d83201fd2f
Former-commit-id: 7017655ac86e7b7837c7b581bf8a1abb86c08b30 Former-commit-id: dcedd4e32e3c7ce302eed94abd2b975a4506df97
280 lines
7.9 KiB
Bash
Executable File
280 lines
7.9 KiB
Bash
Executable File
#!/bin/csh -f
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#
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# make ChloroDB's
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#
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# usage: copy genbank/embl files into 'DB_DIR/download'
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# usage: [create a paramter.sh file in 'DB_DIR']
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# usage: go_chlorodb [DB_DIR]
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#
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unsetenv ORG_SOURCED
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setenv ORG_HOME `dirname $0`/../../../..
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source $ORG_HOME/scripts/csh_init.sh
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#
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# which DB to process
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#
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set DB_BASE = $DATA_DIR/cds/chlorodb # default location
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if ($#Argv > 0) then
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set DB_BASE = $Argv[1]; Shift
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endif
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set DB_BASE = `cd $DB_BASE && pwd -P`
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NeedDir $DB_BASE/download
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if (! -d $DB_BASE/info) mkdir $DB_BASE/info
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if (! -d $DB_BASE/fasta) mkdir $DB_BASE/fasta
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cd $DB_BASE/info
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#
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# params
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#
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if (! -e $DB_BASE/parameters.sh) then
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Notify "no $DB_BASE/parameters.sh found : creating one for you"
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@ n = `find $DB_BASE/download -maxdepth 1 -type f -print | wc -l`
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@ cor_cutoff = $n / 2
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@ atg_cutoff = $n / 10
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@ dbs_cutoff = $n / 4
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if ($cor_cutoff == 0) @ cor_cutoff = 1
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if ($atg_cutoff == 0) @ atg_cutoff = 1
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if ($dbs_cutoff == 0) @ dbs_cutoff = 1
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echo "# sourced file" > $DB_BASE/parameters.sh
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echo "" >> $DB_BASE/parameters.sh
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echo "set CORE_NCDS_CUTOFF = $cor_cutoff" >> $DB_BASE/parameters.sh
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echo "set CORE_START_ATG_CUTOFF = $atg_cutoff" >> $DB_BASE/parameters.sh
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echo "set CORE_START_DFT_CUTOFF = $atg_cutoff" >> $DB_BASE/parameters.sh
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echo "set CORE_START_OTH_CUTOFF = 10" >> $DB_BASE/parameters.sh
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echo "set CORE_STOP_CUTOFF = $cor_cutoff" >> $DB_BASE/parameters.sh
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echo "set CORE_SPLICE_CUTOFF = $atg_cutoff" >> $DB_BASE/parameters.sh
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echo "" >> $DB_BASE/parameters.sh
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echo "set SHEL_NCDS_CUTOFF = 10" >> $DB_BASE/parameters.sh
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echo "" >> $DB_BASE/parameters.sh
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echo "set CORE_DELTA = Inf" >> $DB_BASE/parameters.sh
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echo "set CORE_COVMIN = 30" >> $DB_BASE/parameters.sh
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echo "set CORE_PMAX = 1e-6" >> $DB_BASE/parameters.sh
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echo "set CORE_IDMIN = 30" >> $DB_BASE/parameters.sh
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echo "set CORE_SIZMIN = $cor_cutoff" >> $DB_BASE/parameters.sh
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echo "" >> $DB_BASE/parameters.sh
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echo "set SHEL_DELTA = 0.5" >> $DB_BASE/parameters.sh
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echo "set SHEL_COVMIN = 30" >> $DB_BASE/parameters.sh
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echo "set SHEL_PMAX = 1e-6" >> $DB_BASE/parameters.sh
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echo "set SHEL_IDMIN = 30" >> $DB_BASE/parameters.sh
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echo "set SHEL_SIZMIN = $dbs_cutoff" >> $DB_BASE/parameters.sh
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echo "" >> $DB_BASE/parameters.sh
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echo "set DUST_DELTA = 0.5" >> $DB_BASE/parameters.sh
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echo "set DUST_COVMIN = 30" >> $DB_BASE/parameters.sh
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echo "set DUST_PMAX = 1e-6" >> $DB_BASE/parameters.sh
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echo "set DUST_IDMIN = 30" >> $DB_BASE/parameters.sh
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echo "set DUST_SIZMIN = 10" >> $DB_BASE/parameters.sh
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Cat $DB_BASE/parameters.sh
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else
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Notify "DB parameters : $DB_BASE/parameters.sh"
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endif
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source $DB_BASE/parameters.sh
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##set CMIN_COD = 0
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##set FMIN_COD = 0.01
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#
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# temporarily uncompress
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#
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set ff = `find $DB_BASE/download -maxdepth 1 -name \*.gz -print`
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if ($#ff != 0) then
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Notify "uncompressing $#ff entries"
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foreach f ($ff)
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gunzip -f $f
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end
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endif
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#
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# convert gbk/embl to fasta
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#
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set ff = `find $DB_BASE/download -maxdepth 1 \( -name \*.gbk -or -name \*.embl \) -print`
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Notify "convert $#ff gbk/embl entries to fasta"
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foreach f ($ff)
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set nom = `basename $f:r`
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set typ = $f:e
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$AwkCmd -f $LIB_DIR/$typ.tofasta.awk $f > $DB_BASE/fasta/$nom.fst
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end
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#
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# get gbk/embl info
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#
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Notify "get gbk/embl info for $#ff entries"
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echo "" | awk -v HEADONLY=1 -f $LIB_DIR/gbk.info.awk > db.info.txt # just get header
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foreach f ($ff)
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set nom = `basename $f:r`
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set typ = $f:e
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$AwkCmd -f $LIB_DIR/$typ.oneliner.awk $f |\
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$AwkCmd -f $LIB_DIR/libutil.awk -f $LIB_DIR/$typ.info.awk |\
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egrep -v '^#' >> db.info.txt
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end
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#
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# get cds info
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#
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Notify "get gbk/embl cds for $#ff entries"
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echo "" | awk -v HEADONLY=1 -f $LIB_DIR/gbk.cds_long.awk > db.cds.txt # just get header
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foreach f ($ff)
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set nom = `basename $f:r`
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set typ = $f:e
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$AwkCmd -f $LIB_DIR/$typ.oneliner.awk $f |\
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$AwkCmd -v FASTA=$DB_BASE/fasta/$nom.fst -f $LIB_DIR/libutil.awk \
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-f $LIB_DIR/$typ.cds_long.awk |\
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egrep -v '^#' >> db.cds.txt
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end
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#
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# get fasta for prots
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#
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Notify "get prots"
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$AwkCmd -f $LIB_DIR/libutil.awk -f $LIB_DIR/cds2fasta.awk db.cds.txt > db.prot.fst
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#
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# get introns
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#
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Notify "get gbk/embl introns for $#ff entries"
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echo "" | awk -v HEADONLY=1 -f $LIB_DIR/gbk.intron.awk > db.intron.txt # just get header
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foreach f ($ff)
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set nom = `basename $f:r`
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set typ = $f:e
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$AwkCmd -f $LIB_DIR/$typ.oneliner.awk $f |\
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$AwkCmd -v FASTA=$DB_BASE/fasta/$nom.fst -f $LIB_DIR/libutil.awk \
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-f $LIB_DIR/$typ.intron.awk |\
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egrep -v '^#' >> db.intron.txt
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end
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#
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# make models
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#
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Notify "Making models"
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echo -n "" > db.models.params.txt
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echo "CORE_NCDS_CUTOFF <- $CORE_NCDS_CUTOFF" >> db.models.params.txt
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echo "CORE_START_ATG_CUTOFF <- $CORE_START_ATG_CUTOFF" >> db.models.params.txt
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echo "CORE_START_DFT_CUTOFF <- $CORE_START_DFT_CUTOFF" >> db.models.params.txt
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echo "CORE_START_OTH_CUTOFF <- $CORE_START_OTH_CUTOFF" >> db.models.params.txt
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echo "CORE_STOP_CUTOFF <- $CORE_STOP_CUTOFF" >> db.models.params.txt
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echo "CORE_SPLICE_CUTOFF <- $CORE_SPLICE_CUTOFF" >> db.models.params.txt
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echo "SHEL_NCDS_CUTOFF <- $SHEL_NCDS_CUTOFF" >> db.models.params.txt
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$LIB_DIR/make.models.r |& Cat
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GetStatus
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OnError then
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Error 2 "model parameter too stringent"
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endif
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#
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# add matrices
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#
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cp -f $PROG_DIR/matrices/* models
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#
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# make subDBs
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#
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if (-e db.core.pat.txt) then
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Notify "Making core DB (take some time... please wait)"
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$PROG_DIR/subdb/go_subdb.sh db.prot.fst db.core.pat.txt \
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$CORE_DELTA $CORE_COVMIN $CORE_PMAX $CORE_IDMIN $CORE_SIZMIN
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# add discarded entries into shell
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if (-e db.core.pat.db/Annot.lst) then
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sort db.core.pat.txt > A_$$
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sort db.core.pat.db/Annot.lst > B_$$
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join -a1 A_$$ B_$$ | awk '(NF==3) {print $0}' > C_$$
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set n = `cat C_$$ | wc -l`
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Notify "transfering $n discarded entries to shell"
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cat C_$$ >> db.shell.pat.txt
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\rm -f ?_$$
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endif
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endif
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if (-e db.shell.pat.txt) then
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Notify "Making shell DB (take some time... please wait)"
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$PROG_DIR/subdb/go_subdb.sh db.prot.fst db.shell.pat.txt \
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$SHEL_DELTA $SHEL_COVMIN $SHEL_PMAX $SHEL_IDMIN $SHEL_SIZMIN
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# add discarded entries into dust
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if (-e db.shell.pat.db/Annot.lst) then
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sort db.shell.pat.txt > A_$$
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sort db.shell.pat.db/Annot.lst > B_$$
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join -a1 A_$$ B_$$ | awk '(NF==3) {print $0}' >> C_$$
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set n = `cat C_$$ | wc -l`
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Notify "transfering $n discarded entries to dust"
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cat C_$$ >> db.dust.pat.txt
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\rm -f ?_$$
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endif
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endif
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if (-e db.dust.pat.txt) then
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Notify "Making dust DB (take some time... please wait)"
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$PROG_DIR/subdb/go_subdb.sh db.prot.fst db.dust.pat.txt \
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$DUST_DELTA $DUST_COVMIN $DUST_PMAX $DUST_IDMIN $DUST_SIZMIN
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endif
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#
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# recompress entries
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#
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set ff = `find $DB_BASE/download -maxdepth 1 -type f -print`
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if ($#ff != 0) then
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Notify "recompressing $#ff entries"
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foreach f ($ff)
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gzip -f $f
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end
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endif
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# compress fasta
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set ff = `find $DB_BASE/fasta -maxdepth 1 -name \*.fst -print`
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if ($#ff != 0) then
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Notify "compressing $#ff fasta entries"
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foreach f ($ff)
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gzip -f $f
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end
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endif
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# install everything in proper directory
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foreach dir ("core" "shell" "dust")
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if (-e $DB_BASE/$dir) \rm -r $DB_BASE/$dir
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if ((-d db.$dir.pat.db) && (-e db.$dir.pat.db/Annot.lst)) then
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Notify "installing $DB_BASE/$dir"
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\mv -f db.$dir.pat.db $DB_BASE/$dir
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endif
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end
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if (-e $DB_BASE/models) \rm -r $DB_BASE/models
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if (-d models) \mv -f models $DB_BASE
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Notify "Done"
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exit 0
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