+ usenaivepairscore="-Z"
+ laof=0.0 # addfull no tokini tsukawareru.
+ lexp=0.0 # addfull no tokini tsukawareru.
+ pgaof=0.0 # local nara iranai
+ pgexp=0.0 # local nara iranai
+ pairspecified=1
+ elif [ "$1" = "--longshortpair" ]; then
+ distance="local"
+ usenaivepairscore="-Z"
+ laof=0.0 # addfull no tokini tsukawareru.
+ lexp=0.0 # addfull no tokini tsukawareru.
+ pgaof=0.0 # local nara iranai
+ pgexp=0.0 # local nara iranai
+ pairspecified=1
elif [ "$1" = "--localpair" ]; then
distance="local"
+ pairspecified=1
+ elif [ "$1" = "--lastpair" ]; then
+ distance="last"
+ pairspecified=1
+ elif [ "$1" = "--multipair" ]; then
+ distance="multi"
+ pairspecified=1
+ elif [ "$1" = "--hybridpair" ]; then
+ distance="hybrid"
+ pairspecified=1
elif [ "$1" = "--scarnapair" ]; then
distance="scarna"
+ pairspecified=1
+ elif [ "$1" = "--dafspair" ]; then
+ distance="dafs"
+ pairspecified=1
elif [ "$1" = "--larapair" ]; then
distance="lara"
+ pairspecified=1
elif [ "$1" = "--slarapair" ]; then
distance="slara"
+ pairspecified=1
elif [ "$1" = "--foldalignpair" ]; then
distance="foldalignlocal"
+ pairspecified=1
elif [ "$1" = "--foldalignlocalpair" ]; then
distance="foldalignlocal"
+ pairspecified=1
elif [ "$1" = "--foldalignglobalpair" ]; then
distance="foldalignglobal"
+ pairspecified=1
elif [ "$1" = "--globalgenafpair" ]; then
distance="globalgenaf"
+ pairspecified=1
+ echo "" 1>&2
+ echo "--globalgenaf is no longer supported!" 1>&2
+ echo "" 1>&2
+ exit 1;
elif [ "$1" = "--localgenafpair" ]; then
distance="localgenaf"
+ pairspecified=1
elif [ "$1" = "--genafpair" ]; then
distance="localgenaf"
+ pairspecified=1
+ elif [ "$1" = "--oldgenafpair" ]; then
+ distance="localgenaf"
+ pairspecified=1
+ oldgenafparam=1
elif [ "$1" = "--memsave" ]; then
memopt=" -M -B " # -B (bunkatsunashi no riyu ga omoidasenai)
elif [ "$1" = "--nomemsave" ]; then
elif [ "$1" = "--nofft" ]; then
fft=0
elif [ "$1" = "--quiet" ]; then
- quiet=1
+ if [ $os = "mingw" ]; then
+ progressfile="nul"
+ else
+ progressfile="/dev/null"
+ fi
elif [ "$1" = "--debug" ]; then
debug=1
elif [ "$1" = "--coreext" ]; then
coreext=" -c "
elif [ "$1" = "--core" ]; then
coreout=1
+ elif [ "$1" = "--adjustdirection" ]; then
+ adjustdirection=1
+ elif [ "$1" = "--adjustdirectionaccurately" ]; then
+ adjustdirection=2
+ elif [ "$1" = "--progress" ]; then
+ shift
+ progressfile="$1"
+ if ! ( expr "$progressfile" : "\/" > /dev/null || expr "$progressfile" : "[A-Za-z]\:" > /dev/null ) ; then
+ echo "Specify a progress file name with the absolute path!" 1>&2
+ exit
+ fi
elif [ "$1" = "--out" ]; then
shift
outputfile="$1"
elif [ "$1" = "--thread" ]; then
shift
+ if ! expr "$1" : "[0-9\-]" > /dev/null ; then
+ echo "Specify the number of threads. Or, use --thread -1" 1>&2
+ exit
+ fi
numthreads=`expr "$1" - 0`
+ elif [ "$1" = "--threadtb" ]; then
+ shift
+ if ! expr "$1" : "[0-9\-]" > /dev/null ; then
+ echo "Specify the number of threads for the iterative step!" 1>&2
+ exit
+ fi
+ numthreadstb=`expr "$1" - 0`
+ elif [ "$1" = "--threadit" ]; then
+ shift
+ if ! expr "$1" : "[0-9\-]" > /dev/null ; then
+ echo "Specify the number of threads for the iterative step!" 1>&2
+ exit
+ fi
+ numthreadsit=`expr "$1" - 0`
+ elif [ "$1" = "--last_subopt" ]; then
+ last_subopt="-S"
+ elif [ "$1" = "--last_once" ]; then
+ last_once="-U"
+ elif [ "$1" = "--last_m" ]; then
+ shift
+ last_m=`expr "$1" - 0`
+ elif [ "$1" = "--last_e" ]; then
+ shift
+ last_e=`expr "$1" - 0`
elif [ "$1" = "--randomseed" ]; then
shift
randomseed=`expr "$1" - 0`
elif [ "$1" = "--scoreout" ]; then
scoreoutarg="-S -B"
elif [ "$1" = "--outnum" ]; then
- scoreoutarg="-n"
+ outnum="-n"
+ elif [ "$1" = "--leavegappyregion" ]; then
+ legacygapopt="-L"
+ elif [ "$1" = "--legacygappenalty" ]; then
+ legacygapopt="-L"
+ elif [ "$1" = "--merge" ]; then
+ shift
+ mergetable="$1"
+ if [ ! -e "$mergetable" ]; then
+ echo "Cannot open $mergetable" 1>&2
+ echo "" 1>&2
+ exit
+ fi
elif [ "$1" = "--addprofile" ]; then
shift
addarg0="-I"
shift
addarg0="-K -I"
addfile="$1"
+ elif [ "$1" = "--addfragments" ]; then
+ shift
+ addarg0="-K -I"
+ addfile="$1"
+ fragment=1
+ elif [ "$1" = "--addfull" ]; then
+ shift
+ addarg0="-K -I"
+ addfile="$1"
+ fragment=-1
+ elif [ "$1" = "--addlong" ]; then
+ shift
+ addarg0="-K -I"
+ addfile="$1"
+ fragment=-2
+ elif [ "$1" = "--smoothing" ]; then
+ add2ndhalfarg=$add2ndhalfarg" -p "
+ elif [ "$1" = "--keeplength" ]; then
+ add2ndhalfarg=$add2ndhalfarg" -Y "
+ elif [ "$1" = "--mapout" ]; then
+ add2ndhalfarg=$add2ndhalfarg" -Z -Y "
+ elif [ "$1" = "--mapoutfile" ]; then
+ shift
+ add2ndhalfarg=$add2ndhalfarg" -Z -Y "
+ mapoutfile="$1"
elif [ "$1" = "--maxiterate" ]; then
shift
iterate=`expr "$1" - 0`
+ if ! expr "$1" : "[0-9]" > /dev/null ; then
+ echo "Specify the number of iterations!" 1>&2
+ exit
+ fi
elif [ "$1" = "--retree" ]; then
shift
cycle=`expr "$1" - 0`
+ if ! expr "$1" : "[0-9]" > /dev/null ; then
+ echo "Specify the number of tree rebuilding!" 1>&2
+ exit
+ fi
+ elif [ "$1" = "--text" ]; then
+ sbstmodel=" -b -2 -a "
+ f2clext="-E"
+ seqtype="-P"
+ fft=0
elif [ "$1" = "--aamatrix" ]; then
shift
sbstmodel=" -b -1 "
aamatrix="$1"
+ if [ ! -e "$aamatrix" ]; then
+ echo "Cannot open $aamatrix" 1>&2
+ echo "" 1>&2
+ exit
+ fi
elif [ "$1" = "--treein" ]; then
shift
treeinopt=" -U "
treein=1
treeinfile="$1"
+ if [ ! -e "$treeinfile" ]; then
+ echo "Cannot open $treeinfile" 1>&2
+ echo "" 1>&2
+ exit
+ fi
+ elif [ "$1" = "--pileup" ]; then
+ treeinopt=" -U "
+ treein=1
+ pileuporshuffle="p"
+ elif [ "$1" = "--randomchain" ]; then
+ treeinopt=" -U "
+ treein=1
+ pileuporshuffle="s"
elif [ "$1" = "--topin" ]; then
shift
treeinopt=" -V "
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" = "--memsavetree" ]; then
+ treeinopt=" -U "
+ treein=1
+ pileuporshuffle="C"
+ elif [ "$1" = "--memsavetreex" ]; then
+ treeinopt=" -U "
+ treein=1
+ pileuporshuffle="c"
+ elif [ "$1" = "--initialramusage" ]; then
+ shift
+ treeinopt=" -U "
+ treein=1
+ initialramusage="$1"
+ pileuporshuffle="c"
elif [ "$1" = "--kappa" ]; then
shift
kappa=" -k $1 "
+ if ! expr "$1" : "[0-9]" > /dev/null ; then
+ echo "Specify kappa value!" 1>&2
+ exit
+ fi
elif [ "$1" = "--fmodel" ]; then
fmodel=" -a "
+ elif [ "$1" = "--nwildcard" ]; then
+ nmodel=" -: "
+ elif [ "$1" = "--nzero" ]; then
+ nmodel=" "
elif [ "$1" = "--jtt" ]; then
shift
sbstmodel=" -j $1"
+# if ! expr "$1" : "[0-9]" > /dev/null ; then
+# echo "Specify pam value!" 1>&2
+# exit
+# fi
elif [ "$1" = "--kimura" ]; then
shift
sbstmodel=" -j $1"
+# if ! expr "$1" : "[0-9]" > /dev/null ; then
+# echo "Specify pam value!" 1>&2
+# exit
+# fi
elif [ "$1" = "--tm" ]; then
shift
sbstmodel=" -m $1"
+# if ! expr "$1" : "[0-9]" > /dev/null ; then
+# echo "Specify pam value!" 1>&2
+# exit
+# fi
elif [ "$1" = "--bl" ]; then
shift
sbstmodel=" -b $1"
+ if ! expr "$1" : "[0-9]" > /dev/null ; then
+ echo "blosum $1?" 1>&2
+ exit
+ fi
elif [ "$1" = "--weighti" ]; then
shift
weighti="$1"
+ if ! expr "$1" : "[0-9]" > /dev/null ; then
+ echo "Specify weighti value!" 1>&2
+ exit
+ fi
elif [ "$1" = "--weightr" ]; then
shift
weightr="$1"
+ if ! expr "$1" : "[0-9]" > /dev/null ; then
+ echo "Specify weightr value!" 1>&2
+ exit
+ fi
elif [ "$1" = "--weightm" ]; then
shift
weightm="$1"
+ if ! expr "$1" : "[0-9]" > /dev/null ; then
+ echo "Specify weightm value!" 1>&2
+ exit
+ fi
elif [ "$1" = "--rnaalifold" ]; then
rnaalifold=1
elif [ "$1" = "--mccaskill" ]; then
mccaskill=1
contrafold=0
+ dafs=0
elif [ "$1" = "--contrafold" ]; then
mccaskill=0
contrafold=1
+ dafs=0
+ elif [ "$1" = "--dafs" ]; then
+ mccaskill=0
+ contrafold=0
+ dafs=1
elif [ "$1" = "--ribosum" ]; then
rnascoremtx=" -s "
elif [ "$1" = "--op" ]; then
shift
gop="$1"
+ if ! expr "$1" : "[0-9]" > /dev/null ; then
+ echo "Specify op!" 1>&2
+ exit
+ fi
+ elif [ "$1" = "--opdist" ]; then
+ shift
+ gopdist="$1"
+ if ! expr "$1" : "[0-9]" > /dev/null ; then
+ echo "Specify opdist!" 1>&2
+ exit
+ fi
+ opdistspecified=1
+ elif [ "$1" = "--allowshift" ]; then
+ allowshift=1
+ elif [ "$1" = "--shiftpenalty" ]; then
+ shift
+ spfactor="$1"
+ if ! expr "$1" : "[0-9]" > /dev/null ; then
+ echo "Specify sf!" 1>&2
+ exit
+ fi
+ shiftpenaltyspecified=1
elif [ "$1" = "--ep" ]; then
shift
- aof="$1"
+# aof="$1"
+ tmpval="$1"
+ aof=`awk "BEGIN{ print -1.0 * \"$tmpval\"}"`
+ if ! expr "$aof" : "[0-9\-]" > /dev/null ; then
+ printf "\nSpecify a number for ep, like --ep 0.1\n" 1>&2
+ printf "'$1' cannot be interpreted as a number..\n\n" 1>&2
+ exit
+ fi
elif [ "$1" = "--rop" ]; then
shift
rgop="$1"
+# Atode check
elif [ "$1" = "--rep" ]; then
shift
rgep="$1"
elif [ "$1" = "--corewin" ]; then
shift
corewin="$1"
+ elif [ "$1" = "--strdir" ]; then
+ shift
+ strdir="$1"
+ elif [ "$1" = "--pdbidlist" ]; then
+ shift
+ pdblist="$1"
+ if [ ! -e "$pdblist" ]; then
+ echo "Cannot open $pdblist" 1>&2
+ echo "" 1>&2
+ exit
+ fi
+ elif [ "$1" = "--pdbfilelist" ]; then
+ shift
+ ownlist="$1"
+ if [ ! -e "$ownlist" ]; then
+ echo "Cannot open $ownlist" 1>&2
+ echo "" 1>&2
+ exit
+ fi
+ elif [ "$1" = "--enrich" ]; then
+ enrich=1
+ enrichseq=1
+ enrichstr=1
+ seektarget=""
+ elif [ "$1" = "--enrichseq" ]; then
+ enrich=1
+ enrichseq=1
+ enrichstr=0
+ seektarget="-seq"
+ elif [ "$1" = "--enrichstr" ]; then
+ enrich=1
+ enrichseq=0
+ enrichstr=1
+ seektarget="-str"
elif [ "$1" = "--seedtable" ]; then
shift
seedtable="y"
shift
seed="m"
seedfiles="$seedfiles $1"
+ elif [ "$1" = "--minimumweight" ]; then
+ shift
+ minimumweight="$1"
+ elif [ "$1" = "--similaritylevel" ]; then
+ shift
+ similarityoffset="$1"
+ elif [ "$1" = "--unalignlevel" ]; then
+ shift
+ unalignlevel="$1"
+ unalignspecified=1
+ elif [ "$1" = "--skipiterate" ]; then
+ shift
+ fixthreshold="$1"
+ elif [ "$1" = "--bunkatsunashi" ]; then
+ bunkatsuopt=" -B "
+ elif [ "$1" = "--sp" ]; then
+ sprigorous=1
+ elif [ "$1" = "--focus" ]; then
+ focusarg=" -= "
+ elif [ "$1" = "--sparsepickup" ]; then
+ shift
+ npickup="$1"
elif [ $progname = "fftns" -o $progname = "nwns" ]; then
if [ "$1" -gt 0 ]; then
cycle=`expr "$1" - 0`
else
echo "Unknown option: $1" 1>&2
er=1;
+# exit 1;
fi
shift
done;
+ echo "" 1>"$progressfile"
# TMPFILE=/tmp/$progname.$$
TMPFILE=`mktemp -dt $progname.XXXXXXXXXX`
echo "mktemp seems to be obsolete. Re-trying without -t" 1>&2
TMPFILE=`mktemp -d /tmp/$progname.XXXXXXXXXX`
fi
+
+# if [ $os = "cygwin" ]; then
+# TMPFILE=`cygpath -w $TMPFILE` unnecessary for cygwin2.7
+# fi
+
umask 077
# mkdir $TMPFILE || er=1
if [ $debug -eq 1 ]; then
- trap "tar cfvz debuginfo.tgz $TMPFILE; rm -rf $TMPFILE " 0
+# trap "tar cfvz debuginfo.tgz $TMPFILE; rm -rf $TMPFILE " 0 # does not work in msys
+ trap "tar cfv - $TMPFILE | gzip -c > debuginfo.tgz; rm -rf $TMPFILE " 0
else
- trap "rm -rf $TMPFILE " 0
+ trap "rm -rf $TMPFILE" 0
fi
if [ $# -eq 1 ]; then
if [ -r "$1" -o "$1" = - ]; then
printf '';
else
echo "$0": Cannot open "$addfile". 1>&2
+ echo "" 1>&2
exit 1;
fi
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 "^$" > $TMPFILE/_aamtx
+ cat "$mergetable" | tr "\r" "\n" | grep -v "^$" > $TMPFILE/_subalignmentstable
cat "$treeinfile" | tr "\r" "\n" | grep -v "^$" > $TMPFILE/_guidetree
cat "$seedtablefile" | tr "\r" "\n" | grep -v "^$" > $TMPFILE/_seedtablefile
cat "$laraparams" | tr "\r" "\n" | grep -v "^$" > $TMPFILE/_lara.params
+ cat "$pdblist" | tr "\r" "\n" | grep -v "^$" > $TMPFILE/pdblist
+ cat "$ownlist" | tr "\r" "\n" | grep -v "^$" > $TMPFILE/ownlist
+
# echo $seedfiles
infilename="$1"
seedfilesintmp="/dev/null"
cat "$1" | tr "\r" "\n" > $TMPFILE/seed$#
else
echo "$0": Cannot open "$1". 1>&2
+ echo "" 1>&2
exit 1;
fi
seednseq=$seednseq" "`grep -c '^[>|=]' $TMPFILE/seed$#`
else
echo "$0": Cannot open "$1". 1>&2
+ echo "" 1>&2
er=1
# exit 1;
fi
else
- echo '$#'"=$#" 1>&2
+# echo '$#'"=$#" 1>&2
er=1
fi
- if [ $os != "linux" ]; then
- numthreads=0
+
+ if [ $numthreads -lt 0 ]; then
+ if [ $os = "linux" ]; then
+ nlogicalcore=`cat /proc/cpuinfo | grep "^processor" | uniq | wc -l`
+ ncoresinacpu=`cat /proc/cpuinfo | grep 'cpu cores' | uniq | awk '{print $4}'`
+ nphysicalcpu=`cat /proc/cpuinfo | grep 'physical id' | sort | uniq | wc -l`
+ if [ $nlogicalcore -eq 0 ]; then
+ echo "Cannot get the number of processors from /proc/cpuinfo" 1>>"$progressfile"
+ exit 1
+ fi
+ if [ ${#ncoresinacpu} -gt 0 -a $nphysicalcpu -gt 0 ]; then
+ numthreads=`expr $ncoresinacpu '*' $nphysicalcpu`
+# if [ $nlogicalcore -gt $numthreads ]; then # Hyperthreading
+# numthreads=`expr $numthreads '+' 1`
+# fi
+ else
+ numthreads=$nlogicalcore
+ fi
+ elif [ $os = "darwin" ]; then
+ numthreads=`sysctl -n hw.physicalcpu`
+ if [ -z $numthreads ]; then
+ echo "Cannot get the number of physical cores from sysctl" 1>>"$progressfile"
+ exit 1
+ fi
+# nlogicalcore=`sysctl -n hw.logicalcpu`
+# if [ $nlogicalcore -gt $numthreads ]; then # Hyperthreading
+# numthreads=`expr $numthreads '+' 1`
+# fi
+ elif [ $os = "mingw" -o $os = "cygwin" ]; then
+ numthreads=`wmic cpu get NumberOfCores | head -2 | tail -1 | awk '{print $1}'`
+ else
+ echo "Cannot count the number of physical cores." 1>>"$progressfile"
+ exit 1
+ fi
+ echo "OS = "$os 1>>"$progressfile"
+ echo "The number of physical cores = " $numthreads 1>>"$progressfile"
+ fi
+
+ if [ $numthreadstb -lt 0 ]; then
+ numthreadstb=$numthreads
+ fi
+
+ if [ $numthreadsit -lt 0 ]; then
+ if [ $numthreads -lt 11 ]; then
+ numthreadsit=$numthreads
+ else
+ numthreadsit=10
+ fi
fi
- if [ $numthreads -eq 0 -a $parallelizationstrategy = "BESTFIRST" ]; then
+ if [ $numthreadsit -eq 0 -a $parallelizationstrategy = "BESTFIRST" ]; then
echo 'Impossible' 1>&2;
exit 1;
fi
+ if [ "$addarg0" != " " ]; then
+ iterate=0 # 2013/03/23
+ "$prefix/countlen" < $TMPFILE/_addfile > $TMPFILE/addsize 2>>"$progressfile"
+ nadd=`awk '{print $1}' $TMPFILE/addsize`
+ if [ $nadd -eq "0" ]; then
+ echo Check $addfile 1>&2
+ exit 1;
+ fi
+ 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
+ else
+ nadd="0"
+ fi
+
if [ $auto -eq 1 ]; then
- "$prefix/countlen" < $TMPFILE/infile > $TMPFILE/size
+ "$prefix/countlen" < $TMPFILE/infile > $TMPFILE/size 2>>"$progressfile"
nseq=`awk '{print $1}' $TMPFILE/size`
nlen=`awk '{print $3}' $TMPFILE/size`
- if [ $nlen -lt 2000 -a $nseq -lt 100 ]; then
+
+ if [ $nlen -lt 3000 -a $nseq -lt 100 ]; then
distance="local"
iterate=1000
+ cycle=1
+ elif [ $nlen -lt 1000 -a $nseq -lt 200 ]; then
+ distance="local"
+ iterate=2
+ cycle=1
elif [ $nlen -lt 10000 -a $nseq -lt 500 ]; then
- distance="sixtuples"
+ distance="ktuples"
iterate=2
- else
- distance="sixtuples"
+ cycle=2
+ elif [ $nseq -lt 50000 ]; then # changed from 10000 2014/Oct/4
+ distance="ktuples"
+ iterate=0
+ cycle=2
+ elif [ $nseq -lt 90000 ]; then # changed from 30000 2014/Oct/4
+ distance="ktuples"
iterate=0
+ cycle=1
+ elif [ $nlen -lt 3000 ]; then
+ distance="parttree"
+ partdist="localalign"
+ algopt=" "
+ algoptit=" "
+# algspecified=1
+ cycle=1
+ else
+ distance="parttree"
+ partdist="ktuples"
+ algopt=" "
+ algoptit=" "
+# algspecified=1
+ cycle=1
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
+
+
+# if [ $nlen -lt 3000 -a $nseq -lt 100 ]; then
+# distance="local"
+# iterate=1000
+# cycle=1
+# elif [ $nlen -lt 1000 -a $nseq -lt 200 ]; then
+# distance="local"
+# iterate=2
+# cycle=1
+# elif [ $nlen -lt 10000 -a $nseq -lt 500 ]; then
+# distance="ktuples"
+# iterate=2
+# cycle=2
+# elif [ $nseq -lt 200000 ]; then
+# distance="ktuples"
+# iterate=0
+# treeinopt=" -U "
+# treein=1
+# pileuporshuffle="a"
+# elif [ $nlen -lt 3000 ]; then
+# distance="parttree"
+# partdist="localalign"
+# algopt=" "
+# algoptit=" "
+## algspecified=1
+# cycle=1
+# else
+# distance="parttree"
+# partdist="ktuples"
+# algopt=" "
+# algoptit=" "
+## algspecified=1
+# cycle=1
+# fi
+
+
+ if [ $fragment -ne 0 ]; then
+ norg=`expr $nseq '-' $nadd`
+ npair=`expr $norg '*' $nadd`
+ echo "nadd = " $nadd 1>>"$progressfile"
+ echo "npair = " $npair 1>>"$progressfile"
+ echo "nseq = " $nseq 1>>"$progressfile"
+ echo "nlen = " $nlen 1>>"$progressfile"
+# nagasa check!
+#
+ if [ $npair -gt 10000000 -o $nlen -gt 500000 ]; then # 2015/Jun
+ distance="ktuples"
+ echo "use ktuples, size=$tuplesize!" 1>>"$progressfile"
+ elif [ $npair -gt 3000000 -o $nlen -gt 100000 ]; then # 2015/Jun
+ distance="multi"
+ weighti="0.0"
+ echo "use multipair, weighti=0.0!" 1>>"$progressfile"
+ else
+ distance="multi"
+ echo "use multipair, weighti=$weighti!" 1>>"$progressfile"
+ fi
+ pairspecified=1
fi
fi
+ if [ `awk "BEGIN {print( 0.0+\"$sueff\" < 0.0 || 0.0+\"$sueff\" > 1.0 )}"` -gt 0 ]; then
+ printf "\n%s\n\n" "The argument of --mixedlinkage must be between 0.0 and 1.0" 1>>"$progressfile"
+ exit 1;
+ fi
+
+ if [ $allowshift -eq 1 ]; then
+ if [ $unalignspecified -ne 1 ]; then
+ unalignlevel="0.8"
+ fi
+ if [ $shiftpenaltyspecified -ne 1 ]; then
+ spfactor="2.00"
+ fi
+ fi
+
+ if [ $opdistspecified -ne 1 ]; then
+ gopdist=$gop
+ fi
+
+ if [ $unalignlevel != "0.0" -o `awk "BEGIN {print( 0.0+\"$spfactor\" < 100.0 )}"` -gt 0 ]; then
+ nmodel=" -: "
+ termgapopt=" "
+ if [ $distance = "localgenaf" ]; then
+ printf "\n%s\n" "The combination of --allowshift and --genafpair (E-INS-i/-1) is not supported." 1>>"$progressfile"
+ printf "%s\n" "Instead, please try --allowshift --globalpair (G-INS-i/-1 in the web version)," 1>>"$progressfile"
+ printf "%s\n\n" "which covers the situation for --genafpair (E-INS-i/-1), too." 1>>"$progressfile"
+ exit 1;
+ fi
+ if [ $distance != "global" -o `awk "BEGIN {print( 0.0+\"$weighti\" < 1.0 )}"` -gt 0 ]; then
+ printf "\n%s\n\n" "At present, --unalignlevel # or --allowshift is supported only with the --globalpair option." 1>>"$progressfile"
+ exit 1;
+ fi
+ if [ $fragment -ne 0 ]; then
+ printf "\n%s\n\n" "At present, --unalignlevel # or --allowshift is not supported with the --addfragments option." 1>>"$progressfile"
+ exit 1;
+ fi
+ fi
+
+ if [ `awk "BEGIN {print( 0.0+\"$spfactor\" < 1.0 )}"` -gt 0 ]; then
+ printf "\n%s\n" "shiftpenalty must be >1." 1>>"$progressfile"
+ exit 1;
+ fi
+
+ if [ `awk "BEGIN {print( 0.0+\"$fixthreshold\" < 0.0 )}"` -gt 0 ]; then
+ printf "\n%s\n\n" "The 'fix' parameter must be >= 0.0" 1>>"$progressfile"
+ exit 1;
+ fi
+
+ if [ `awk "BEGIN {print( 0.0+\"$unalignlevel\" < 0.0 || 0.0+\"$unalignlevel\" > 1.0 )}"` -gt 0 ]; then
+ printf "\n%s\n\n" "The 'unalignlevel' parameter must be between 0.0 and 1.0" 1>>"$progressfile"
+ exit 1;
+ fi
+ if [ `awk "BEGIN {print( 0.0+\"$unalignlevel\" > 0.0 )}"` -gt 0 ]; then
+ laof="0"
+ lexp="0"
+ pgaof="0"
+ pgexp="0"
+ LEXP="0"
+ GEXP="0"
+ termgapopt=" "
+# if [ $auto -eq 1 -o $fragment -ne 0 -o $iterate -gt 0 ]; then
+ if [ $fragment -ne 0 ]; then
+ printf "\n%s\n\n" "At present, the 'unalignlevel > 0' mode is not supported with the --addfragments option." 1>>"$progressfile"
+ exit 1;
+ fi
+ if [ $distance = "parttree" ]; then
+ printf "\n%s\n\n" "At present, the 'unalignlevel > 0' mode is not supported in the (dp)parttree option." 1>>"$progressfile"
+ exit 1;
+ fi
+ if [ $distance = "localgenaf" ]; then
+ printf "\n%s\n" "The --genafpair is not supported in the 'unalignlevel > 0' mode." 1>>"$progressfile"
+ printf "%s\n" "Instead, please try --unalignlevel xx --globalpair," 1>>"$progressfile"
+ printf "%s\n\n" "which covers the situation for --genafpair (E-INS-i), too." 1>>"$progressfile"
+ exit 1;
+ fi
+# if [ $distance != "ktuples" -a `awk "BEGIN {print( 0.0+\"$weighti\" > 0.0 )}"` -gt 0 -a $iterate -gt 0 ]; then
+# printf "\n%s\n\n" "Please add --weighti 0.0, for now." 1>>"$progressfile"
+# exit 1;
+# fi
+ fi
+
+ if [ `awk "BEGIN {print( 0.0+\"$similarityoffset\" != 0.0 && 0.0+\"$unalignlevel\" != 0.0 )}"` -gt 0 ]; then
+ printf "\n%s\n\n" "Do not simultaneously specify --similaritylevel and --unalignlevel" 1>>"$progressfile"
+ exit 1;
+ fi
+
+ if [ `awk "BEGIN {print( 0.0+\"$similarityoffset\" < -1.0 || 0.0+\"$similarityoffset\" > 1.0 )}"` -gt 0 ]; then
+ printf "\n%s\n\n" "Similarity must be between -1.0 and +1.0" 1>>"$progressfile"
+ exit 1;
+ fi
+ aof=`awk "BEGIN{print 0.0 + \"$similarityoffset\" + $aof}"`
+ laof=`awk "BEGIN{print 0.0 + \"$similarityoffset\" + $laof}"`
+ pgaof=`awk "BEGIN{print 0.0 + \"$similarityoffset\" + $pgaof}"`
+
+
if [ $parallelizationstrategy = "BESTFIRST" -o $parallelizationstrategy = "BAATARI0" ]; then
iteratelimit=254
else
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
+ elif [ $mccaskill -eq 1 -o $dafs -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 $rnascoremtx "
rnaoptit=" -F "
fi
- model="$sbstmodel $kappa $fmodel"
+# if [ $algspecified -eq 0 ]; then
+# if [ $distance = "parttree" ]; then
+# algopt=" -Q "
+# algoptit=" "
+# else
+# algopt=" "
+# algoptit=" "
+# fi
+# fi
+
+ if [ $sprigorous -eq 1 ]; then
+ algopt=" -@ "
+ if [ $iterate -gt 0 ]; then
+ if [ $numthreadsit -eq 0 ]; then
+ algoptit=" -@ -B -Z -z 1000 "
+ else
+ echo "" 1>>"$progressfile"
+ echo "At present, the combination of --sp and iterative refinement is supported only in a single thread." 1>>"$progressfile"
+ echo "Please try \"--thread -1 --threadit 0\", which runs the iterative refinment calculation on a single thread." 1>>"$progressfile"
+ echo "" 1>>"$progressfile"
+ exit 1;
+# algoptit=" -@ -B -z 1000 "
+ fi
+ fi
+ termgapopt=" "
+ fft=0
+ memopt=" -N "
+ fi
+
+ model="$sbstmodel $kappa $fmodel $nmodel"
if [ $er -eq 1 ]; then
echo "------------------------------------------------------------------------------" 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 " MBE 30:772-780 (2013), NAR 30:3059-3066 (2002)" 1>&2
# echo "------------------------------------------------------------------------------" 1>&2
# echo " % mafft in > out" 1>&2
echo "------------------------------------------------------------------------------" 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 "--thread # : Number of threads (if unsure, --thread -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
exit 1
fi
fi
+ if [ $distance = "last" -o $distance = "lastmulti" ]; then
+ if [ ! -x "$prefix/lastal" -o ! -x "$prefix/lastdb" ]; then
+ echo "" 1>&2
+ echo "== Install LAST ============================================================" 1>&2
+ echo "LAST (Kielbasa, Wan, Sato, Horton, Frith 2011 Genome Res. 21:487) is required." 1>&2
+ echo "http://last.cbrc.jp/" 1>&2
+ echo "http://mafft.cbrc.jp/alignment/software/xxxxxxx.html " 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
exit 1
fi
fi
- if [ $distance = "scarna" ]; then
+ if [ $distance = "scarna" -o $mccaskill -eq 1 ]; then
if [ ! -x "$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 "http://mafft.cbrc.jp/alignment/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
+ if [ $distance = "dafs" -o $dafs -eq 1 ]; then
+ if [ ! -x "$prefix/dafs" ]; 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 "== Install DAFS===========================================================" 1>&2
+ echo "DAFS (Sato et al. Journal 2012 issue:page) is required." 1>&2
+ echo "http://www.ncrna.org/ " 1>&2
echo "==========================================================================" 1>&2
echo "" 1>&2
exit 1
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
+ weighti="0.0" # 2016Jul31, tbfast.c kara idou
+# if [ $distance = "global" -o $distance = "local" -o $distance = "localgenaf" -o $distance = "globalgenaf" ]; then # 2012/04, localpair --> local alignment distance
+# if [ $distance = "global" ]; then
+# distance="distonly"
+# fi
if [ $treeout -eq 1 ]; then
parttreeoutopt="-t"
groupsize=1
fi
if [ $distout -eq 1 ]; then
distoutopt="-y -T"
+ if [ $treeout -eq 0 ]; then
+ treeoutopt=""
+ fi
fi
else
if [ $treeout -eq 1 ]; then
cycle=3
fi
- if [ $nseq -gt 4000 -a $iterate -gt 1 ]; then
+ if [ $nseq -gt 60000 -a $iterate -gt 1 ]; then # 2014/Oct/22, test
echo "Too many sequences to perform iterative refinement!" 1>&2
echo "Please use a progressive method." 1>&2
exit 1
fi
+ if [ $distance = "lastmulti" -o $distance = "multi" ]; then
+ if [ $fragment -eq 0 ]; then
+ echo 'Specify --addfragments too' 1>&2
+ exit 1
+ fi
+ fi
+
+ if [ $fragment -ne 0 ]; then
+ if [ $pairspecified -eq 0 ]; then
+ distance="multi"
+ fi
+ if [ $distance != "multi" -a $distance != "hybrid" -a $distance != "lastmulti" -a $distance != "local" -a $distance != "last" -a $distance != "ktuples" -a $distance != "ktuplesmulti" ]; then
+ echo 'Specify --multipair, --lastmultipair, --lastpair, --localpair, --6merpair, --6mermultipair or --hybridpair' 1>&2
+ exit 1
+ fi
+ fi
+
+ if [ "$memopt" = " -M -B " -a "$distance" != "ktuples" ]; then
+ echo "Impossible" 1>&2
+ exit 1
+ fi
+
+ if [ $distance = "parttree" ]; then
+ if [ $mergetable != "/dev/null" ]; then
+ echo "The combination of (dp)parttree and merge is Impossible. " 1>&2
+ exit 1
+ fi
+ if [ $addfile != "/dev/null" ]; then
+ echo "The combination of (dp)parttree and add(fragments) is Impossible. " 1>&2
+ exit 1
+ fi
+ 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=" -U " # -U -l -> fast
+ cycle=1
+ elif [ $partdist = "fasta" ]; then
+ splitopt=" -S "
+ cycle=1
+ else
+ splitopt=" "
+ fi
+ fi
- if [ $distance = "sixtuples" -a \( $seed = "x" -a $seedtable = "x" \) ]; then
- localparam=" "
- elif [ $distance = "sixtuples" -a \( $seed != "x" -o $seedtable != "x" \) ]; then
+ if [ \( $distance = "ktuples" -o $distance = "ktuplesmulti" \) -a \( $seed = "x" -a $seedtable = "x" -a $ownlist = "/dev/null" -a $pdblist = "/dev/null" -a $enrichstr -eq 0 \) ]; then
+ localparam=""
+ weighti="0.0"
+ elif [ \( $distance = "ktuples" -o $distance = "ktuplesmulti" \) -a \( $seed != "x" -o $seedtable != "x" -o $ownlist != "/dev/null" -o $pdblist != "/dev/null" -o $enrichstr -eq 1 \) ]; then
if [ $cycle -lt 2 ]; then
- cycle=2 # nazeda
+ cycle=2 # disttbfast ha seed hi-taiou # chuui 2014Aug21
fi
if [ $iterate -lt 2 ]; then
echo "############################################################################" 1>&2
fi
localparam="-l "$weighti
elif [ $distance = "parttree" ]; then
- localparam=" "
+ localparam=""
+ weighti="0.0"
if [ $groupsize -gt -1 ]; then
cycle=1
fi
else
- localparam=" -l "$weighti
+ localparam="-B -l "$weighti # weighti=0 demo bunkatsu nashi
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=" "
+ if [ $oldgenafparam -ne 1 ]; then
+ laof="0.0"
+ lexp="0.0"
+# LEXP="0.0" # default = 0.0
+ usenaivepairscore="-Z"
fi
fi
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 [ $f2clext = "-E" -a $anysymbol -gt 0 ]; then
+ echo '' 1>&2
+ echo 'At present, the combination of --text and ( --anysymbol or --preservecase ) is impossible.' 1>&2
+ echo '' 1>&2
+ exit 1
+ fi
+
+ if [ $f2clext = "-E" -a $aamatrix != "/dev/null" ]; then
+ echo '' 1>&2
+ echo 'At present, the combination of --text and (--aamatrix) is impossible.' 1>&2
+ echo '' 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
+ if [ ! -s $TMPFILE/_guidetree ]; then
+ if [ $distance != "ktuples" ]; then
+ echo "Not supported yet" 1>>"$progressfile"
+ exit 1
+ fi
+ if [ $pileuporshuffle = "p" ]; then
+ echo "pileup" > $TMPFILE/_guidetree
+# weightopt=" -u " -> disttbfast.c?
+# numthreadstb=0 -> disttbfast.c
+ cycle=1 # disttbfast. shitei
+ elif [ $pileuporshuffle = "s" ]; then
+ echo "shuffle $randomseed" > $TMPFILE/_guidetree
+# numthreadstb=0 -> disttbfast.c
+# weightopt=" -u " -> disttbfast.c?
+ cycle=1 # disttbfast.c dem shitei
+ elif [ $pileuporshuffle = "C" ]; then
+ echo "very compact" > $TMPFILE/_guidetree
+ elif [ $pileuporshuffle = "c" ]; then
+ echo "compact " "$initialramusage" > $TMPFILE/_guidetree
+ elif [ $pileuporshuffle = "a" ]; then
+ echo "auto $randomseed 200" > $TMPFILE/_guidetree
+ fi
+ fi
fi
- if [ "$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;
+ if [ $nadd -gt "0" ]; then
+ if [ $fragment -eq "1" ]; then
+ addarg="$addarg0 $nadd -g -0.01"
+ addsinglearg=""
+ cycle=1 # chuui 2014Aug25
+ elif [ $fragment -eq "-1" ]; then
+ addarg="$addarg0 $nadd"
+ addsinglearg="-V" # allowlongadds, 2014/04/02
+ cycle=1 # chuui 2014Aug25
+ elif [ $fragment -eq "-2" ]; then
+ addarg="$addarg0 $nadd"
+ addsinglearg="-V" # allowlongadds + smoothing
+ add2ndhalfarg=$add2ndhalfarg" -p "
+ cycle=1 # chuui 2014Aug25
+ usenaivepairscore="-Z" # 2015Jun01
+ laof=0.0 # 2015Jun01
+ lexp=0.0 # 2015Jun01
+ else
+ addarg="$addarg0 $nadd"
+ addsinglearg=""
fi
- addarg="$addarg0 $nadd"
- cycle=1
+
+# cycle=1 # chuui 2014Aug19
iterate=0
- if [ $seed != "x" -o $seedtable != "x" ]; then
- echo 'Impossible' 1>&2;
- echo 'Use either ONE of --seed, --seedtable, --addprofile and --add.' 1>&2
- exit 1;
+# treealg=" -q " ## 2012/01/24 ## removed 2012/02/06
+ fi
+
+
+ if [ -z "$localparam" -a $fragment -eq 0 -a $distance != "parttree" ]; then
+# echo "use disttbfast"
+# echo cycle = $cycle
+ cycletbfast=1 # tbfast wo jikkou shinai
+ cycledisttbfast=$cycle # disttbfast ni -E cycle wo watasu
+ if [ $cycledisttbfast -eq 0 ]; then # --treeout de tsukau
+ cycledisttbfast=1
fi
+ else
+# echo "use tbfast"
+# echo cycle = $cycle
+ cycletbfast=$cycle # 1 ijou nara jikkou
+ cycledisttbfast=1 # disttbfast ha ikkai dake
fi
- if [ $mccaskill -eq 1 -o $rnaalifold -eq 1 -o $contrafold -eq 1 ]; then
- if [ $distance = "sixtuples" ]; then
+# echo localparam=
+# echo $localparam
+# echo cycletbfast=
+# echo $cycletbfast
+# echo cycledisttbfast=
+# echo $cycledisttbfast
+
+#exit
+
+ if [ $adjustdirection -gt 0 -a $seed != "x" ]; then
+ echo '' 1>&2
+ echo 'The combination of --adjustdirection(accurately) and --seed is not supported.' 1>&2
+ echo '' 1>&2
+ exit 1
+ fi
+
+
+ if [ $mccaskill -eq 1 -o $dafs -eq 1 -o $rnaalifold -eq 1 -o $contrafold -eq 1 ]; then
+ if [ $distance = "ktuples" ]; then
echo 'Not supported.' 1>&2
- echo 'Please add --globalpair, --localpair, --scarnapair,' 1>&2
+ echo 'Please add --globalpair, --localpair, --scarnapair, --dafspair' 1>&2
echo '--larapair, --slarapair, --foldalignlocalpair or --foldalignglobalpair' 1>&2
exit 1
fi
+ if [ $f2clext = "-E" ]; then
+ echo '' 1>&2
+ echo 'For RNA alignment, the --text mode is impossible.' 1>&2
+ echo '' 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"
+# cycle ga atode henkou sareru node koko de strategy no namae wo kimeru.
+# kokokara
+ if [ $pileuporshuffle = "p" ]; then
+ strategy="Pileup-"
+ elif [ $pileuporshuffle = "s" ]; then
+ strategy="Randomchain-"
+ elif [ $mccaskill -eq 1 -o $dafs -eq 1 -o $rnaalifold -eq 1 -o $contrafold -eq 1 ]; then
+ if [ $distance = "scarna" -o $distance = "dafs" -o $distance = "lara" -o $distance = "slara" -o $distance = "foldalignlocal" -o $distance = "foldalignglobal" ]; then
+ strategy="X-"
elif [ $distance = "global" -o $distance = "local" -o $distance = "localgenaf" -o "globalgenaf" ]; then
- strategy="Q-I"
+ strategy="Q-"
fi
elif [ $distance = "fasta" -a $sw -eq 0 ]; then
- strategy="F-I"
+ strategy="F-"
elif [ $distance = "fasta" -a $sw -eq 1 ]; then
- strategy="H-I"
+ strategy="H-"
elif [ $distance = "blast" ]; then
- strategy="B-I"
+ strategy="B-"
elif [ $distance = "global" -o $distance = "distonly" ]; then
- strategy="G-I"
+ strategy="G-"
elif [ $distance = "local" ]; then
- strategy="L-I"
+ strategy="L-"
+ elif [ $distance = "last" ]; then
+ strategy="Last-"
+ elif [ $distance = "hybrid" ]; then
+ strategy="Hybrid-"
+ elif [ $distance = "multi" ]; then
+ strategy="Multi-"
+ elif [ $distance = "lastmulti" ]; then
+ strategy="LastMulti-"
elif [ $distance = "localgenaf" ]; then
- strategy="E-I"
+ strategy="E-"
elif [ $distance = "globalgenaf" ]; then
- strategy="K-I"
+ strategy="K-"
elif [ $fft -eq 1 ]; then
strategy="FFT-"
else
strategy="NW-"
fi
+# if [ `echo "$weighti>0.0" | bc` -gt 0 ]; then
+ if [ `awk "BEGIN {print(0.0+\"$weighti\">0.0)}"` -gt 0 ]; then
+ strategy=$strategy"I"
+ fi
strategy=$strategy"NS-"
if [ $iterate -gt 0 ]; then
strategy=$strategy"i"
else
strategy=$strategy"PartTree-"$cycle
fi
+ elif [ $fragment -eq 1 ]; then
+ strategy=$strategy"fragment"
+ elif [ $fragment -eq -1 ]; then
+ strategy=$strategy"full"
+ elif [ $fragment -eq -2 ]; then
+ strategy=$strategy"long"
else
strategy=$strategy$cycle
fi
fi
if [ $outputformat = "clustal" -a $outorder = "aligned" ]; then
- outputopt=" -c $strategy -r $TMPFILE/order "
+ outputopt=" -c $strategy -r $TMPFILE/order $f2clext "
elif [ $outputformat = "clustal" -a $outorder = "input" ]; then
- outputopt=" -c $strategy "
+ outputopt=" -c $strategy $f2clext "
elif [ $outputformat = "phylip" -a $outorder = "aligned" ]; then
outputopt=" -y -r $TMPFILE/order "
elif [ $outputformat = "phylip" -a $outorder = "input" ]; then
else
outputopt="null"
fi
+# kokomade
+
+
- (
- cd $TMPFILE;
+# ( # 2017/Mar/17
+ pushd $TMPFILE > /dev/null;
- if [ $quiet -gt 0 ]; then
+ cat /dev/null > pre
- if [ $anysymbol -eq 1 ]; then
- mv infile orig
- "$prefix/replaceu" -i orig > infile 2>/dev/null || exit 1
+# echo "nseq = " $nseq 1>>"$progressfile"
+# echo "distance = " $distance 1>>"$progressfile"
+# echo "iterate = " $iterate 1>>"$progressfile"
+# echo "cycle = " $cycle 1>>"$progressfile"
+
+ if [ $anysymbol -eq 1 ]; then
+ mv infile orig
+ "$prefix/replaceu" $seqtype -i orig > infile 2>>"$progressfile" || exit 1
+ fi
+
+ if [ $mergetable != "/dev/null" ]; then
+ if [ $nadd -gt "0" ]; then
+ echo "Impossible" 1>&2
+ exit 1
fi
+# if [ $seed != "x" -o $seedtable != "x" ]; then
+# echo "This version does not support the combination of merge and seed." 1>&2
+# exit 1
+# fi
+# iterate=0 # 2013/04/16
+ mergearg="-H $seedoffset"
+ 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
+ if [ $adjustdirection -gt 0 ]; then
+ if [ $fragment -ne 0 ]; then
+ fragarg="-F" #
else
- cat /dev/null > hat3.seed
+ fragarg="-F" # 2014/02/06, do not consider other additional sequences, even in the case of --add
fi
-# cat hat3.seed
+ if [ $adjustdirection -eq 1 ]; then
+ "$prefix/makedirectionlist" $fragarg -C $numthreads -m -I $nadd -i infile -t 0.00 -r 5000 -o a > _direction 2>>"$progressfile"
+ elif [ $adjustdirection -eq 2 ]; then
+ "$prefix/makedirectionlist" $fragarg -C $numthreads -m -I $nadd -i infile -t 0.00 -r 100 -o a -d > _direction 2>>"$progressfile"
+ fi
+ "$prefix/setdirection" $mergearg -d _direction -i infile > infiled 2>>"$progressfile" || exit
+ mv infiled infile
+ if [ $anysymbol -eq 1 ]; then
+ "$prefix/setdirection" $mergearg -d _direction -i orig -r > origd 2>>"$progressfile" || exit
+ mv origd orig
+ fi
+ fi
+ if [ $seed != "x" -o $seedtable != "x" ]; then
+ if [ $pdblist != "/dev/null" -o $ownlist != "/dev/null" ]; then
+ echo "The combination of --seed and (--pdbidlist or --pdbfilelist) is impossible." 1>>"$progressfile"
+ exit 1
+ fi
+ if [ $enrich -eq 1 ]; then
+ echo "The combination of --seed and (--enrich, --enrichseq or --enrichstr) is impossible at present." 1>>"$progressfile"
+ exit 1
+ fi
+ fi
- 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
+ if [ $enrich -eq 1 ]; then
+ if [ $ownlist != "/dev/null" ]; then
+ echo "Warning: Sequence homologs of the structures given with the --pdbfilelist option cannot be collected.\n" 1>>"$progressfile"
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 $treealg -i infile > pre 2>/dev/null || exit 1
- mv hat3.seed hat3
+ echo "SEEKQUENCER (http://sysimm.ifrec.osaka-u.ac.jp/seekquencer/) is" 1>>"$progressfile"
+ if [ $pdblist != "/dev/null" ]; then
+ echo "collecting homoplogs of the input sequences and the structures given with the --pdbidlist option." 1>>"$progressfile"
+ perl "$prefix/seekquencer_premafft.pl" $seektarget -run thread -trd 2 -seqd uniref90 -blim 1000 -noin -seqf infile -idf pdblist -out seekout -mod mafftash-split 2>>"seekerr"
+ seekres="$?"
else
- "$prefix/disttbfast" -O $outnum $addarg -C $numthreads $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $algopt $treealg $scoreoutarg < infile > pre 2>/dev/null || exit 1
- mv hat3.seed hat3
+ echo "collecting homologs of the input sequences." 1>>"$progressfile"
+ perl "$prefix/seekquencer_premafft.pl" $seektarget -run thread -trd 2 -seqd uniref90 -blim 1000 -noin -seqf infile -out seekout -mod mafftash-split 2>>"seekerr"
+ seekres="$?"
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 $treealg -i infile > pre 2>/dev/null || exit 1
+ cat seekerr 1>>"$progressfile"
+
+ if [ $seekres -ne "0" ]; then
+ echo "Error in SEEKQUENCER" 1>>"$progressfile"
+ exit 1;
+ fi
+ echo "Done." 1>>"$progressfile"
+
+ if [ $enrichseq -eq 1 ]; then
+# cat seekout.seq >> infile
+ if [ $anysymbol -eq 1 ]; then
+ "$prefix/replaceu" $seqtype -i seekout.seq -o $nseq >> infile
+ cat seekout.seq >> orig
else
- "$prefix/tbfast" -O $outnum -C $numthreads $rnaopt $weightopt $treeoutopt $distoutopt $memopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $localparam $algopt -J $treealg $scoreoutarg < pre > /dev/null 2>&1 || exit 1
+ "$prefix/replaceu" $seqtype -i seekout.seq | sed 's/_os_[0-9]*_oe_//' >> infile
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
+ if [ $enrichstr -eq 1 ]; then
+ nseekstr=`wc -l < seekout.str`
+ if [ $nseekstr -gt 1 ]; then
+ cat seekout.str >> pdblist
+ pdblist="tsukaimasu"
fi
- "$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
+ fi
+ if [ $seed != "x" ]; then
+ mv infile infile2
if [ $anysymbol -eq 1 ]; then
- mv infile orig
- "$prefix/replaceu" -i orig > infile || exit 1
+ 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 $seednseq >> "$progressfile"
+# echo $#
+ while [ $# -gt 1 ]
+ do
+ shift
+# echo "num="$#
- if [ $seed != "x" ]; then
- mv infile infile2
if [ $anysymbol -eq 1 ]; then
- mv orig orig2
- cat /dev/null > orig
+ cat seed$# >> orig
+ "$prefix/replaceu" $seqtype -i seed$# -o $seedoffset > clean 2>>"$progressfile" || exit 1
+ mv clean seed$#
fi
- cat /dev/null > infile
- cat /dev/null > hat3.seed
- seedoffset=0
-# echo "seednseq="$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;
+ "$prefix/multi2hat3s" -t $nseq -o $seedoffset -i seed$# >> infile 2>>"$progressfile" || exit 1
+ cat hat3 >> hat3.seed
+# echo "$1"
+ seedoffset=`expr $seedoffset + $1`
+# echo "$1"
# echo "seedoffset="$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 [ $seedtable != "x" ]; then
- cat _seedtablefile > hat3.seed
+ done;
+# echo "seedoffset="$seedoffset
+ if [ $anysymbol -eq 1 ]; then
+ "$prefix/replaceu" $seqtype -i orig2 -o $seedoffset >> infile 2>>"$progressfile" || exit 1 # yarinaoshi
+ cat orig2 >> orig
else
- cat /dev/null > hat3.seed
+ cat infile2 >> infile
fi
-# cat hat3.seed
+ elif [ $seedtable != "x" ]; then
+ cat _seedtablefile > hat3.seed
+ elif [ $pdblist != "/dev/null" -o $ownlist != "/dev/null" ]; then
+ mv infile infile2
+ if [ $anysymbol -eq 1 ]; then
+ mv orig orig2
+ cat /dev/null > orig
+ fi
+ cat /dev/null > infile
+
+ echo "strdir = " 1>>"$progressfile"
+ echo $strdir 1>>"$progressfile"
+
+ echo "Calling DASH (http://sysimm.ifrec.osaka-u.ac.jp/dash/)" 1>>"$progressfile"
+ perl "$prefix/mafftash_premafft.pl" -p pdblist -o ownlist -d "$strdir" 2>>"dasherr"
+ dashres="$?"
+ cat dasherr 1>>"$progressfile"
- 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
+ if [ $dashres -ne "0" ]; then
+ echo "Error in DASH" 1>>"$progressfile"
+ 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 $laof -L < infile > /dev/null || exit 1
+ echo "Done." 1>>"$progressfile"
+
+ seedoffset=`grep -c '^[>|=]' instr | head -1 `
+
+ echo "# of structures = " 1>>"$progressfile"
+ echo $seedoffset 1>>"$progressfile"
+ mv hat3 hat3.seed
+
+ if [ $anysymbol -eq 1 ]; then
+ cat instr >> orig
+ "$prefix/replaceu" $seqtype -i instr -o 0 > clean 2>>"$progressfile" || exit 1
+ mv clean infile
+
+ "$prefix/replaceu" $seqtype -i orig2 -o $seedoffset >> infile 2>>"$progressfile" || exit 1 # yarinaoshi
+ cat orig2 >> orig
+ else
+ cat instr > infile
+ cat infile2 >> infile
+ fi
+ else
+ cat /dev/null > hat3.seed
+ fi
+# cat hat3.seed
+
+
+
+
+ if [ $mccaskill -eq 1 ]; then
+ "$prefix/mccaskillwrap" -s -C $numthreads -d "$prefix" -i infile > hat4 2>>"$progressfile" || exit 1
+ elif [ $dafs -eq 1 ]; then
+ "$prefix/mccaskillwrap" -G -C $numthreads -d "$prefix" -i infile > hat4 2>>"$progressfile" || exit 1
+ elif [ $contrafold -eq 1 ]; then
+ "$prefix/contrafoldwrap" -d "$prefix" -i infile > hat4 2>>"$progressfile" || exit 1
+ fi
+ if [ $distance = "fasta" ]; then
+ "$prefix/dndfast7" $swopt < infile > /dev/null 2>>"$progressfile" || exit 1
+ cat hat3.seed hat3 > hatx
+ mv hatx hat3
+ "$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>>"$progressfile" || exit 1
+ elif [ $distance = "blast" ]; then
+ "$prefix/dndblast" < infile > /dev/null 2>>"$progressfile" || exit 1
+ cat hat3.seed hat3 > hatx
+ mv hatx hat3
+ "$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>>"$progressfile" || exit 1
+ elif [ $distance = "foldalignlocal" ]; then
+ "$prefix/pairlocalalign" -C $numthreads $seqtype $foldalignopt $model -g $lexp -f $lgop -Q $spfactor -h $laof -H -d "$prefix" < infile > /dev/null 2>>"$progressfile" || exit 1
+ cat hat3.seed hat3 > hatx
+ mv hatx hat3
+ "$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>>"$progressfile" || exit 1
+ elif [ $distance = "foldalignglobal" ]; then
+ "$prefix/pairlocalalign" -C $numthreads $seqtype $foldalignopt $model -g $pgexp -f $pggop -Q $spfactor -h $pgaof -H -o -global -d "$prefix" < infile > /dev/null 2>>"$progressfile" || exit 1
+ cat hat3.seed hat3 > hatx
+ mv hatx hat3
+ "$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>>"$progressfile" || exit 1
+ elif [ $distance = "slara" ]; then
+ "$prefix/pairlocalalign" -C $numthreads -p $laraparams $seqtype $model -f $lgop -Q $spfactor -T -d "$prefix" < infile > /dev/null 2>>"$progressfile" || exit 1
+ cat hat3.seed hat3 > hatx
+ mv hatx hat3
+ "$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>>"$progressfile" || exit 1
+ elif [ $distance = "lara" ]; then
+ "$prefix/pairlocalalign" -C $numthreads -p $laraparams $seqtype $model -f $lgop -Q $spfactor -B -d "$prefix" < infile > /dev/null 2>>"$progressfile" || exit 1
+ cat hat3.seed hat3 > hatx
+ mv hatx hat3
+ "$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>>"$progressfile" || exit 1
+ elif [ $distance = "scarna" ]; then
+# "$prefix/pairlocalalign" -C $numthreads $seqtype $model -f $pggop -Q $spfactor -s -d "$prefix" < infile > /dev/null 2>>"$progressfile" || exit 1
+# cat hat3.seed hat3 > hatx
+# mv hatx hat3
+# "$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>>"$progressfile" || exit 1
+ "$prefix/tbfast" _ -C $numthreads $seqtype $model -f $pggop -Q $spfactor -s -d "$prefix" _ -+ $iterate -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>>"$progressfile" || exit 1
+ elif [ $distance = "dafs" ]; then
+ "$prefix/pairlocalalign" -C $numthreads $seqtype $model -f $pggop -Q $spfactor -G -d "$prefix" < infile > /dev/null 2>>"$progressfile" || exit 1
+ cat hat3.seed hat3 > hatx
+ mv hatx hat3
+ "$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>>"$progressfile" || exit 1
+ elif [ $distance = "global" ]; then
+# "$prefix/pairlocalalign" -u $unalignlevel $localparam -C $numthreads $seqtype $model -g $pgexp -f $pggop -Q $spfactor -h $pgaof -A $usenaivepairscore $focusarg < infile > /dev/null 2>>"$progressfile" || exit 1
+# cat hat3.seed hat3 > hatx
+# mv hatx hat3
+# "$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg $focusarg < infile > /dev/null 2>>"$progressfile" || exit 1
+ "$prefix/tbfast" _ -u $unalignlevel $localparam -C $numthreads $seqtype $model -g $pgexp -f $pggop -Q $spfactor -h $pgaof -A $usenaivepairscore $focusarg _ -+ $iterate -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg $focusarg < infile > /dev/null 2>>"$progressfile" || exit 1
+
+ elif [ $distance = "local" ]; then
+ if [ $fragment -ne 0 ]; then
+ "$prefix/pairlocalalign" $localparam $addarg -C $numthreads $seqtype $model -g $lexp -f $lgop -Q $spfactor -h $laof -L $usenaivepairscore < infile > /dev/null 2>>"$progressfile" || 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 $GEXP -K < infile > /dev/null || exit 1
+ "$prefix/addsingle" -Q 100 $legacygapopt -O $outnum $addsinglearg $addarg $add2ndhalfarg -C $numthreads $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>>"$progressfile" || exit 1
+ else
+# "$prefix/pairlocalalign" -u $unalignlevel $localparam -C $numthreads $seqtype $model -g $lexp -f $lgop -Q $spfactor -h $laof -L $usenaivepairscore $focusarg < infile > /dev/null 2>>"$progressfile" || exit 1
+# addarg wo watasanai
+# cat hat3.seed hat3 > hatx
+# mv hatx hat3
+# "$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $termgapopt $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg $focusarg < infile > /dev/null 2>>"$progressfile" || exit 1
+ "$prefix/tbfast" _ -u $unalignlevel $localparam -C $numthreads $seqtype $model -g $lexp -f $lgop -Q $spfactor -h $laof -L $usenaivepairscore $focusarg _ -+ $iterate -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $termgapopt $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg $focusarg < infile > /dev/null 2>>"$progressfile" || exit 1
+ fi
+ elif [ $distance = "globalgenaf" ]; then
+ "$prefix/pairlocalalign" -u $unalignlevel $localparam -C $numthreads $seqtype $model -g $pgexp -f $pggop -Q $spfactor -h $pgaof -O $GGOP -E $GEXP -K $usenaivepairscore < infile > /dev/null 2>>"$progressfile" || exit 1
+ cat hat3.seed hat3 > hatx
+ mv hatx hat3
+ "$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>>"$progressfile" || exit 1
+ elif [ $distance = "localgenaf" ]; then
+# "$prefix/pairlocalalign" -u $unalignlevel $localparam -C $numthreads $seqtype $model -g $lexp -f $lgop -Q $spfactor -h $laof -O $LGOP -E $LEXP -N $usenaivepairscore $focusarg < infile > /dev/null 2>>"$progressfile" || exit 1
+# cat hat3.seed hat3 > hatx
+# mv hatx hat3
+# "$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $termgapopt $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg $focusarg < infile > /dev/null 2>>"$progressfile" || exit 1
+ "$prefix/tbfast" _ -u $unalignlevel $localparam -C $numthreads $seqtype $model -g $lexp -f $lgop -Q $spfactor -h $laof -O $LGOP -E $LEXP -N $usenaivepairscore $focusarg _ -+ $iterate -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $termgapopt $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg $focusarg < infile > /dev/null 2>>"$progressfile" || exit 1
+ elif [ $distance = "last" ]; then
+ if [ $fragment -ne 0 ]; then
+ "$prefix/pairlocalalign" $addarg -C $numthreads $seqtype $model -e $last_e -w $last_m -g $lexp -f $lgop -Q $spfactor -h $laof -R $last_subopt $last_once -d "$prefix" < infile > /dev/null 2>>"$progressfile" || exit 1
cat hat3.seed hat3 > hatx
mv hatx hat3
- "$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 $LEXP -N < infile > /dev/null || exit 1
+ "$prefix/addsingle" -Q 100 $legacygapopt -O $outnum $addsinglearg $addarg $add2ndhalfarg -C $numthreads $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>>"$progressfile" || exit 1
+ else
+ "$prefix/pairlocalalign" -C $numthreads $seqtype $model -e $last_e -w $last_m -g $lexp -f $lgop -Q $spfactor -h $laof -R $last_subopt $last_once -d "$prefix" < infile > /dev/null 2>>"$progressfile" || exit 1
+# addarg wo watasanai
cat hat3.seed hat3 > hatx
mv hatx hat3
- "$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 $treealg -i infile > pre || exit 1
- mv hat3.seed hat3
+ "$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $termgapopt $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>>"$progressfile" || exit 1
+ fi
+ elif [ $distance = "lastmulti" ]; then
+ "$prefix/dndpre" $model -M 2 $addarg -C $numthreads $seqtype $model -g $lexp -f $lgop -Q $spfactor -h $laof < infile > /dev/null 2>>"$progressfile" || exit 1
+ mv hat2 hat2i
+ "$prefix/pairlocalalign" $addarg -C $numthreads $seqtype $model -e $last_e -w $last_m -g $lexp -f $lgop -Q $spfactor -h $laof -r $last_subopt $last_once -d "$prefix" < infile > /dev/null 2>>"$progressfile" || exit 1
+ cat hat3.seed hat3 > hatx
+ mv hat2 hat2n
+ mv hatx hat3
+ if [ $fragment -ne 0 ]; then
+ "$prefix/addsingle" -Q 100 $legacygapopt -d -O $outnum $addsinglearg $addarg $add2ndhalfarg -C $numthreads $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>>"$progressfile" || exit 1
+ else
+ echo "Impossible" 1>&2
+ exit 1
+ fi
+ elif [ $distance = "multi" ]; then
+ "$prefix/dndpre" $model -M 2 $addarg -C $numthreads $seqtype $model -g $lexp -f $lgop -h $laof $usenaivepairscore < infile > /dev/null 2>>"$progressfile" || exit 1
+ mv hat2 hat2i
+ "$prefix/pairlocalalign" $localparam $addarg -C $numthreads $seqtype $model -g $lexp -f $lgop -Q $spfactor -h $laof -Y $usenaivepairscore < infile > /dev/null 2>>"$progressfile" || exit 1
+ cat hat3.seed hat3 > hatx
+ mv hat2 hat2n
+ mv hatx hat3
+ if [ $fragment -ne 0 ]; then
+ "$prefix/addsingle" -Q 100 $legacygapopt -d -O $outnum $addsinglearg $addarg $add2ndhalfarg -C $numthreads $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>>"$progressfile" || exit 1
+ else
+ echo "Impossible" 1>&2
+ exit 1
+ fi
+ elif [ $distance = "hybrid" ]; then
+ "$prefix/pairlocalalign" $addarg -C $numthreads $seqtype $model -g $lexp -f $lgop -Q $spfactor -h $laof -Y < infile > /dev/null 2>>"$progressfile" || exit 1
+ cat hat3.seed hat3 > hatx
+ mv hatx hat3
+ "$prefix/disttbfast" -E 1 -s $unalignlevel $legacygapopt -W $tuplesize $termgapopt $outnum $addarg $add2ndhalfarg -C $numthreadstb $memopt $weightopt $treeinopt $treeoutopt -T -y $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $algopt $treealg $scoreoutarg < infile > /dev/null 2>>"$progressfile" || exit 1
+ if [ $fragment -ne 0 ]; then
+ "$prefix/addsingle" -Q 100 $legacygapopt -O $outnum $addsinglearg $addarg $add2ndhalfarg -C $numthreads $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>>"$progressfile" || exit 1
else
- "$prefix/disttbfast" -O $outnum $addarg -C $numthreads $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h "-"$aof $param_fft $algopt $treealg $scoreoutarg < infile > pre || exit 1
+ "$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $termgapopt $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>>"$progressfile" || exit 1
+ fi
+# elif [ $distance = "distonly" ]; then
+# "$prefix/pairlocalalign" -C $numthreads $seqtype $model -g $pgexp -f $pggop -Q $spfactor -h $pgaof -t < infile > /dev/null 2>>"$progressfile" || exit 1
+# "$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>>"$progressfile" || exit 1
+ elif [ $distance = "parttree" ]; then
+ "$prefix/splittbfast" $legacygapopt $algopt $splitopt $partorderopt $parttreeoutopt $memopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof -p $partsize -s $groupsize $treealg $outnum -i infile > pre 2>>"$progressfile" || exit 1
+ mv hat3.seed hat3
+ elif [ $distance = "ktuplesmulti" ]; then
+# "$prefix/dndpre" $model -M 1 $addarg -C $numthreads $seqtype $model -g $lexp -f $lgop -h $laof < infile > /dev/null 2>>"$progressfile" || exit 1
+# mv hat2 hat2i
+# "$prefix/disttbfast" -E 1 -s $unalignlevel $legacygapopt -W $tuplesize $termgapopt $outnum $addarg $add2ndhalfarg -C $numthreadstb $memopt $weightopt $treeinopt $treeoutopt -T -y $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $algopt $treealg $scoreoutarg < infile > /dev/null 2>>"$progressfile" || exit 1
+# mv hat2 hat2n
+ if [ $fragment -ne 0 ]; then
+ "$prefix/addsingle" -Q 100 $legacygapopt -d -W $tuplesize -O $outnum $addsinglearg $addarg $add2ndhalfarg -C $numthreads $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>>"$progressfile" || exit 1
+# "$prefix/addsingle" -Q 100 $legacygapopt -d -O $outnum $addsinglearg $addarg $add2ndhalfarg -C $numthreads $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>>"$progressfile" || exit 1
+ else
+ echo "Impossible" 1>&2
+ exit 1
+ fi
+ else
+ if [ $fragment -ne 0 ]; then
+ "$prefix/addsingle" -Q 100 $legacygapopt -W $tuplesize -O $outnum $addsinglearg $addarg $add2ndhalfarg -C $numthreads $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>>"$progressfile" || exit 1
+ else
+ "$prefix/disttbfast" -q $npickup -E $cycledisttbfast -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg -W $tuplesize $termgapopt $outnum $addarg $add2ndhalfarg -C $numthreadstb $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $algopt $treealg $scoreoutarg < infile > pre 2>>"$progressfile" || 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
+ while [ $cycletbfast -gt 1 ]
+ do
+ if [ $distance = "parttree" ]; then
+ mv pre infile
+ "$prefix/splittbfast" $legacygapopt -Z $algopt $splitopt $partorderopt $parttreeoutopt $memopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof -p $partsize -s $groupsize $treealg $outnum -i infile > pre 2>>"$progressfile" || exit 1
+ else
+ "$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $termgapopt $outnum -C $numthreadstb $rnaopt $weightopt $treeoutopt $distoutopt $memopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt -J $treealg $scoreoutarg < pre > /dev/null 2>>"$progressfile" || exit 1
+# fragment>0 no baai, nanimoshinai
+# seed youchuui!!
+ fi
+ cycletbfast=`expr $cycletbfast - 1`
+ done
+ if [ $iterate -gt 0 ]; then
+ if [ $distance = "ktuples" ]; then
+ "$prefix/dndpre" $model -M 2 -C $numthreads < pre > /dev/null 2>>"$progressfile" || exit 1
fi
+ "$prefix/dvtditr" -W $minimumweight $bunkatsuopt -E $fixthreshold -s $unalignlevel $legacygapopt $mergearg $outnum -C $numthreadsit -t $randomseed $rnaoptit $memopt $scorecalcopt $localparam -z 50 $seqtype $model -f "-"$gop -Q $spfactor -h $aof -I $iterate $weightopt $treeinopt $algoptit $treealg -p $parallelizationstrategy $scoreoutarg < pre > /dev/null 2>>"$progressfile" || exit 1
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
+ "$prefix/restoreu" $add2ndhalfarg -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 [ $distance = "foldalignglobal" ]; then
- echo "Pairwise alignments were computed by FOLDALIGN (global)" 1>&2
- echo "(Havgaard et al., 2007, PLoS Computational Biology 3:e193)." 1>&2
+
+
+
+ echo '' 1>>"$progressfile"
+ if [ $mccaskill -eq 1 ]; then
+ echo "RNA base pairing probaility was calculated by the McCaskill algorithm (1)" 1>>"$progressfile"
+ echo "implemented in Vienna RNA package (2) and MXSCARNA (3), and then" 1>>"$progressfile"
+ echo "incorporated in the iterative alignment process (4)." 1>>"$progressfile"
+ echo "(1) McCaskill, 1990, Biopolymers 29:1105-1119" 1>>"$progressfile"
+ echo "(2) Hofacker et al., 2002, J. Mol. Biol. 319:3724-3732" 1>>"$progressfile"
+ echo "(3) Tabei et al., 2008, BMC Bioinformatics 9:33" 1>>"$progressfile"
+ echo "(4) Katoh and Toh, 2008, BMC Bioinformatics 9:212" 1>>"$progressfile"
+ echo "" 1>>"$progressfile"
+ elif [ $contrafold -eq 1 ]; then
+ echo "RNA base pairing probaility was calculated by the CONTRAfold algorithm (1)" 1>>"$progressfile"
+ echo "and then incorporated in the iterative alignment process (4)." 1>>"$progressfile"
+ echo "(1) Do et al., 2006, Bioinformatics 22:e90-98" 1>>"$progressfile"
+ echo "(2) Katoh and Toh, 2008, BMC Bioinformatics 9:212" 1>>"$progressfile"
+ echo "" 1>>"$progressfile"
+ fi
+ if [ $pdblist != "/dev/null" -o $ownlist != "/dev/null" ]; then
+ echo "Input structures are decomposed into structural domains using" 1>>"$progressfile"
+ echo "Protein Domain Parser (Alexandrov & Shindyalov 2003)." 1>>"$progressfile"
+ echo "Domain pairs are aligned using the rash function in" 1>>"$progressfile"
+ echo "the ASH structural alignment package (Standley et al. 2007)." 1>>"$progressfile"
+ fi
+ if [ $pdblist != "/dev/null" ]; then
+ echo "Pre-computed alignments stored in " 1>>"$progressfile"
+ echo "DASH (http://sysimm.ifrec.osaka-u.ac.jp/dash/) are used. " 1>>"$progressfile"
+ fi
+ if [ $distance = "fasta" -o $partdist = "fasta" ]; then
+ echo "Pairwise alignments were computed by FASTA" 1>>"$progressfile"
+ echo "(Pearson & Lipman, 1988, PNAS 85:2444-2448)" 1>>"$progressfile"
+ fi
+ if [ $distance = "blast" ]; then
+ echo "Pairwise alignments were computed by BLAST" 1>>"$progressfile"
+ echo "(Altschul et al., 1997, NAR 25:3389-3402)" 1>>"$progressfile"
+ fi
+ if [ $distance = "last" -o $distance = "lastmulti" ]; then
+ echo "Pairwise alignments were computed by LAST" 1>>"$progressfile"
+ echo "http://last.cbrc.jp/" 1>>"$progressfile"
+ echo "Kielbasa, Wan, Sato, Horton, Frith 2011 Genome Res. 21:487" 1>>"$progressfile"
+ fi
+ if [ $distance = "scarna" ]; then
+ echo "Pairwise alignments were computed by MXSCARNA" 1>>"$progressfile"
+ echo "(Tabei et al., 2008, BMC Bioinformatics 9:33)." 1>>"$progressfile"
+ fi
+ if [ $distance = "dafs" ]; then
+ echo "Pairwise alignments were computed by DAFS" 1>>"$progressfile"
+ echo "(Sato et al., 2012,,,,)." 1>>"$progressfile"
+ fi
+ if [ $distance = "lara" -o $distance = "slara" ]; then
+ echo "Pairwise alignments were computed by LaRA" 1>>"$progressfile"
+ echo "(Bauer et al., 2007, BMC Bioinformatics 8:271)." 1>>"$progressfile"
+ fi
+ if [ $distance = "foldalignlocal" ]; then
+ echo "Pairwise alignments were computed by FOLDALIGN (local)" 1>>"$progressfile"
+ echo "(Havgaard et al., 2007, PLoS Computational Biology 3:e193)." 1>>"$progressfile"
+ fi
+ if [ $distance = "foldalignglobal" ]; then
+ echo "Pairwise alignments were computed by FOLDALIGN (global)" 1>>"$progressfile"
+ echo "(Havgaard et al., 2007, PLoS Computational Biology 3:e193)." 1>>"$progressfile"
+ fi
+# printf "\n" 1>>"$progressfile"
+ echo 'Strategy:' 1>>"$progressfile"
+ printf ' '$strategy 1>>"$progressfile"
+ echo ' ('$performance')' 1>>"$progressfile"
+ echo ' '$explanation 1>>"$progressfile"
+ echo '' 1>>"$progressfile"
+ echo "If unsure which option to use, try 'mafft --auto input > output'." 1>>"$progressfile"
+ echo "For more information, see 'mafft --help', 'mafft --man' and the mafft page." 1>>"$progressfile"
+ echo "" 1>>"$progressfile"
+ echo "The default gap scoring scheme has been changed in version 7.110 (2013 Oct)." 1>>"$progressfile"
+ echo "It tends to insert more gaps into gap-rich regions than previous versions." 1>>"$progressfile"
+ echo "To disable this change, add the --leavegappyregion option." 1>>"$progressfile"
+# echo "If long gaps are expected, try 'mafft --ep 0.0 --auto input > output'." 1>>"$progressfile"
+# echo "If the possibility of long gaps can be excluded, add '--ep 0.123'." 1>>"$progressfile"
+ if [ $distance = "localgenaf" -o $distance = "globalgenaf" ]; then
+ echo "" 1>>"$progressfile"
+ if [ $oldgenafparam -eq 1 ]; then
+ echo "Obsolete parameters used for this calculation." 1>>"$progressfile"
+ echo "Also try the new parameters for E-INS-i, by not specifying --oldgenafpair." 1>>"$progressfile"
+ else
+ echo "Parameters for the E-INS-i option have been changed in version 7.243 (2015 Jun)." 1>>"$progressfile"
+ echo "To switch to the old parameters, use --oldgenafpair, instead of --genafpair." 1>>"$progressfile"
fi
- printf "\n" 1>&2
- echo 'Strategy:' 1>&2
- printf ' '$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
- )
+ echo '' 1>>"$progressfile"
+
+
+ if [ $pdblist != "/dev/null" -o $ownlist != "/dev/null" ]; then
+ cat dasherr >>"$progressfile"
+ fi
+
+# ) # 2017/Mar/17
+ popd > /dev/null;
+
if [ "$outputfile" = "" ]; then
if [ "$outputopt" = "null" ]; then
cat < $TMPFILE/pre || exit 1
else
- "$prefix/f2cl" -n $namelength $outputopt < $TMPFILE/pre || exit 1
+ "$prefix/f2cl" -n $namelength $outputopt < $TMPFILE/pre 2>>/dev/null || exit 1
fi
else
if [ "$outputopt" = "null" ]; then
cat < $TMPFILE/pre > "$outputfile" || exit 1
else
- "$prefix/f2cl" -n $namelength $outputopt < $TMPFILE/pre > "$outputfile" || exit 1
+ "$prefix/f2cl" -n $namelength $outputopt < $TMPFILE/pre > "$outputfile" 2>>/dev/null || exit 1
fi
fi
cp $TMPFILE/infile.tree "$infilename.tree"
fi
+ if [ -s $TMPFILE/GuideTree ]; then # --merge no toki dake
+ cp $TMPFILE/GuideTree .
+ fi
+
if [ $distout -eq 1 ]; then
cp $TMPFILE/hat2 "$infilename.hat2"
fi
+ if [ $npickup -ne 0 ]; then
+ cp $TMPFILE/notused "$infilename.notused"
+ fi
+
+ if [ -s $TMPFILE/_deletemap ]; then
+ if [ "$mapoutfile" = "/dev/null" ]; then
+ cp $TMPFILE/_deletemap "$addfile.map"
+ else
+ cp $TMPFILE/_deletemap "$mapoutfile"
+ fi
+ fi
+
exit 0;
fi
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( " Copyright (c) 2016 Kazutaka Katoh\n" ) > "/dev/tty";
+ printf( " MBE 30:772-780 (2013), NAR 30:3059-3066 (2002)\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( "Additional arguments? (--ep #, --op #, --kappa #, etc)\n" ) > "/dev/tty";
+ printf( "Additional arguments? (--ep # --op # --kappa # etc)\n" ) > "/dev/tty";
printf( "@ " ) > "/dev/tty";
res = getline < "/dev/tty";
close( "/dev/tty" );
printf( "\n" ) > "/dev/tty";
}
system( command );
- command = sprintf( "less \"%s\"", outfile );
+ command = sprintf( "more \"%s\"", outfile );
system( command );
printf( "Press Enter to exit." ) > "/dev/tty";
res = getline < "/dev/tty";
git://source.jalview.org / jabaws.git / blobdiff