#! /bin/bash
er=0;
myself=`dirname "$0"`/`basename "$0"`; export myself
version="v7.505 (2022/Apr/10)"; export version
LANG=C; export LANG
os=`uname`
progname=`basename "$0"`
windows="no"
if [ `echo $os | grep -i cygwin` ]; then
os="cygwin"
windows="yes"
elif [ `echo $os | grep -i msys` ]; then
os="msys"
windows="yes"
elif [ `echo $os | grep -i mingw` ]; then
os="mingw"
windows="yes"
elif [ `echo $os | grep -i darwin` ]; then
os="darwin"
elif [ `echo $os | grep -i sunos` ]; then
os="sunos"
elif [ `echo $os | grep -i linux` ]; then
os="linux"
else
os="unix"
fi
#export os # iranai
if [ "$windows" = "yes" ]; then
echo "" 1>&2
echo "It may take a while before the calculation starts" 1>&2
echo "if being scanned by anti-virus software." 1>&2
echo "Also consider using a faster version for Windows 10:" 1>&2
echo "https://mafft.cbrc.jp/alignment/software/wsl.html" 1>&2
fi
if [ "$MAFFT_BINARIES" ]; then
prefix="$MAFFT_BINARIES"
else
prefix="$BIRCH/bin-$BIRCH_PLATFORM/mafftdir/libexec/mafft"
fi
export prefix # iranai
if [ $# -gt 0 ]; then
if [ "$1" = "--man" ]; then
man "$prefix/mafft.1"
exit 0;
fi
fi
if [ -x "$prefix/version" ]; then
# versionbin=`"$prefix/version" | awk '{print $1}'` # for cygwin
versionbin=`"$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 "Please send a problem report to katoh@ifrec.osaka-u.ac.jp," 1>&2
echo "if this problem remains." 1>&2
echo "" 1>&2
# exit 1
# er=1
fi
defaultiterate=0
defaultcycle=2
defaultgop="1.53"
#defaultaof="0.123"
defaultaof="0.000"
defaultlaof="0.100"
defaultlgop="-2.00"
defaultfft=1
defaultrough=0
defaultdistance="ktuples"
#defaultdistance="local"
defaultweighti="2.7"
defaultweightr="0.0"
defaultweightm="1.0"
defaultdafs=0
defaultmccaskill=0
defaultcontrafold=0
defaultalgopt=" "
defaultalgoptit=" "
defaultsbstmodel=" -b 62 "
defaultfmodel=" "
defaultkappa=" "
if [ $progname = "xinsi" -o $progname = "mafft-xinsi" ]; then
defaultfft=1
defaultcycle=1
defaultiterate=1000
defaultdistance="scarna"
defaultweighti="3.2"
defaultweightr="8.0"
defaultweightm="2.0"
defaultmccaskill=1
defaultcontrafold=0
defaultdafs=0
defaultalgopt=" -A "
defaultalgoptit=" -AB " ## chui
defaultaof="0.0"
defaultsbstmodel=" -b 62 "
defaultkappa=" "
defaultfmodel=" " # 2013/06/18
elif [ $progname = "qinsi" -o $progname = "mafft-qinsi" ]; then
defaultfft=1
defaultcycle=1
defaultiterate=1000
defaultdistance="global"
defaultweighti="3.2"
defaultweightr="8.0"
defaultweightm="2.0"
defaultmccaskill=1
defaultcontrafold=0
defaultdafs=0
defaultalgopt=" -A "
defaultalgoptit=" -AB " ## chui
defaultaof="0.0"
defaultsbstmodel=" -b 62 "
defaultkappa=" "
defaultfmodel=" " # 2013/06/18
elif [ $progname = "linsi" -o $progname = "mafft-linsi" ]; then
defaultfft=0
defaultcycle=1
defaultiterate=1000
defaultdistance="local"
elif [ $progname = "ginsi" -o $progname = "mafft-ginsi" ]; then
defaultfft=1
defaultcycle=1
defaultiterate=1000
defaultdistance="global"
elif [ $progname = "einsi" -o $progname = "mafft-einsi" ]; then
defaultfft=0
defaultcycle=1
defaultiterate=1000
defaultdistance="localgenaf"
elif [ $progname = "fftns" -o $progname = "mafft-fftns" ]; then
defaultfft=1
defaultcycle=2
defaultdistance="ktuples"
elif [ $progname = "fftnsi" -o $progname = "mafft-fftnsi" ]; then
defaultfft=1
defaultcycle=2
defaultiterate=2
defaultdistance="ktuples"
elif [ $progname = "nwns" -o $progname = "mafft-nwns" ]; then
defaultfft=0
defaultcycle=2
defaultdistance="ktuples"
elif [ $progname = "nwnsi" -o $progname = "mafft-nwnsi" ]; then
defaultfft=0
defaultcycle=2
defaultiterate=2
defaultdistance="ktuples"
fi
outputfile=""
namelength=-1
anysymbol=0
parallelizationstrategy="BAATARI2"
kappa=$defaultkappa
sbstmodel=$defaultsbstmodel
fmodel=$defaultfmodel
nmodel=" "
gexp=0
gop=$defaultgop
gopdist=$defaultgop
aof=$defaultaof
cycle=$defaultcycle
iterate=$defaultiterate
fft=$defaultfft
rough=$defaultrough
distance=$defaultdistance
forcefft=0
memopt=" "
weightopt=" "
GGOP="-6.00"
LGOP="-6.00"
LEXP="-0.000"
GEXP="-0.000"
lgop=$defaultlgop
lexp="-0.100"
laof=$defaultlaof
pggop="-2.00"
pgexp="-0.10"
pgaof="0.10"
rgop="-1.530"
rgep="-0.000"
seqtype=" "
weighti=$defaultweighti
weightr=$defaultweightr
weightm=$defaultweightm
rnaalifold=0
dafs=$defaultdafs
mccaskill=$defaultmccaskill
contrafold=$defaultcontrafold
progressfile="/dev/stderr"
anchorfile="/dev/null"
anchoropt=""
maxanchorseparation=1000
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="ktuples"
partorderopt=" -x "
treeout=0
nodeout=0
distout=0
treein=0
topin=0
treeinopt=" "
seedfiles="/dev/null"
seedtablefile="/dev/null"
pdblist="/dev/null"
ownlist="/dev/null"
strdir="$PWD"
scorematrix="/dev/null"
textmatrix="/dev/null"
treeinfile="/dev/null"
codonposfile="/dev/null"
codonscorefile="/dev/null"
rnascoremtx=" "
laraparams="/dev/null"
foldalignopt=" "
treealg=" -X 0.1 "
sueff="1.0"
maxambiguous="1.0"
dofilter=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 # ato de kezuru
enrichseq=0 # ato de kezuru
enrichstr=0 # ato de kezuru
seektarget="" # ato de kezuru
dashserver="https://sysimm.org/dash/REST1.0/"
newdash=0
newdash_originalsequenceonly=0
exclude_ho=0
fixthreshold="0.0"
bunkatsuopt=" "
npickup=0
minimumweight="0.00001" # 2016/Mar
usenaivepairscore=" "
oldgenafparam=0
sprigorous=0
treeext="none"
initialramusage="20GB"
focusarg=" "
lhlimit=" "
mpiscript="/dev/null"
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
auto=1
elif [ "$1" = "--anysymbol" ]; then
anysymbol=1
elif [ "$1" = "--preservecase" ]; then
anysymbol=1
elif [ "$1" = "--clustalout" ]; then
outputformat="clustal"
elif [ "$1" = "--phylipout" ]; then
outputformat="phylip"
elif [ "$1" = "--reorder" ]; then
outorder="aligned"
partorderopt=" "
elif [ "$1" = "--inputorder" ]; then
outorder="input"
partorderopt=" -x "
elif [ "$1" = "--unweight" ]; then
weightopt=" -u "
elif [ "$1" = "--termgappenalty" ]; then
termgapopt=" "
elif [ "$1" = "--alga" ]; then
algopt=" "
algoptit=" "
# algspecified=1
elif [ "$1" = "--algq" ]; then
algopt=" -Q "
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="ktuples"
elif [ "$1" = "--dpparttree" ]; then
distance="parttree"
partdist="localalign"
elif [ "$1" = "--fastaparttree" ]; then
distance="parttree"
partdist="fasta"
elif [ "$1" = "--treeout" ]; then
treeout=1
elif [ "$1" = "--nodeout" ]; then
nodeout=1
treeout=1
elif [ "$1" = "--distout" ]; then
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=" -X 1.0 "
sueff="1.0"
elif [ "$1" = "--minimumlinkage" ]; then
treealg=" -X 0.0 "
sueff="0.0"
elif [ "$1" = "--mixedlinkage" ]; then
shift
sueff="$1"
treealg=" -X $1"
elif [ "$1" = "--maxambiguous" ]; then
shift
maxambiguous="$1"
dofilter=1
elif [ "$1" = "--codonpos" ]; then
shift
codonposfile="$1"
if [ ! -e "$codonposfile" ]; then
echo "Cannot open $codonposfile" 1>&2
echo "" 1>&2
exit
fi
codonposopt=" -R "
elif [ "$1" = "--codonscore" ]; then
shift
codonscorefile="$1"
if [ ! -e "$codonscorefile" ]; then
echo "Cannot open $codonscorefile" 1>&2
echo "" 1>&2
exit
fi
codonscoreopt=" -S "
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="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
memopt=" -N "
elif [ "$1" = "--nuc" ]; then
seqtype="-D" # Deleted space, 2018/Dec
elif [ "$1" = "--amino" ]; then
seqtype="-P" # Deleted space, 2018/Dec
elif [ "$1" = "--fft" ]; then
fft=1
forcefft=1
elif [ "$1" = "--nofft" ]; then
fft=0
elif [ "$1" = "--quiet" ]; then
# if [ $os = "msys" ]; 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" = "--oneiteration" ]; then
oneiterationopt=" -r "
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" = "--skipanchorsremoterthan" ]; then
shift
if ! expr "$1" : "[0-9]" > /dev/null ; then
echo "Specify maximum gap length between anchors." 1>&2
exit
fi
maxanchorseparation=`expr "$1" - 0`
elif [ "$1" = "--anchors" ]; then
shift
anchorfile="$1"
anchoropt=" -l "
# memopt=" -M -B " # ato de kentou
# memopt=" -N " # no memsave
if [ ! -e "$anchorfile" ]; then
echo "Cannot open $anchorfile" 1>&2
echo "" 1>&2
exit
fi
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 "Check the argument after --threadtb, the number of threads for the progressive step." 1>&2
exit
fi
numthreadstb=`expr "$1" - 0`
elif [ "$1" = "--threadit" ]; then
shift
if ! expr "$1" : "[0-9\-]" > /dev/null ; then
echo "Check the argument after --threadit, 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" = "--bestfirst" ]; then
parallelizationstrategy="BESTFIRST"
elif [ "$1" = "--adhoc0" ]; then
parallelizationstrategy="BAATARI0"
elif [ "$1" = "--adhoc1" ]; then
parallelizationstrategy="BAATARI1"
elif [ "$1" = "--adhoc2" ]; then
parallelizationstrategy="BAATARI2"
elif [ "$1" = "--simplehillclimbing" ]; then
parallelizationstrategy="BAATARI2"
elif [ "$1" = "--scoreout" ]; then
scoreoutarg="-S -B"
elif [ "$1" = "--outnum" ]; then
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"
addfile="$1"
elif [ "$1" = "--add" ]; then
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" = "--addtotop" ]; then
shift
addarg0="-K -I"
addfile="$1"
fragment=-3
elif [ "$1" = "--smoothing" ]; then
add2ndhalfarg=$add2ndhalfarg" -p "
elif [ "$1" = "--keeplength" ]; then
add2ndhalfarg=$add2ndhalfarg" -Y "
elif [ "$1" = "--compactmapout" ]; then
add2ndhalfarg=$add2ndhalfarg" -z -Y "
elif [ "$1" = "--compactmapoutfile" ]; then
shift
add2ndhalfarg=$add2ndhalfarg" -z -Y "
mapoutfile="$1"
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" = "--aamatrix" ]; then
shift
f2clext="-N"
sbstmodel=" -b -1 "
scorematrix="$1"
if [ ! -e "$scorematrix" ]; then
echo "Cannot open $scorematrix" 1>&2
echo "" 1>&2
exit
fi
elif [ "$1" = "--textmatrix" ]; then
shift
f2clext="-E"
seqtype="-P"
fft=0
sbstmodel=" -b -2 -a "
scorematrix="$1"
if [ ! -e "$scorematrix" ]; then
echo "Cannot open $scorematrix" 1>&2
echo "" 1>&2
exit
fi
elif [ "$1" = "--text" ]; then
f2clext="-E"
seqtype="-P"
fft=0
sbstmodel=" -b -2 -a "
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
treeext="pileup"
elif [ "$1" = "--randomchain" ]; then
# treeinopt=" -U "
# treein=1
# pileuporshuffle="s"
treeext="randomchain"
elif [ "$1" = "--topin" ]; then
shift
treeinopt=" -V "
treein=1
treeinfile="$1"
echo "The --topin option has been disabled." 1>&2
echo "There was a bug in version < 6.530." 1>&2
echo "This bug has not yet been fixed." 1>&2
exit 1
elif [ "$1" = "--mpi" ]; then
mpiscript="$prefix/mpiscript"
elif [ "$1" = "--large" ]; then
treeext="memsavetree"
elif [ "$1" = "--memsavetree" ]; then
treeext="memsavetree"
elif [ "$1" = "--memsavetreex" ]; then
treeext="memsavetreex"
elif [ "$1" = "--stepadd" ]; then
treeext="stepadd"
elif [ "$1" = "--youngestlinkage" ]; then
treeext="youngestlinkage"
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
f2clext="-N"
sbstmodel=" -j $1"
# if ! expr "$1" : "[0-9]" > /dev/null ; then
# echo "Specify pam value!" 1>&2
# exit
# fi
elif [ "$1" = "--kimura" ]; then
shift
f2clext="-N"
sbstmodel=" -j $1"
# if ! expr "$1" : "[0-9]" > /dev/null ; then
# echo "Specify pam value!" 1>&2
# exit
# fi
elif [ "$1" = "--tm" ]; then
shift
f2clext="-N"
sbstmodel=" -m $1"
# if ! expr "$1" : "[0-9]" > /dev/null ; then
# echo "Specify pam value!" 1>&2
# exit
# fi
elif [ "$1" = "--bl" ]; then
shift
f2clext="-N"
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" = "--exp" ]; then
shift
# gexp="$1"
tmpval="$1"
gexp=`awk "BEGIN{ print -1.0 * \"$tmpval\"}"`
if ! expr "$gexp" : "[0-9\-]" > /dev/null ; then
printf "\nSpecify a number for exp, like --exp 0.1\n" 1>&2
printf "'$1' cannot be interpreted as a number..\n\n" 1>&2
exit
fi
elif [ "$1" = "--ep" ]; then
shift
# 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" = "--lop" ]; then
shift
lgop="$1"
elif [ "$1" = "--LOP" ]; then
shift
LGOP="$1"
elif [ "$1" = "--lep" ]; then
shift
laof="$1"
elif [ "$1" = "--lexp" ]; then
shift
lexp="$1"
elif [ "$1" = "--LEXP" ]; then
shift
LEXP="$1"
elif [ "$1" = "--GEXP" ]; then
shift
GEXP="$1"
elif [ "$1" = "--GOP" ]; then
shift
GGOP="$1"
elif [ "$1" = "--gop" ]; then
shift
pggop="$1"
elif [ "$1" = "--gep" ]; then
shift
pgaof="$1"
elif [ "$1" = "--gexp" ]; then
shift
pgexp="$1"
elif [ "$1" = "--laraparams" ]; then
shift
laraparams="$1"
elif [ "$1" = "--corethr" ]; then
shift
corethr="$1"
elif [ "$1" = "--corewin" ]; then
shift
corewin="$1"
elif [ "$1" = "--strdir" ]; then
shift
strdir="$1"
elif [ "$1" = "--pdbidlist" ]; then
echo "--pdbidlist is temporarily unavailable, 2018/Dec." 1>&2
echo "" 1>&2
exit
shift
pdblist="$1"
if [ ! -e "$pdblist" ]; then
echo "Cannot open $pdblist" 1>&2
echo "" 1>&2
exit
fi
elif [ "$1" = "--pdbfilelist" ]; then
echo "--pdbfilelist is temporarily unavailable, 2018/Dec." 1>&2
echo "" 1>&2
exit
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 [ "$1" = "--dash" ]; then
newdash=1
if [ "$distance" != "local" -a "$distance" != "localgenaf" ]; then # 2021/Oct
distance="global"
fi
if [ "$iterate" -eq 0 ]; then # 2021/Oct
iterate=3
fi
elif [ "$1" = "--dashserver" ]; then
shift
dashserver="$1"
elif [ "$1" = "--originalseqonly" ]; then
newdash_originalsequenceonly=1
elif [ "$1" = "--excludehomologs" ]; then # works with --dash only
exclude_ho=1
elif [ "$1" = "--seedtable" ]; then
shift
seedtable="y"
seedtablefile="$1"
elif [ "$1" = "--seed" ]; then
shift
seed="m"
seedfiles="$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" = "--lhlimit" ]; then # atode namae henkou
shift
lhlimit=" -q $1 "
elif [ "$1" = "--sparsepickup" ]; then
shift
npickup="$1"
elif [ $progname = "fftns" -o $progname = "nwns" ]; then
if [ "$1" -gt 0 ]; then
cycle=`expr "$1" - 0`
fi
else
echo "Unknown option: $1" 1>&2
er=1;
# exit 1;
fi
shift
done;
# echo "" 1>"$progressfile"
if [ $treeext = "memsavetree" ] || [ $treeext = "stepadd" ]; then
if [ $distance != "ktuples" ]; then
# auto -> memsave && globalpair ha erabarenai node,
# ~/maffttmp wo tsukau noha meijiteki ni shitei saretatoki dake.
if [ ! "$MAFFT_TMPDIR" ]; then # space is acceptable, 2018/Mar/17
MAFFT_TMPDIR="$HOME/maffttmp"
mkdir -p "$MAFFT_TMPDIR" || exit
fi
fi
fi
if [ ! "$MAFFT_TMPDIR" ]; then
MAFFT_TMPDIR="$TMPDIR"
fi
TMPFILE=`env TMPDIR="$MAFFT_TMPDIR" mktemp -dt "$progname.XXXXXXXXXX"`
if [ $? -ne 0 ]; then
echo "mktemp seems to be obsolete. Re-trying without -t" 1>&2
mkdir -p "$MAFFT_TMPDIR/tmp" 1>&2
TMPFILE=`mktemp -d "$MAFFT_TMPDIR/tmp/$progname.XXXXXXXXXX"`
fi
# lfs getstripe $TMPFILE 2>/dev/null && lfs setstripe -c 1 $TMPFILE # 2017/Oct
lfs getstripe "$TMPFILE" > /dev/null 2>&1 && lfs setstripe -c 1 "$TMPFILE" > /dev/null 2>&1 # 2018/Feb
if [ $os = "cygwin" ]; then
TMPFILE=`cygpath -w "$TMPFILE"` # necessary to pass path to f2cl on cyswin, somehow unnecessary in msys.
fi
# umask 077 # 2021/Jan
# mkdir "$TMPFILE" || er=1
function removetmpfile() { # for MPI
while true
do
rm -rf "$TMPFILE" && break
echo Retrying to remove "$TMPFILE". It may take several seconds. 1>&2
sleep 2
done
}
if [ $debug -eq 1 ]; then
# 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 $TMPFILE " 0 15
trap "popd > /dev/null 2>&1; tar cfv - \"$TMPFILE\" | gzip -c > debuginfo.tgz; removetmpfile" 0 15
else
# trap "rm -rf $TMPFILE" 0 15
trap "removetmpfile" 0 15
fi
if [ $# -eq 1 ]; then
if [ -r "$1" -o "$1" = - ]; then
if [ -r "$addfile" ]; then
printf '';
else
echo "$0": Cannot open "$addfile". 1>&2
echo "" 1>&2
exit 1;
fi
cat "$1" | tr "\r" "\n" > "$TMPFILE/infile"
echo "" >> "$TMPFILE/infile"
cat "$addfile" | tr "\r" "\n" | grep -v "^$" > "$TMPFILE/_addfile"
if [ $dofilter -eq 1 ]; then
# mv "$TMPFILE/infile" "$TMPFILE/_tofilter"
# "$prefix/filter" -m $maxambiguous $seqtype -i "$TMPFILE/_tofilter" > "$TMPFILE/infile" 2>>"$progressfile" || exit 1
mv "$TMPFILE/_addfile" "$TMPFILE/_tofilter"
"$prefix/filter" -m $maxambiguous $seqtype -i "$TMPFILE/_tofilter" > "$TMPFILE/_addfile" 2>>"$progressfile" || exit 1
fi
cat "$TMPFILE/_addfile" >> "$TMPFILE/infile"
cat "$scorematrix" | tr "\r" "\n" | grep -v "^$" > "$TMPFILE/_aamtx"
cat "$mergetable" | tr "\r" "\n" | grep -v "^$" > "$TMPFILE/_subalignmentstable"
cat "$treeinfile" | tr "\r" "\n" | grep -v "^$" > "$TMPFILE/_guidetree"
cat "$codonposfile" | tr "\r" "\n" | grep -v "^$" > "$TMPFILE/_codonpos"
cat "$codonscorefile" | tr "\r" "\n" | grep -v "^$" > "$TMPFILE/_codonscore"
cat "$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 "$ownlist" | tr "\r" "\n" | grep -v "^$" > "$TMPFILE/ownlist"
cat "$anchorfile" | tr "\r" "\n" | grep -v "^$" > "$TMPFILE/_externalanchors"
SAVEIFS=$IFS
# Fixed a bug: 'n' was misinterpreted as delimiter, 2020/Jun/19
IFS=$'\n'
filelist="$1
$addfile
$scorematrix
$mergetable
$treeinfile
$codonposfile
$codonscorefile
$seedtablefile
$laraparams
$pdblist
$ownlist"
for f in $filelist; do
file "$f" 2>/dev/null | grep -e 'UTF-16' -e 'UTF-32' >& /dev/null && printf "$f: UTF-16 or UTF-32? Convert this file to ASCII\n\n" 1>&2 && exit 1;
done
IFS=$SAVEIFS
# echo $seedfiles
infilename="$1"
seedfilesintmp="/dev/null"
seednseq="0"
set $seedfiles > /dev/null
while [ $# -gt 1 ];
do
shift
if [ -r "$1" ]; then
cat "$1" | tr "\r" "\n" > "$TMPFILE/seed$#"
file "$1" | grep -e 'UTF-16' -e 'UTF-32' >& /dev/null && printf "$1: UTF-16 or UTF-32? Convert this file to ASCII\n\n" 1>&2 && exit 1;
else
echo "$0": Cannot open "$1". 1>&2
echo "" 1>&2
exit 1;
fi
seednseq=$seednseq" "`grep -c '^[>|=]' "$TMPFILE/seed$#"`
seedfilesintmp=$seedfilesintmp" "seed$#
done
# ls $TMPFILE
# echo $seedfilesintmp
# echo $seednseq
else
echo "$0": Cannot open "$1". 1>&2
echo "" 1>&2
er=1
# exit 1;
fi
else
# echo '$#'"=$#" 1>&2
er=1
fi
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 $numthreads '+' 1`
# fi
elif [ "$windows" = "yes" ]; then
# numthreads=`wmic cpu get NumberOfCores | head -2 | tail -1 | awk '{print $1}'`
numthreads=`wmic cpu get NumberOfCores | awk 'BEGIN{n=0} {n+=$1} END{print n}'`
else
echo "Cannot count the number of physical cores." 1>>"$progressfile"
exit 1
fi
echo "OS = "$os 1>>"$progressfile"
echo "The number of physical cores = " $numthreads 1>>"$progressfile"
fi
if [ $numthreadstb -lt 0 ]; then
if [ $numthreads -lt 16 -o "$mpiscript" != "/dev/null" ]; then # mpi: museigen, multithread: 16 made
# if [ $numthreads -lt 31 ]; then
numthreadstb=$numthreads
else
numthreadstb=16
fi
fi
if [ $numthreadsit -lt 0 ]; then
if [ $numthreads -lt 8 ]; then
numthreadsit=$numthreads
else
numthreadsit=8
fi
fi
if [ $numthreadsit -eq 0 -a $parallelizationstrategy = "BESTFIRST" ]; then
echo 'Impossible' 1>&2;
exit 1;
fi
if [ "$addarg0" != " " ]; then
# iterate=0 # 2013/03/23 -> commented out, 2017/12
"$prefix/countlen" < "$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" 2>>"$progressfile"
nseq=`awk '{print $1}' "$TMPFILE/size"`
nlen=`awk '{print $3}' "$TMPFILE/size"`
if [ $nlen -lt 3000 -a $nseq -lt 100 ]; then
distance="local"
iterate=1000
cycle=1
treeext="none"
elif [ $nlen -lt 1000 -a $nseq -lt 200 ]; then
distance="local"
iterate=2
cycle=1
treeext="none"
elif [ $nlen -lt 10000 -a $nseq -lt 500 ]; then
distance="ktuples"
iterate=2
cycle=2
treeext="none"
elif [ $nseq -lt 20000 ]; then # changed from 10000 2014/Oct/4
distance="ktuples"
iterate=0
cycle=2
treeext="none"
elif [ $nseq -lt 100000 ]; then # changed from 50000 2017/Nov/24
distance="ktuples"
iterate=0
cycle=2
if [ $fragment -eq 0 -a "$mergetable" = "/dev/null" ]; then
treeext="memsavetree"
fi
elif [ $nseq -lt 200000 ]; then # changed from 90000 2017/Nov/24
distance="ktuples"
iterate=0
cycle=1
if [ $fragment -eq 0 -a "$mergetable" = "/dev/null" ]; then
treeext="memsavetree"
fi
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 [ $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"
if [ $norg -eq 0 ]; then
echo "" 1>>"$progressfile"
echo "The reference sequence was removed because of ambiguous letters?" 1>>"$progressfile"
echo "" 1>>"$progressfile"
exit 1;
fi
# nagasa check!
# if [ $npair -gt 10000000 -o $nlen -gt 5000 ]; then # 2017/Oct
if [ $npair -gt 10000000 -o $nlen -gt 5000 -o $nadd -gt 500000 ]; then # 2021/Dec pairlocalalign to buntan
distance="ktuples"
echo "use ktuples, size=$tuplesize!" 1>>"$progressfile"
# elif [ $npair -gt 3000000 -o $nlen -gt 5000 ]; then # 2017/Oct
elif [ $npair -gt 3000000 -o $nlen -gt 5000 ]; then # 2017/Oct
distance="multi"
weighti="0.0"
echo "use multipair, weighti=0.0!" 1>>"$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>>"$progressfile"
exit 1;
fi
if [ `awk "BEGIN {print( 0.0+\"$maxambiguous\" < 0.0 || 0.0+\"$maxambiguous\" > 1.0 )}"` -gt 0 ]; then
printf "\n%s\n\n" "The argument of --maxambiguous must be between 0.0 and 1.0" 1>>"$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
iteratelimit=16
fi
if [ $iterate -gt $iteratelimit ]; then #??
iterate=$iteratelimit
fi
if [ $rnaalifold -eq 1 ]; then
rnaopt=" -e $rgep -o $rgop -c $weightm -r $weightr -R $rnascoremtx "
# rnaoptit=" -o $rgop -BT -c $weightm -r $weightr -R "
rnaoptit=" -o $rgop -F -c $weightm -r $weightr -R "
elif [ $mccaskill -eq 1 -o $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 "
else
rnaopt=" "
rnaoptit=" -F "
fi
# 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 " MAFFT" $version 1>&2
# echo "" 1>&2
# echo " Input format: fasta" 1>&2
# echo "" 1>&2
# echo " Usage: `basename $0` [options] inputfile > outputfile" 1>&2
echo " https://mafft.cbrc.jp/alignment/software/" 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 "" 1>&2
echo "High speed:" 1>&2
echo " % mafft in > out" 1>&2
echo " % mafft --retree 1 in > out (fast)" 1>&2
echo "" 1>&2
echo "High accuracy (for <~200 sequences x <~2,000 aa/nt):" 1>&2
echo " % mafft --maxiterate 1000 --localpair in > out (% linsi in > out is also ok)" 1>&2
echo " % mafft --maxiterate 1000 --genafpair in > out (% einsi in > out)" 1>&2
echo " % mafft --maxiterate 1000 --globalpair in > out (% ginsi in > out)" 1>&2
echo "" 1>&2
echo "If unsure which option to use:" 1>&2
echo " % mafft --auto in > out" 1>&2
echo "" 1>&2
# echo "Other options:" 1>&2
echo "--op # : Gap opening penalty, default: 1.53" 1>&2
echo "--ep # : Offset (works like gap extension penalty), default: 0.0" 1>&2
echo "--maxiterate # : Maximum number of iterative refinement, default: 0" 1>&2
echo "--clustalout : Output: clustal format, default: fasta" 1>&2
echo "--reorder : Outorder: aligned, default: input order" 1>&2
echo "--quiet : Do not report progress" 1>&2
echo "--thread # : Number of threads (if unsure, --thread -1)" 1>&2
echo "--dash : Add structural information (Rozewicki et al, submitted)" 1>&2
# echo "" 1>&2
# echo " % mafft --maxiterate 1000 --localpair in > out (L-INS-i)" 1>&2
# echo " most accurate in many cases, assumes only one alignable domain" 1>&2
# echo "" 1>&2
# echo " % mafft --maxiterate 1000 --genafpair in > out (E-INS-i)" 1>&2
# echo " works well if many unalignable residues exist between alignable domains" 1>&2
# echo "" 1>&2
# echo " % mafft --maxiterate 1000 --globalpair in > out (G-INS-i)" 1>&2
# echo " suitable for globally alignable sequences " 1>&2
# echo "" 1>&2
# echo " % mafft --maxiterate 1000 in > out (FFT-NS-i)" 1>&2
# echo " accurate and slow, iterative refinement method " 1>&2
# echo "" 1>&2
# echo "If the input sequences are long (~1,000,000nt)," 1>&2
# echo " % mafft --retree 1 --memsave --fft in > out (FFT-NS-1-memsave, new in v5.8)" 1>&2
# echo "" 1>&2
# echo "If many (~5,000) sequences are to be aligned," 1>&2
# echo "" 1>&2
# echo " % mafft --retree 1 [--memsave] --nofft in > out (NW-NS-1, new in v5.8)" 1>&2
# echo "" 1>&2
# echo " --localpair : All pairwise local alignment information is included" 1>&2
# echo " to the objective function, default: off" 1>&2
# echo " --globalpair : All pairwise global alignment information is included" 1>&2
# echo " to the objective function, default: off" 1>&2
# echo " --op # : Gap opening penalty, default: $defaultgop " 1>&2
# echo " --ep # : Offset (works like gap extension penalty), default: $defaultaof " 1>&2
# echo " --bl #, --jtt # : Scoring matrix, default: BLOSUM62" 1>&2
# echo " Alternatives are BLOSUM (--bl) 30, 45, 62, 80, " 1>&2
# echo " or JTT (--jtt) # PAM. " 1>&2
# echo " --nuc or --amino : Sequence type, default: auto" 1>&2
# echo " --retree # : The number of tree building in progressive method " 1>&2
# echo " (see the paper for detail), default: $defaultcycle " 1>&2
# echo " --maxiterate # : Maximum number of iterative refinement, default: $defaultiterate " 1>&2
# if [ $defaultfft -eq 1 ]; then
# echo " --fft or --nofft: FFT is enabled or disabled, default: enabled" 1>&2
# else
# echo " --fft or --nofft: FFT is enabled or disabled, default: disabled" 1>&2
# fi
# echo " --memsave: Memory saving mode" 1>&2
# echo " (for long genomic sequences), default: off" 1>&2
# echo " --clustalout : Output: clustal format, default: fasta" 1>&2
# echo " --reorder : Outorder: aligned, default: input order" 1>&2
# echo " --quiet : Do not report progress" 1>&2
# echo "-----------------------------------------------------------------------------" 1>&2
exit 1;
fi
if [ $sw -eq 1 ]; then
swopt=" -A "
else
swopt=" "
fi
if [ $distance = "fasta" -o $partdist = "fasta" ]; then
if [ ! "$FASTA_4_MAFFT" ]; then
FASTA_4_MAFFT=`which fasta34`
fi
if [ ! -x "$FASTA_4_MAFFT" ]; then
echo "" 1>&2
echo "== Install FASTA ========================================================" 1>&2
echo "This option requires the fasta34 program (FASTA version x.xx or higher)" 1>&2
echo "installed in your PATH. If you have the fasta34 program but have renamed" 1>&2
echo "(like /usr/local/bin/myfasta), set the FASTA_4_MAFFT environment variable" 1>&2
echo "to point your fasta34 (like setenv FASTA_4_MAFFT /usr/local/bin/myfasta)." 1>&2
echo "=========================================================================" 1>&2
echo "" 1>&2
exit 1
fi
fi
if [ $distance = "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
echo "== Install LaRA =========================================================" 1>&2
echo "This option requires LaRA (Bauer et al. http://www.planet-lisa.net/)." 1>&2
echo "The executable have to be renamed to 'mafft_lara' and installed into " 1>&2
echo "the $prefix directory. " 1>&2
echo "A configuration file of LaRA also have to be given" 1>&2
echo "mafft-xinsi --larapair --laraparams parameter_file" 1>&2
echo "mafft-xinsi --slarapair --laraparams parameter_file" 1>&2
echo "=========================================================================" 1>&2
echo "" 1>&2
exit 1
fi
if [ ! -s "$laraparams" ]; then
echo "" 1>&2
echo "== Configure LaRA =======================================================" 1>&2
echo "A configuration file of LaRA have to be given" 1>&2
echo "mafft-xinsi --larapair --laraparams parameter_file" 1>&2
echo "mafft-xinsi --slarapair --laraparams parameter_file" 1>&2
echo "=========================================================================" 1>&2
echo "" 1>&2
exit 1
fi
fi
if [ $distance = "foldalignlocal" -o $distance = "foldalignglobal" ]; then
if [ ! -x "$prefix/foldalign210" ]; then
echo "" 1>&2
echo "== Install FOLDALIGN ====================================================" 1>&2
echo "This option requires FOLDALIGN (Havgaard et al. http://foldalign.ku.dk/)." 1>&2
echo "The executable have to be renamed to 'foldalign210' and installed into " 1>&2
echo "the $prefix directory. " 1>&2
echo "=========================================================================" 1>&2
echo "" 1>&2
exit 1
fi
fi
if [ $distance = "scarna" -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://mafft.cbrc.jp/alignment/software/source.html " 1>&2
echo "==========================================================================" 1>&2
echo "" 1>&2
exit 1
fi
fi
if [ $distance = "dafs" -o $dafs -eq 1 ]; then
if [ ! -x "$prefix/dafs" ]; then
echo "" 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
fi
fi
if [ $contrafold -eq 1 ]; then
if [ ! -x "$prefix/contrafold" ]; then
echo "" 1>&2
echo "== Install CONTRAfold ===================================================" 1>&2
echo "This option requires CONTRAfold" 1>&2
echo "(Do et al. http://contra.stanford.edu/contrafold/)." 1>&2
echo "The executable 'contrafold' have to be installed into " 1>&2
echo "the $prefix directory. " 1>&2
echo "=========================================================================" 1>&2
echo "" 1>&2
exit 1
fi
fi
#old
# if [ $treeout -eq 1 ]; then
# parttreeoutopt="-t"
# if [ $cycle -eq 0 ]; then
# treeoutopt="-t -T"
# groupsize=1
# iterate=0
# if [ $distance = "global" -o $distance = "local" -o $distance = "localgenaf" -o $distance = "globalgenaf" ]; then
# distance="distonly"
# fi
# else
# treeoutopt="-t"
# fi
# else
# parttreeoutopt=" "
# if [ $cycle -eq 0 ]; then
# treeoutopt="-t -T"
# iterate=0
# if [ $distance = "global" -o $distance = "local" -o $distance = "localgenaf" -o $distance = "globalgenaf" ]; then
# distance="distonly"
# fi
# else
# treeoutopt=" "
# fi
# fi
#new
if [ $cycle -eq 0 ]; then
if [ $nodeout -eq 1 ]; then
treeoutopt="-^ -T"
else
treeoutopt="-t -T"
fi
iterate=0
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
else
parttreeoutopt=" "
fi
if [ $distout -eq 1 ]; then
distoutopt="-y -T"
if [ $treeout -eq 0 ]; then
treeoutopt=""
fi
fi
else
if [ $nodeout -eq 1 ]; then
if [ $iterate -gt 0 ]; then
echo "The --nodeout option supports only progressive method (--maxiterate 0) for now." 1>&2
exit 1
fi
parttreeoutopt="-t"
treeoutopt="-^"
elif [ $treeout -eq 1 ]; then
parttreeoutopt="-t"
treeoutopt="-t"
else
parttreeoutopt=" "
treeoutopt=" "
fi
if [ $distout -eq 1 ]; then
distoutopt="-y"
fi
fi
#
formatcheck=`grep -c '^[[:blank:]]\+>' "$TMPFILE/infile" | head -1 `
if [ $formatcheck -gt 0 ]; then
echo "The first character of a description line must be " 1>&2
echo "the greater-than (>) symbol, not a blank." 1>&2
echo "Please check the format around the following line(s):" 1>&2
grep -n '^[[:blank:]]\+>' "$TMPFILE/infile" 1>&2
exit 1
fi
nseq=`grep -c '^[>|=]' "$TMPFILE/infile" | head -1 `
if [ $nseq -eq 2 ]; then
cycle=1
fi
if [ $cycle -gt 3 ]; then
cycle=3
fi
if [ $nseq -gt 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 [ \( $distance = "ktuples" -o $distance = "ktuplesmulti" \) -a \( $seed = "x" -a $seedtable = "x" -a $ownlist = "/dev/null" -a $pdblist = "/dev/null" -a $enrichstr -eq 0 -a $newdash -eq 0 \) ]; then
localparam=""
weighti="0.0"
elif [ \( $distance = "ktuples" -o $distance = "ktuplesmulti" \) -a \( $seed != "x" -o $seedtable != "x" -o $ownlist != "/dev/null" -o $pdblist != "/dev/null" -o $enrichstr -eq 1 -o $newdash -eq 1 \) ]; then
if [ $cycle -lt 2 ]; then
cycle=2 # disttbfast ha seed hi-taiou # chuui 2014Aug21
fi
if [ $iterate -lt 2 ]; then
echo "############################################################################" 1>&2
echo "# Warning:" 1>&2
echo "# Progressive alignment method is incompatible with the --seed option." 1>&2
echo "# Automatically switched to the iterative refinement method." 1>&2
echo "# " 1>&2
echo "# Also consider using the '--add' option, which is compatible with" 1>&2
echo "# the progressive method and FASTER than the '--seed' option." 1>&2
echo "# Usage is:" 1>&2
echo "# % mafft --add newSequences existingAlignment > output" 1>&2
echo "############################################################################" 1>&2
iterate=2
fi
localparam="-l "$weighti
elif [ $distance = "parttree" ]; then
localparam=""
weighti="0.0"
if [ $groupsize -gt -1 ]; then
cycle=1
fi
else
# localparam="-B -l "$weighti # weighti=0 demo bunkatsu nashi
localparam="-l "$weighti # -B (bunkatsunashi) ha dvtditr.c de taiou (17/Jan/15)
if [ $cycle -gt 1 ]; then # 09/01/08
cycle=1
fi
fi
if [ $distance = "localgenaf" -o $distance = "globalgenaf" ]; then
aof="0.000"
if [ $oldgenafparam -ne 1 ]; then
laof="0.0"
lexp="0.0"
# LEXP="0.0" # default = 0.0
usenaivepairscore="-Z"
fi
fi
# if [ $nseq -gt 5000 ]; then
# fft=0
# fi
if [ $forcefft -eq 1 ]; then
param_fft=" -G "
fft=1
elif [ $fft -eq 1 ]; then
param_fft=" -F "
else
param_fft=" "
fi
if [ $seed != "x" -a $seedtable != "x" ]; then
echo 'Use either one of seedtable and seed. Not both.' 1>&2
exit 1
fi
if [ $f2clext = "-E" -a $anysymbol -gt 0 ]; then
echo '' 1>&2
echo 'The combination of --text and ( --anysymbol or --preservecase ) is impossible.' 1>&2
echo '' 1>&2
exit 1
fi
# if [ $f2clext = "-E" -a $scorematrix != "/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
memsavetree=0
if [ $treeext != "none" ]; then
if [ $distance == "ktuples" ]; then
treein=1
treeinopt=" -U "
if [ $treeext == "randomchain" ]; then
echo "shuffle $randomseed" > "$TMPFILE/_guidetree"
cycle=1 # disttbfast.c dem shitei
elif [ $treeext == "pileup" ]; then
echo "pileup" > "$TMPFILE/_guidetree"
cycle=1 # disttbfast. shitei
elif [ $treeext == "memsavetree" ]; then
echo "very compact" > "$TMPFILE/_guidetree"
memsavetree=1
elif [ $treeext == "memsavetreex" ]; then
echo "compact " "$initialramusage" > "$TMPFILE/_guidetree"
memsavetree=1
elif [ $treeext == "stepadd" ]; then
echo "stepadd" > "$TMPFILE/_guidetree"
memsavetree=1
elif [ $treeext == "youngestlinkage" ]; then
echo "youngestlinkage" > "$TMPFILE/_guidetree"
memsavetree=1
else
echo "error in mafft.tmpl"
exit
fi
else # globalpair, localpair, genafpair, oldgenafpair
# treein, treeinopt ha kimaranai
if [ $treeext == "memsavetree" -o $treeext == "stepadd" ]; then
memsavetree=1
else
echo "With globalpair, localpair or genafpair," 1>>"$progressfile"
echo "Use --large, --minimumlinkage, --averagelinkage or --mixedlinkage." 1>>"$progressfile"
echo "--$treeext is supported only with --6merpair." 1>>"$progressfile"
echo '' 1>>"$progressfile"
exit
fi
fi
if [ $iterate -gt 0 ]; then
echo 'Iterative refinment is not supported for --large or --'$treeext 1>>"$progressfile"
echo '' 1>>"$progressfile"
exit 1
fi
if [ $fragment -ne 0 ]; then
echo '--addfragments, --addfull or --addlong is not yet supported for --large or --'$treeext 1>>"$progressfile"
echo "Use --add newsequences --$treeext" 1>>"$progressfile"
echo "Or, --addfragments (long, full) newsequences, without --"$treeext 1>>"$progressfile"
echo '' 1>>"$progressfile"
exit 1
fi
if [ "$mergetable" != "/dev/null" ]; then # 2018/Mar/2
echo '--merge is not yet supported for --large or --'$treeext 1>>"$progressfile"
echo "Use --merge without --"$treeext 1>>"$progressfile"
echo '' 1>>"$progressfile"
exit 1
fi
fi
if [ $nadd -gt "0" ]; then
if [ $fragment -eq "1" ]; then
addarg="$addarg0 $nadd -g -0.01"
addsinglearg=""
cycle=1 # chuui 2014Aug25
iterate=0
elif [ $fragment -eq "-1" ]; then
addarg="$addarg0 $nadd"
addsinglearg="-V" # allowlongadds, 2014/04/02
cycle=1 # chuui 2014Aug25
iterate=0
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
iterate=0
elif [ $fragment -eq "-3" ]; then
addarg="$addarg0 $nadd"
addsinglearg="-x" # add to top, 2021/12/31
cycle=1 # chuui 2014Aug25
iterate=0
else
addarg="$addarg0 $nadd"
addsinglearg=""
# iterate=1 # iterate ha shitei dori
bunkatsuopt=" -B " # fftnsi demo bunktasu shinai
if [ "$add2ndhalfarg" != " " ]; then
if [ $auto -eq 1 -o $iterate -gt 0 ]; then
# echo '' 1>>"$progressfile"
# echo 'The --keeplength and --mapout options are not supported' 1>>"$progressfile"
# echo 'with the --auto or --maxiterate >0 options.' 1>>"$progressfile"
# echo 'Use the --maxiterate 0 option (= progressive method).' 1>>"$progressfile"
# echo '' 1>>"$progressfile"
# exit 1
iterate=0
fi
fi
fi
# cycle=1 # chuui 2014Aug19
# iterate=0
# treealg=" -q " ## 2012/01/24 ## removed 2012/02/06
else
if [ "$add2ndhalfarg" != " " ]; then
echo '' 1>>"$progressfile"
echo 'The --keeplength and --mapout options are supported' 1>>"$progressfile"
echo 'only with --add, --addfragments or --addlong.' 1>>"$progressfile"
echo '' 1>>"$progressfile"
exit 1
fi
fi
if [ "$codonposfile" != "/dev/null" -o "$codonscorefile" != "/dev/null" ]; then
if [ $nadd -eq "0" -o $fragment -eq "0" ]; then
echo '' 1>>"$progressfile"
echo "'--codonpos' and '--codonscore' options are supported only with the '--6merpair --addfragments' option." 1>>"$progressfile"
echo '' 1>>"$progressfile"
exit 1
fi
if [ $distance != "ktuples" ]; then # ato de taiou
echo '' 1>>"$progressfile"
echo "'--codonpos' and '--codonscore' options are supported only with the '--6merpair --addfragments' option, at this point." 1>>"$progressfile"
echo '' 1>>"$progressfile"
exit 1
fi
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
# 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, --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
# cycle ga atode henkou sareru node koko de strategy no namae wo kimeru.
# kokokara
if [ $treeext = "pileup" ]; then
strategy="Pileup-"
elif [ $treeext = "randomchain" ]; 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-"
fi
elif [ $distance = "fasta" -a $sw -eq 0 ]; then
strategy="F-"
elif [ $distance = "fasta" -a $sw -eq 1 ]; then
strategy="H-"
elif [ $distance = "blast" ]; then
strategy="B-"
elif [ $distance = "global" -o $distance = "distonly" ]; then
strategy="G-"
elif [ $distance = "local" ]; then
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-"
elif [ $distance = "globalgenaf" ]; then
strategy="K-"
elif [ $fft -eq 1 ]; then
strategy="FFT-"
else
strategy="NW-"
fi
if [ $memsavetree -eq 1 ]; then
strategy=$strategy"large-"
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"
elif [ $distance = "parttree" ]; then
if [ $partdist = "fasta" ]; then
strategy=$strategy"FastaPartTree-"$cycle
elif [ $partdist = "localalign" ]; then
strategy=$strategy"DPPartTree-"$cycle
else
strategy=$strategy"PartTree-"$cycle
fi
elif [ $fragment -eq 1 ]; then
strategy=$strategy"fragment"
elif [ $fragment -eq -1 ]; then
strategy=$strategy"full"
elif [ $fragment -eq -2 ]; then
strategy=$strategy"long"
elif [ $fragment -eq -3 ]; then
strategy=$strategy"top"
else
strategy=$strategy$cycle
fi
explanation='?'
performance='Not tested.'
if [ $strategy = "F-INS-i" ]; then
explanation='Iterative refinement method (<'$iterate') with LOCAL pairwise alignment information'
performance='Most accurate, but very slow'
elif [ $strategy = "L-INS-i" ]; then
explanation='Iterative refinement method (<'$iterate') with LOCAL pairwise alignment information'
performance='Probably most accurate, very slow'
elif [ $strategy = "E-INS-i" ]; then
explanation='Iterative refinement method (<'$iterate') with LOCAL pairwise alignment with generalized affine gap costs (Altschul 1998)'
performance='Suitable for sequences with long unalignable regions, very slow'
elif [ $strategy = "G-INS-i" ]; then
explanation='Iterative refinement method (<'$iterate') with GLOBAL pairwise alignment information'
performance='Suitable for sequences of similar lengths, very slow'
elif [ $strategy = "X-INS-i" ]; then
explanation='RNA secondary structure information is taken into account.'
performance='For short RNA sequences only, extremely slow'
elif [ $strategy = "F-INS-1" ]; then
explanation='Progressive method incorporating LOCAL pairwise alignment information'
elif [ $strategy = "L-INS-1" ]; then
explanation='Progressive method incorporating LOCAL pairwise alignment information'
elif [ $strategy = "G-INS-1" ]; then
explanation='Progressive method incorporating GLOBAL pairwise alignment information'
elif [ $strategy = "FFT-NS-i" -o $strategy = "NW-NS-i" ]; then
explanation='Iterative refinement method (max. '$iterate' iterations)'
if [ $iterate -gt 2 ]; then
performance='Accurate but slow'
else
performance='Standard'
fi
elif [ $strategy = "FFT-NS-2" -o $strategy = "NW-NS-2" ]; then
explanation='Progressive method (guide trees were built '$cycle' times.)'
performance='Fast but rough'
elif [ $strategy = "FFT-NS-1" -o $strategy = "NW-NS-1" ]; then
explanation='Progressive method (rough guide tree was used.)'
performance='Very fast but very rough'
fi
if [ $outputformat = "clustal" -a $outorder = "aligned" ]; then
outputopt=" -c $strategy -r $TMPFILE/order $f2clext "
elif [ $outputformat = "clustal" -a $outorder = "input" ]; then
outputopt=" -c $strategy $f2clext "
elif [ $outputformat = "phylip" -a $outorder = "aligned" ]; then
outputopt=" -y -r $TMPFILE/order "
elif [ $outputformat = "phylip" -a $outorder = "input" ]; then
outputopt=" -y "
elif [ $outputformat = "pir" -a $outorder = "aligned" ]; then
outputopt=" -f -r $TMPFILE/order "
else
outputopt="-f"
fi
if [ $newdash_originalsequenceonly -eq 1 ]; then
outputopt="$outputopt -d "
fi
# kokomade
pushd "$TMPFILE" > /dev/null
cat /dev/null > pre
# 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 [ $adjustdirection -gt 0 ]; then
if [ $fragment -ne 0 ]; then
fragarg="-F" #
else
fragarg="-F" # 2014/02/06, do not consider other additional sequences, even in the case of --add
fi
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
if [ $newdash -eq 1 ]; then
echo "The combination of --seed and --dash is impossible at present." 1>>"$progressfile"
exit 1
fi
fi
# 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
# 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
# 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
# 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/replaceu" $seqtype -i seekout.seq | sed 's/_os_[0-9]*_oe_//' >> infile
# fi
#
# fi
# if [ $enrichstr -eq 1 ]; then
# nseekstr=`wc -l < seekout.str`
# if [ $nseekstr -gt 1 ]; then
# cat seekout.str >> pdblist
# pdblist="tsukaimasu"
# fi
# fi
# 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 $seednseq >> "$progressfile"
# echo $#
while [ $# -gt 1 ]
do
shift
# echo "num="$#
if [ $anysymbol -eq 1 ]; then
cat seed$# >> orig
"$prefix/replaceu" $seqtype -i seed$# -o $seedoffset > clean 2>>"$progressfile" || exit 1
mv clean seed$#
fi
"$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
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 infile2 >> infile
fi
elif [ $seedtable != "x" ]; then
cat _seedtablefile > hat3.seed
elif [ $newdash -eq 1 ]; then
seemstobe=`"$prefix/countlen" -i infile | awk '{print $6}'`
if [ $seemstobe = "d" -a "x$seqtype" != "x-P" ]; then
echo "" 1>>"$progressfile"
echo "Error: This data seems to be nucleotide sequences." 1>>"$progressfile"
echo "Add the --amino flag if this is surely protein." 1>>"$progressfile"
echo "" 1>>"$progressfile"
exit 1;
fi
if [ $anysymbol -eq 1 ]; then
mv orig infile # replaceu wo mukouka
fi
# sed 's/-//g' infile > dashin # gap nozoku
awk '{if(/^>/)print; else {gsub( /-/,"" ); print;}}' infile > dashin
if [ ! -x "$prefix/dash_client" -o ! -x "$prefix/dash_client" ]; then
echo "" 1>&2
echo "== Install DASH client =====================================================" 1>&2
echo "To use this feature, uncomment the following line in Makefile" 1>&2
echo "DASH_CLIENT = dash_client" 1>&2
echo "and re-compile the source." 1>&2
echo "Note that it requires the 'Go' compiler." 1>&2
echo "============================================================================" 1>&2
echo "" 1>&2
exit 1
fi
echo "Calling DASH (https://sysimm.org/dash/)" 1>>"$progressfile"
"$prefix/dash_client" -url "$dashserver" -i dashin -sequences dashsequences -hat3 hat3.seed 1>>"$progressfile"
dashres="$?"
if [ $dashres -ne "0" ]; then
echo "Error in DASH" 1>>"$progressfile"
echo "To enable this feature, compile with DASH_CLIENT=dash_client. Go compiler is necessary." 1>>"$progressfile"
exit 1;
fi
if [ $exclude_ho -eq 1 ]; then # amari yokunai
awk 'BEGIN{out=1} !/^>_addedbymaffte_/{if(out) print; out=1} /^>_addedbymaffte_/{out=0}' dashsequences | sed 's/>DASH_/>DASH|/' > ho_excluded
mv ho_excluded dashsequences
fi
if [ "$mergetable" != "/dev/null" ]; then # 2020/Apr/30
ndash=`grep -c '>DASH_' dashsequences | head -1`
# echo "ndash = " $ndash
awk "{for( i=1;i<=NF;i++){if(0+\$i==0)break; printf( \"%d \", $ndash+\$i); } print \"\" }" _subalignmentstable > _subalignmentstableshifted
mv _subalignmentstableshifted _subalignmentstable
cp dashsequences dashsequences.bk
awk "BEGIN{nout=0} {if(\$1~/^>/) nout++; if( nout <= $ndash ) print;}" dashsequences > infile2
cat infile >> infile2
cp infile2 dashsequences
fi
sed 's/>DASH_/>DASH|/' dashsequences > renamed
mv renamed dashsequences
echo "Done." 1>>"$progressfile"
# cat hat3.seed
seedoffset=`grep -c '^[>|=]' dashsequences | head -1 `
echo "# of structures = " 1>>"$progressfile"
echo $seedoffset 1>>"$progressfile"
if [ $anysymbol -eq 1 ]; then
cat dashsequences >> orig
"$prefix/replaceu" $seqtype -i dashsequences -o 0 > clean 2>>"$progressfile" || exit 1
mv clean infile
# "$prefix/replaceu" $seqtype -i orig2 -o $seedoffset >> infile 2>>"$progressfile" || exit 1 # yarinaoshi
# cat orig2 >> orig
else
cat dashsequences > 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" -a $memsavetree -eq 1 ]; then
if [ "$mpiscript" != "/dev/null" ]; then
sh $mpiscript "$prefix/nodepair_mpi" $lhlimit -u $unalignlevel $localparam $seqtype $model -g $pgexp -f $pggop -Q $spfactor -h $pgaof -A $usenaivepairscore $focusarg $treeinopt $treeoutopt -i infile > /dev/null 2>>"$progressfile" || exit 1
else
"$prefix/nodepair" $lhlimit -u $unalignlevel $localparam -C $numthreads $seqtype $model -g $pgexp -f $pggop -Q $spfactor -h $pgaof -A $usenaivepairscore $focusarg $treeinopt $treeoutopt -i infile > /dev/null 2>>"$progressfile" || exit 1
fi
echo 'nodepair' > _guidetree
"$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt -U $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" -a $memsavetree -eq 1 ]; then
if [ "$mpiscript" != "/dev/null" ]; then
sh $mpiscript "$prefix/nodepair_mpi" $lhlimit -u $unalignlevel $localparam $seqtype $model -g $lexp -f $lgop -Q $spfactor -h $laof -L $usenaivepairscore $focusarg $treeinopt $treeoutopt -i infile > /dev/null 2>>"$progressfile" || exit 1
else
"$prefix/nodepair" $lhlimit -u $unalignlevel $localparam -C $numthreads $seqtype $model -g $lexp -f $lgop -Q $spfactor -h $laof -L $usenaivepairscore $focusarg $treeinopt $treeoutopt -i infile > /dev/null 2>>"$progressfile" || exit 1
fi
echo 'nodepair' > _guidetree
"$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $termgapopt $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt -U $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 = "localgenaf" -a $memsavetree -eq 1 ]; then
"$prefix/nodepair" $lhlimit -u $unalignlevel $localparam -C $numthreads $seqtype $model -g $lexp -f $lgop -Q $spfactor -h $laof -O $LGOP -E $LEXP -N $usenaivepairscore $focusarg $treeinopt $treeoutopt -i infile > /dev/null 2>>"$progressfile" || exit 1
echo 'nodepair' > _guidetree
"$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $termgapopt $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt -U $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 = "global" -a $memsavetree -eq 0 ]; then
"$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" -a $memsavetree -eq 0 ]; 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/addsingle" $codonposopt $codonscoreopt -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 $treealg < infile > /dev/null 2>>"$progressfile" || exit 1
else
"$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" -a $memsavetree -eq 0 ]; then
"$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/addsingle" $codonposopt $codonscoreopt -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 $treealg < infile > /dev/null 2>>"$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" -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" $codonposopt $codonscoreopt -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 $treealg < infile > /dev/null 2>>"$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" $codonposopt $codonscoreopt -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 $treealg < infile > /dev/null 2>>"$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 $numthreads-$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" $codonposopt $codonscoreopt -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 $treealg < infile > /dev/null 2>>"$progressfile" || exit 1
else
"$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 $numthreads-$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" $codonposopt $codonscoreopt -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 $treealg < infile > /dev/null 2>>"$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 $treealg < infile > /dev/null 2>>"$progressfile" || exit 1
else
echo "Impossible" 1>&2
exit 1
fi
else
if [ $fragment -ne 0 ]; then
"$prefix/addsingle" $codonposopt $codonscoreopt -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 $treealg < infile > /dev/null 2>>"$progressfile" || exit 1
else
"$prefix/disttbfast" -q $npickup -E $cycledisttbfast -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg -W $tuplesize $termgapopt $outnum $addarg $add2ndhalfarg -C $numthreads-$numthreadstb $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -g $gexp -f "-"$gop -Q $spfactor -h $aof $param_fft $algopt $treealg $scoreoutarg $anchoropt -x $maxanchorseparation $oneiterationopt < infile > pre 2>>"$progressfile" || exit 1
mv hat3.seed hat3
fi
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" $seqtype $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 -K $nadd < pre > /dev/null 2>>"$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" $add2ndhalfarg -a pre -i orig > restored || exit 1
mv restored pre
fi
echo '' 1>>"$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>>"$progressfile"
fi
fi
echo '' 1>>"$progressfile"
if [ $pdblist != "/dev/null" -o $ownlist != "/dev/null" ]; then
# cat dasherr >>"$progressfile"
echo '' >>"$progressfile"
fi
popd > /dev/null
if [ "$outputopt" != "-f" -o "$windows" = "yes" ]; then # Windows deha kaigyo code wo f2cl de modosu.
# ln -s "$TMPFILE/order" _order$$ # f2cl ga space ari filename ni taiou shiteinainode
# cp "$TMPFILE/order" _order$$ # ln -s no error wo sakeru
if [ "$outputfile" = "" ]; then
"$prefix/f2cl" -n $namelength $outputopt < "$TMPFILE/pre" 2>"/dev/null" || exit 1
else
"$prefix/f2cl" -n $namelength $outputopt < "$TMPFILE/pre" > "$outputfile" 2>"/dev/null" || exit 1
fi
# rm _order$$
else
if [ "$outputfile" = "" ]; then
cat < "$TMPFILE/pre" || exit 1
else
cat < "$TMPFILE/pre" > "$outputfile" || exit 1
fi
fi
if [ $treeout -eq 1 ]; then
cp "$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
prog="awk"
#tmpawk=`which nawk 2>/dev/null | awk '{print $1}'`
#if [ -x "$tmpawk" ]; then
# prog="$tmpawk"
#fi
#
#tmpawk=`which gawk 2>/dev/null | awk '{print $1}'`
#if [ -x "$tmpawk" ]; then
# prog="$tmpawk"
#fi
# 2017/May/12, Windows no gawk wo sakeru tame
#echo "prog="$prog 1>&2
umask 077
(
$prog '
BEGIN {
prefix = ENVIRON["prefix"];
version = ENVIRON["version"];
myself = ENVIRON["myself"];
pwd = ENVIRON["mafft_working_dir"]; # from mafft.bat on windows
if( pwd == "" ) pwd = ENVIRON["PWD"];
while( 1 )
{
options = ""
printf( "\n" ) > "/dev/tty";
printf( "---------------------------------------------------------------------\n" ) > "/dev/tty";
printf( "\n" ) > "/dev/tty";
printf( " MAFFT %s\n", version ) > "/dev/tty";
printf( "\n" ) > "/dev/tty";
# printf( " Copyright (c) 2002- Kazutaka Katoh\n" ) > "/dev/tty";
printf( " MBE 30:772-780 (2013), NAR 30:3059-3066 (2002)\n" ) > "/dev/tty";
printf( " https://mafft.cbrc.jp/alignment/software/\n" ) > "/dev/tty";
printf( "---------------------------------------------------------------------\n" ) > "/dev/tty";
printf( "\n" ) > "/dev/tty";
while( 1 )
{
printf( "\n" ) > "/dev/tty";
printf( "Input file? (FASTA format; Folder=%s)\n@ ", pwd ) > "/dev/tty";
res = getline < "/dev/tty";
close( "/dev/tty" )
if( res == 0 || NF == 0 )
continue;
infile = sprintf( "%s", $0 );
res = getline < infile;
close( infile );
if( res == -1 )
{
printf( "%s: No such file.\n\n", infile ) > "/dev/tty";
printf( "Filename extension (eg., .txt) must be typed, if any.\n\n" ) > "/dev/tty";
}
else if( res == 0 )
printf( "%s: Empty.\n", infile ) > "/dev/tty";
else
{
printf( "OK. infile = %s\n\n", infile ) > "/dev/tty";
break;
}
}
nseq = 0;
while( 1 )
{
printf( "\n" ) > "/dev/tty";
printf( "Output file?\n" ) > "/dev/tty";
printf( "@ " ) > "/dev/tty";
res = getline < "/dev/tty";
close( "/dev/tty" );
if( res == 0 || NF == 0 )
continue;
else
{
outfile = sprintf( "%s", $0 );
printf( "OK. outfile = %s\n\n", outfile ) > "/dev/tty";
break;
}
}
while( 1 )
{
outargs = "";
printf( "\n" ) > "/dev/tty";
printf( "Output format?\n" ) > "/dev/tty";
printf( " 1. Clustal format / Sorted\n" ) > "/dev/tty";
printf( " 2. Clustal format / Input order\n" ) > "/dev/tty";
printf( " 3. Fasta format / Sorted\n" ) > "/dev/tty";
printf( " 4. Fasta format / Input order\n" ) > "/dev/tty";
printf( " 5. Phylip format / Sorted\n" ) > "/dev/tty";
printf( " 6. Phylip format / Input order\n" ) > "/dev/tty";
printf( "@ " ) > "/dev/tty";
res = getline < "/dev/tty";
close( "/dev/tty" );
# printf( "res=%d, NF=%d\n", res, NF );
resnum = 0 + $1;
# printf( "resnum=%d\n", resnum );
if( resnum < 1 || 6 < resnum )
continue;
else
{
if( resnum == 1 )
outargs = "--clustalout --reorder";
else if( resnum == 2 )
outargs = "--clustalout --inputorder";
else if( resnum == 3 )
outargs = "--reorder";
else if( resnum == 4 )
outargs = "--inputorder";
else if( resnum == 5 )
outargs = "--phylipout --reorder";
else if( resnum == 6 )
outargs = "--phylipout --inputorder";
else
continue;
printf( "OK. arguments = %s\n\n", outargs ) > "/dev/tty";
break;
}
}
while( 1 )
{
arguments = "";
printf( "\n" ) > "/dev/tty";
printf( "Strategy?\n" ) > "/dev/tty";
printf( " 1. --auto\n" ) > "/dev/tty";
printf( " 2. FFT-NS-1 (fast)\n" ) > "/dev/tty";
printf( " 3. FFT-NS-2 (default)\n" ) > "/dev/tty";
printf( " 4. G-INS-i (accurate)\n" ) > "/dev/tty";
printf( " 5. L-INS-i (accurate)\n" ) > "/dev/tty";
printf( " 6. E-INS-i (accurate)\n" ) > "/dev/tty";
printf( "@ " ) > "/dev/tty";
res = getline < "/dev/tty";
close( "/dev/tty" );
# printf( "res=%d, NF=%d\n", res, NF );
resnum = 0 + $1;
# printf( "resnum=%d\n", resnum );
if( resnum < 1 || 6 < resnum )
continue;
else
{
if( resnum == 1 )
arguments = "--auto";
else if( resnum == 2 )
arguments = "--retree 1";
else if( resnum == 3 )
arguments = "--retree 2";
else if( resnum == 4 )
arguments = "--globalpair --maxiterate 16";
else if( resnum == 5 )
arguments = "--localpair --maxiterate 16";
else if( resnum == 6 )
arguments = "--genafpair --maxiterate 16";
else
arguments = sprintf( "%s", $0 );
printf( "OK. arguments = %s %s\n\n", arguments, outargs ) > "/dev/tty";
break;
}
}
while( 1 )
{
printf( "\n" ) > "/dev/tty";
printf( "Additional arguments? (--ep # --op # --kappa # etc)\n" ) > "/dev/tty";
printf( "@ " ) > "/dev/tty";
res = getline < "/dev/tty";
close( "/dev/tty" );
if( res == 0 || NF == 0 )
{
break;
}
else
{
addargs = sprintf( "%s", $0 );
printf( "OK. arguments = %s %s %s\n\n", addargs, arguments, outargs ) > "/dev/tty";
break;
}
}
arguments = sprintf( "%s %s %s", addargs, arguments, outargs );
print ""
command = sprintf( "\"%s\" %s \"%s\" > \"%s\"", myself, arguments, infile, outfile );
gsub( /\\/, "/", command );
printf( "command=\n%s\n", command ) > "/dev/tty";
while( 1 )
{
go = 0;
printf( "Type Y or just enter to run this command.\n" ) > "/dev/tty";
printf( "@ " ) > "/dev/tty";
res = getline < "/dev/tty";
close( "/dev/tty" );
if( res == 0 )
continue;
else if( NF == 0 || $0 ~ /^[Yy]/ )
{
go=1;
break;
}
else
break;
}
if( go ) break;
printf( "\n" ) > "/dev/tty";
printf( "\n" ) > "/dev/tty";
}
system( command );
command = sprintf( "more \"%s\"", outfile );
system( command );
printf( "Press Enter to exit." ) > "/dev/tty";
res = getline < "/dev/tty";
}
'
)
exit 0;