diff --git a/CORE/.GDEmenus b/CORE/.GDEmenus index 76ae008..40d513f 100644 --- a/CORE/.GDEmenus +++ b/CORE/.GDEmenus @@ -1,7 +1,7 @@ -1menu:File +menu:File item:test cmask output -itemmethod: kedit in1 +itemmethod: textedit in1 in:in1 informat:colormask @@ -44,9 +44,6 @@ itemhelp:readseq.help arg:FORMAT argtype:choice_list -argchoice:FASTA:8 -argchoice:NEXUS:17 -argchoice:Phylip v3.3:12 argchoice:IG/Stanford:1 argchoice:GenBank:2 argchoice:NBRF:3 @@ -206,7 +203,7 @@ informat:gde insave: item:Clustal alignment -itemmethod:(tr '%#' '>'clus_in;clustalw -quicktree -output=PIR -infile=clus_in -align > in1.rpt;sed "s/>DL;/#/g" < clus_in.pir> in1;$REPORT gde in1;/bin/rm -f clus_in* in1* )& +itemmethod:(tr '%#' '>'clus_in;clustalv /output=PIR /infile=clus_in /align /ktup=$KTUP /window=$WIN $Trans /fixedgap=$FIXED /floatgap=$FLOAT > in1.rpt;sed "s/>DL;/#/g" < clus_in.pir> in1;$REPORT gde in1; /bin/rm -f clus_in* in1* )& itemhelp:clustal_help @@ -248,7 +245,7 @@ arg:REPORT argtype:chooser arglabel:View assembly report? argchoice:No: -argchoice:Yes:kedit in1.rpt& +argchoice:Yes:textedit in1.rpt& in:in1 @@ -270,25 +267,6 @@ informat:flat out:out1 outformat:colormask -item:Phrap -itemmethod:readseq in1 -a -f8 > OUTPUTFILE;/bin/rm -f OUTFILE.tmp; phrap OUTPUTFILE; readseq -a -f2 OUTPUTFILE.contigs > out1;/bin/rm -rf OUTPUT*; - -in:in1 -informat:genbank - -out:out1 -outformat:genbank - -item:SNAP -itemmethod: cat in1 > infile;/usr/local/bio/GDE/bin/fasta2snap.pl > outfile; /usr/bin/X11/xterm -e /home/tulio/bio/SNAP/SNAP.pl outfile; kedit backg*; kedit summ*; sheeltool /home/tulio/bio/codons-xyplot.pl codons.*; kedit codon.data; /bin/rm -rf back* codon* summ*; - -in:in1 -informat:flat -out:out1 -outformat:text - - - item:Find all itemmethod:findall $SEARCH $PRCNT $CASE $UT -match $MAT -mismatch $MIS < in1 > out1; @@ -381,19 +359,66 @@ out:out1 outformat:gde +item:MFOLD +itemmethod:(tr 'a-z' 'A-Z' < seqGB > .GDE.tmp.caps; ZUKERGDE.sh .GDE.tmp.caps $CT $GDE_HELP_DIR/ZUKER/ > out1 && $METHOD < out1; Zuk_to_gen < $CT >file.gen; gde file.gen& textedit RegionTable; /bin/rm -f RegionTable out1 seqGB* .GDE.tmp.caps)& +itemhelp:MFOLD.help + +in:seqGB +informat:genbank +insave: + +arg:METHOD +argtype:chooser +arglabel:RNA type +argchoice:Fold Linear RNA:lrna +argchoice:Fold Circular RNA:crna + +arg:CT +argtype:text +arglabel:Pairing(ct) File Name +argtext:mfold_out + + +item:Draw Secondary structure +itemmethod:(LoopTool $TEMPLATE in1 ; /bin/rm -f in1) & +itemhelp:LoopTool.help + +arg:TEMPLATE +argtype:chooser +arglabel:Use template file ./loop.temp? +argchoice:No: +argchoice:Yes:-t loop.temp + +in:in1 +informat:genbank +insave: + +item:Highlight helix +itemmethod:readseq -a -f8 in1 | sed "s/>HELIX/\"HELIX/" > in1.flat; sho_helix < in1.flat > out1;rm in1.flat +itemhelp:sho_helix.help + +in:in1 +informat:genbank + +out:out1 +outformat:colormask + + #Menu for DNA/RNA item:blastn -itemmethod:(sed "s/[#%]/>/" in1.f; /usr/local/bio/blast/blastall -p blastn -d $BLASTDBDNA -i in1.f -W $WORDLEN -M $MATCH > in1.tmp; kedit in1.tmp; rm in1*)& +itemmethod:(sed "s/[#%]/>/" in1.f; blastn $BLASTDB in1.f W=$WORDLEN M=$MATCH N=$MMSCORE > in1.tmp; textedit in1.tmp; rm in1*)& in:in1 informat:flat insave: -arg:BLASTDBDNA +arg:BLASTDB argtype:choice_list arglabel:Which Database -argchoice:HIV-1 Seq. Db.:/usr/local/bio/db/DNA/hiv17-08-01.fasta2 +argchoice:genbank:$GDE_HELP_DIR/BLAST/genbank +argchoice:genbank update:$GDE_HELP_DIR/BLAST/genupdate + arg:WORDLEN argtype:slider arglabel:Word Size @@ -416,18 +441,16 @@ argmax:-1 argvalue:-5 item:blastx -itemmethod:(sed "s/[#%]/>/" in1.f; /usr/local/bio/blast/blastall -p blastx -d $BLASTDB -i in1.f -W $WORDLEN -M PAM30 > in1.tmp; /usr/openwin/bin/kedit in1.tmp; rm in1*)& - - +itemmethod:(sed "s/[#%]/>/" in1.f; cp $GDE_HELP_DIR/BLAST/PAM??? .; blastx $BLASTDB in1.f W=$WORDLEN M=$Matrix C=$CODE> in1.tmp; textedit in1.tmp; rm in1* PAM???)& in:in1 informat:flat insave: -arg:BLASTDBDNA +arg:BLASTDB argtype:choice_list arglabel:Which Database -argchoice:HIV Proteins:/usr/local/bio/db/hiv17-08-01.PROT.fasta +argchoice:pir1:$GDE_HELP_DIR/BLAST/pir argchoice:genpept:$GDE_HELP_DIR/BLAST/genpept arg:WORDLEN @@ -440,13 +463,12 @@ argvalue:3 arg:Matrix arglabel:Substitution Matrix: argtype:choice_list -argchoice:PAM30:PAM30 -argchoice:PAM70:PAM70 +argchoice:PAM120:PAM120 +argchoice:PAM250:PAM250 arg:CODE argtype:choice_list arglabel:Genetic Code - argchoice:Standard or Universal:0 argchoice:Vertebrate Mitochondrial:1 argchoice:Yeast Mitochondrial:2 @@ -457,57 +479,119 @@ argchoice:Protozoan Mitochondrial:6 argchoice:Plant Mitochondrial:7 argchoice:Echinodermate Mitochondrial:8 -item:------------------------ -item:Add a new DNA blast db -itemmethod:xterm -e formatdb -i $sourcefile -p F -o T; /usr/local/bio/GDE/bin/installBLASTDB.pl $sourcefile $menuname; +item:FASTA (DNA/RNA) +itemmethod:(sed "s/[#%]/>/"in1.fasta;fasta -Q -d $NUMOFALN $MATRIX in1.fasta $DBASE > in1.out; textedit in1.out;\rm in1*) & +itemhelp:FASTA.help -arg:sourcefile -argtype:text -arglabel: enter the file name +in:in1 +informat:flat -arg:menuname -argtype:text -arglabel: enter the name of the DB +arg:DBASE +argtype:choice_list +arglabel:Database +argchoice:GenBank Primate:$GDE_HELP_DIR/FASTA/GENBANK/gbpri.seq\ 1 +argchoice:GenBank Rodent:$GDE_HELP_DIR/FASTA/GENBANK/gbrod.seq\ 1 +argchoice:GenBank all Mammal:$GDE_HELP_DIR/FASTA/GENBANK/gbmam.seq\ 1 +argchoice:GenBank verteBrates:$GDE_HELP_DIR/FASTA/GENBANK/gbvrt.seq\ 1 +argchoice:GenBank Inverts:$GDE_HELP_DIR/FASTA/GENBANK/gbinv.seq\ 1 +argchoice:GenBank pLants:$GDE_HELP_DIR/FASTA/GENBANK/gbpln.seq\ 1 +argchoice:GenBank Struct RNA:$GDE_HELP_DIR/FASTA/GENBANK/gbrna.seq\ 1 +argchoice:GenBank euk. Organelles:$GDE_HELP_DIR/FASTA/GENBANK/gborg.seq\ 1 +argchoice:GenBank phaGe:$GDE_HELP_DIR/FASTA/GENBANK/gbphg.seq\ 1 +argchoice:GenBank bacTeria:$GDE_HELP_DIR/FASTA/GENBANK/gbbct.seq\ 1 +argchoice:GenBank sYnthetic:$GDE_HELP_DIR/FASTA/GENBANK/gbsyn.seq\ 1 +argchoice:GenBank Viral:$GDE_HELP_DIR/FASTA/GENBANK/gbvrl.seq\ 1 +argchoice:GenBank Unannotated:$GDE_HELP_DIR/FASTA/GENBANK/gbuna.seq\ 1 +arg:NUMOFALN +argtype:slider +arglabel:Number of Alignment to Report +argmin:1 +argmax:100 +argvalue:20 -#Sequence dataset -menu:seq. datasets +arg:MATRIX +arglabel:Which SMATRIX +argtype:choice_list +argchoice:Default: +argchoice:altdiag.mat:-s $GDE_HELP_DIR/FASTA/MATRIX/altdiag.mat +argchoice:altprot.mat:-s $GDE_HELP_DIR/FASTA/MATRIX/altprot.mat +argchoice:dna.mat:-s $GDE_HELP_DIR/FASTA/MATRIX/dna.mat +argchoice:prot.mat:-s $GDE_HELP_DIR/FASTA/MATRIX/prot.mat +menu:Protein -item:------------- -item:add a new dataset -itemmethod:mkdir db; cp $file db/ ;xterm -e /usr/local/bio/GDE/newDATASET.pl $name $file +item:Clustal Protein Alignment +itemmethod:(tr '%#"' '>' clus_in;clustalv /output=PIR /infile=clus_in /align /ktup=$KTUP /window=$WIN $Matrx /fixedgap=$FIXED /floatgap=$FLOAT > in1.rpt;sed "s/>P1;/%/g" < clus_in.pir > in1;$REPORT gde in1;/bin/rm -f in1* clus_in* )& +itemhelp:clustal_help -arg:name -argtype:text -arglabel:Enter the dataset name ? +arg:KTUP +argtype:slider +arglabel:K-tuple size for pairwise search +argmin:1 +argmax:10 +argvalue:2 -arg:file -argtype:text -arglabel:Enter the dataset file (in FASTA) ? +arg:WIN +argtype:slider +arglabel:Window size +argmin:1 +argmax:10 +argvalue:4 +arg:Matrx +argtype:chooser +arglabel:Weighting matrix +argchoice:PAM 250:PAM250 +argchoice:PAM 100:PAM100 +argchoice:Identity:ID + +arg:FIXED +argtype:slider +arglabel:Fixed gap penalty +argmin:1 +argmax:100 +argvalue:10 + +arg:FLOAT +arglabel:Floating gap penalty +argtype:slider +argmin:1 +argmax:100 +argvalue:10 + +arg:REPORT +argtype:chooser +arglabel:View assembly report? +argchoice:No: +argchoice:Yes:textedit in1.rpt& + +in:in1 +informat:flat +insave: #Menu for Protein -menu:protein -item:blastp -itemmethod:(sed "s/[#%]/>/" in1.f; cp /usr/local/bio/db/PAM30; /usr/local/bio/blast/blastall -p blastp -d $BLASTDBPROT -i in1.f -W $WORDLEN -M $Matrix > in1.tmp; /usr/openwin/bin/kedit in1.tmp; rm in1* PAM30)& +item:blastp +itemmethod:(sed "s/[#%]/>/" in1.f; cp $GDE_HELP_DIR/BLAST/PAM??? .; blastp $BLASTDB in1.f W=$WORDLEN M=$Matrix > in1.tmp;textedit in1.tmp; rm in1* PAM???)& in:in1 informat:flat insave: -arg:BLASTDBPROT +arg:BLASTDB argtype:choice_list arglabel:Which Database -argchoice:HIV Proteins:/usr/local/bio/db/hiv17-08-01.PROT.fasta +argchoice:pir:$GDE_HELP_DIR/BLAST/pir +argchoice:genpept:$GDE_HELP_DIR/BLAST/genpept +argchoice:local:$GDE_HELP_DIR/BLAST/local_db arg:Matrix -barglabel:Substitution Matrix: +arglabel:Substitution Matrix: argtype:choice_list -argchoice:PAM30:PAM30 -argchoice:PAM70:PAM70 +argchoice:PAM120:PAM120 +argchoice:PAM250:PAM250 arg:WORDLEN argtype:slider @@ -517,7 +601,7 @@ argmax:5 argvalue:3 item:tblastn -itemmethod:(sed "s/[#%]/>/" in1.f; cp /usr/local/bio/db/PAM??? .; tblastn $BLASTDB in1.f W=$WORDLEN M=$Matrix C=$CODE > in1.tmp; kedit in1.tmp; rm in1* PAM???)& +itemmethod:(sed "s/[#%]/>/" in1.f; cp $GDE_HELP_DIR/BLAST/PAM??? .; tblastn $BLASTDB in1.f W=$WORDLEN M=$Matrix C=$CODE > in1.tmp; textedit in1.tmp; rm in1* PAM???)& in:in1 informat:flat @@ -532,8 +616,8 @@ argchoice:genbank update:$GDE_HELP_DIR/BLAST/genupdate arg:Matrix arglabel:Substitution Matrix: argtype:choice_list -argchoice:PAM30:PAM30 -argchoice:PAM70:PAM70 +argchoice:PAM120:PAM120 +argchoice:PAM250:PAM250 arg:WORDLEN argtype:slider @@ -555,6 +639,90 @@ argchoice:Protozoan Mitochondrial:6 argchoice:Plant Mitochondrial:7 argchoice:Echinodermate Mitochondrial:8 +item:blast3 +itemmethod:(sed "s/[#%]/>/" in1.f; cp $GDE_HELP_DIR/BLAST/PAM??? .; blast3 $BLASTDB in1.f W=$WORDLEN M=$Matrix > in1.tmp;textedit in1.tmp; rm in1* PAM???)& + +in:in1 +informat:flat +insave: + +arg:BLASTDB +argtype:choice_list +arglabel:Which Database +argchoice:pir1:$GDE_HELP_DIR/BLAST/pir +argchoice:genpept:$GDE_HELP_DIR/BLAST/genpept + +arg:Matrix +arglabel:Substitution Matrix: +argtype:choice_list +argchoice:PAM120:PAM120 +argchoice:PAM250:PAM250 + +arg:WORDLEN +argtype:slider +arglabel:Word Size +argmin:1 +argmax:5 +argvalue:3 + +item:FASTA (Protein) +itemmethod:(sed "s/[#%]/>/"in1.fasta;fasta -Q -d $NUMOFALN $MATRIX in1.fasta $DBASE > in1.out; textedit in1.out;\rm in1*) & +itemhelp:FASTA.help + +in:in1 +informat:flat + +arg:DBASE +argtype:choice_list +arglabel:Database +argchoice:NBRF PIR1:$GDE_HELP_DIR/FASTA/PIR/pir1.dat\ 2 +argchoice:NBRF PIR2:$GDE_HELP_DIR/FASTA/PIR/pir2.dat\ 2 +argchoice:NBRF PIR3:$GDE_HELP_DIR/FASTA/PIR/pir3.dat\ 2 + + +arg:NUMOFALN +argtype:slider +arglabel:Number of Alignment to Report +argmin:1 +argmax:100 +argvalue:20 + +arg:MATRIX +arglabel:Which SMATRIX +argtype:choice_list +argchoice:Default: +argchoice:Minimum mutation matrix:-s $GDE_HELP_DIR/FASTA/MATRIX/codaa.mat +argchoice:Identity matrix:-s $GDE_HELP_DIR/FASTA/MATRIX/idnaa.mat +argchoice:Identity matrix for mismatches:-s $GDE_HELP_DIR/FASTA/MATRIX/idpaa.mat +argchoice:PAM250:-s $GDE_HELP_DIR/FASTA/MATRIX/pam250.mat +argchoice:PAM120:-s $GDE_HELP_DIR/FASTA/MATRIX/pam120.mat + +menu:Seq management + +item:Assemble Contigs +itemmethod:(sed "s/#/>/"in1.tmp; CAP2 in1.tmp $OVERLAP $PMATCH > out1;/bin/rm -f in1.tmp) +itemhelp:CAP2.help + +arg:OVERLAP +argtype:slider +arglabel:Minimum overlap? +argmin:5 +argmax:100 +argvalue:20 + +arg:PMATCH +argtype:slider +arglabel:Percent match required within overlap +argmin:25 +argmax:100 +argvalue:90 + +in:in1 +informat:flat + +out:out1 +outformat:gde +outoverwrite: item:Map View itemmethod:(mapview in1 -pbl $PBL -npp $NPP; /bin/rm -f in1)& @@ -585,69 +753,114 @@ argvalue:2 argmin:1 argmax:5 -item:-------------------------- -item:Add a new Protein blast db -itemmethod:xterm -e formatdb -i $sourcefile -p T -o T; /usr/local/bio/GDE/bin/installBLASTDBPROT.pl $sourcefile $menuname; -arg:sourcefile +item:Restriction sites +itemmethod:(cp $ENZ in1.tmp ; $PRE_EDIT Restriction in1.tmp in1 > out1 ; rm in1.tmp); +itemhelp:Restriction.help + +arg:ENZ argtype:text -arglabel: Enter the file (in FASTA) +arglabel:Enzyme file +argtext:$GDE_HELP_DIR/DATA_FILES/enzymes -arg:menuname -argtype:text -arglabel: Enter the name of the DB +arg:PRE_EDIT +argtype:chooser +arglabel:Edit enzyme file first? +argchoice:Yes:textedit in1.tmp; +argchoice:No: -#Phylogenetic Menu +in:in1 +informat:flat + +out:out1 +outformat:colormask menu:Phylogeny +item:DeSoete Tree fit +itemmethod: (readseq -a -f8 in1>in1.flat;count -t $CORR in1.flat> in1.tmp ; lsadt in1.out ; $DISPLAY_FUNC in1.out;/bin/rm -f in1* )& +itemhelp:lsadt.help + +in:in1 +informat:genbank +insave: +inmask: + +arg:CORR +arglabel:Distance correction? +argtype:chooser +argchoice:Olsen:-c=olsen +argchoice:Jukes/Cantor:-c=jukes +argchoice:None:-c=none + +arg:INIT +arglabel:Initial parameter estimate +argtype:choice_list +argchoice:uniformly distributed random numbers:1 +argchoice:error-perturbed data:2 +argchoice:original distance data from input matrix:3 + +arg:SEED +argtype:slider +arglabel:Random number seed +argmin:0 +argmax:65535 +argvalue:12345 + +arg:DISPLAY_FUNC +argtype:chooser +arglabel:View tree using +argchoice:TextEdit:textedit +argchoice:Treetool:treetool < + item:Phylip help -itemmethod:(netscape /usr/local/bio/phylip/doc/$FILE)& +itemmethod:(textedit $GDE_HELP_DIR/PHYLIP/$FILE)& arg:FILE argtype:choice_list arglabel:Which program? -argchoice:clique:clique.html -argchoice:consense:consense.html -argchoice:contchar:contchar.html -argchoice:contml:contml.html -argchoice:contrast:contrast.html -argchoice:discrete:discrete.html -argchoice:distance:distance.html -argchoice:dnaboot:dnaboot.html -argchoice:dnacomp:dnacomp.html -argchoice:dnadist:dnadist.html -argchoice:dnainvar:dnainvar.html -argchoice:dnaml:dnaml.html -argchoice:dnamlk:dnamlk.html -argchoice:dnamove:dnamove.html -argchoice:dnapars:dnapars.html -argchoice:dnapenny:dnapenny.html -argchoice:dollop:dollop.html -argchoice:dolmove:dolmove.html -argchoice:dolpenny:dolpenny.html -argchoice:draw:draw.html -argchoice:drawgram:drawgram.html -argchoice:drawtree:drawtree.html -argchoice:factor:factor.html -argchoice:fitch:fitch.html -argchoice:gendist:gendist.html -argchoice:kitsch:kitsch.html -argchoice:main:main.html -argchoice:mix:mix.html -argchoice:move:move.html -argchoice:neighbor:neighbor.html -argchoice:penny:penny.html -argchoice:protpars:protpars.html -argchoice:read.me.general:read.me.general.html -argchoice:restml:restml.html -argchoice:seqboot:seqboot.html -argchoice:sequence:sequence.html +argchoice:boot:boot.doc +argchoice:clique:clique.doc +argchoice:consense:consense.doc +argchoice:contchar:contchar.doc +argchoice:contml:contml.doc +argchoice:contrast:contrast.doc +argchoice:discrete:discrete.doc +argchoice:distance:distance.doc +argchoice:dnaboot:dnaboot.doc +argchoice:dnacomp:dnacomp.doc +argchoice:dnadist:dnadist.doc +argchoice:dnainvar:dnainvar.doc +argchoice:dnaml:dnaml.doc +argchoice:dnamlk:dnamlk.doc +argchoice:dnamove:dnamove.doc +argchoice:dnapars:dnapars.doc +argchoice:dnapenny:dnapenny.doc +argchoice:dolboot:dolboot.doc +argchoice:dollop:dollop.doc +argchoice:dolmove:dolmove.doc +argchoice:dolpenny:dolpenny.doc +argchoice:draw:draw.doc +argchoice:drawgram:drawgram.doc +argchoice:drawtree:drawtree.doc +argchoice:factor:factor.doc +argchoice:fitch:fitch.doc +argchoice:gendist:gendist.doc +argchoice:kitsch:kitsch.doc +argchoice:main:main.doc +argchoice:mix:mix.doc +argchoice:move:move.doc +argchoice:neighbor:neighbor.doc +argchoice:penny:penny.doc +argchoice:protpars:protpars.doc +argchoice:read.me.general:read.me.general.doc +argchoice:restml:restml.doc +argchoice:seqboot:seqboot.doc +argchoice:sequence:sequence.doc - -item:Phylip 3.5 -itemmethod:(rm -f outfile ; readseq -a -f12 in1 | sed "s/ YF//1" > infile;$PREEDIT /usr/bin/X11/xterm -e $PROGRAM;kedit outfile; treetool outtree; rm in1 )& +item:Phylip 3.4 +itemmethod:(rm -f outfile ; readseq -a -f12 in1 | sed "s/ YF//1" > infile;$PREEDIT shelltool $PROGRAM;textedit outfile;rm in1 )& arg:PROGRAM argtype:choice_list @@ -666,81 +879,358 @@ arg:PREEDIT argtype:chooser arglabel:Edit input before running? argchoice:No: -argchoice:Yes:kedit infile; +argchoice:Yes:textedit infile; in:in1 informat:genbank inmask: insave: - - - -item:Phylip DNA Distance methods -itemmethod:(readseq -a -f12 in1 | sed "s/ YF//1" > infile ;$PROG mv -f outfile infile; /usr/bin/X11/xterm -e dnadist;mv -f outfile infile; cp infile $DNA; /usr/bin/X11/xterm -e neighbor; cp outtree intree; cp outfile $NEI; $PROGRAM kedit outfile; cp outtree $TREE; treetool outtree; /bin/rm -f in1 infile outfile intree outtree)& -arg:EXPLAIN -argtype:text -arglabel:To produce a bootstraped tree choose DNADIST+NEIGHOR+CONSENSE - - +item:Phylip Distance methods +itemmethod:(readseq -a -f12 in1 | sed "s/ YF//1" > infile ; $PREEDIT shelltool dnadist;mv -f outfile infile;$PROGRAM textedit outfile;/bin/rm -f in1 infile outfile)& + arg:PROGRAM arglabel:Which method? argtype:chooser -argchoice:DNADIST+NEIGHBOR: -argchoice:DNADIST+NEIGHOR+CONSENSE: /usr/bin/X11/xterm -e consense; - -arg:PROG -arglabel:Run ? -argtype:chooser -argchoice:Run without Bootstrap: -argchoice:Run with Bootstrap: /usr/bin/X11/xterm -e seqboot; - -arg:DNA -argtype:text -arglabel:Name of DNADIST outfile? - -arg:NEI -argtype:text -arglabel:Name of NEIGHBOR outfile? - -arg:TREE -argtype:text -arglabel:Name of TREEFILE ? +argchoice:DNADIST:mv -f infile outfile; +argchoice:Fitch:shelltool fitch; +argchoice:Kitsch:shelltool kitsch; +argchoice:Neighbor:shelltool neighbor; arg:PREEDIT argtype:chooser arglabel:Edit input before running? argchoice:No: -argchoice:Yes:kedit infile; +argchoice:Yes:textedit infile; in:in1 informat:genbank inmask: insave: -item:Phylip PROTEIN Distance methods -itemmethod:(readseq -a -f12 in1 > infile ;$PROG mv -f outfile infile; /usr/bin/X11/xterm -e protdist;mv -f outfile infile; /usr/bin/X11/xterm -e neighbor; cp outtree intree; $PROGRAM kedit outfile;treetool outtree;/bin/rm -f in1 infile outfile)& - -arg:PROGRAM -arglabel:Which method? -argtype:chooser -argchoice:PROTDIST+NEIGHBOR: -argchoice:PROTDIST+NEIGHOR+CONSENSE: /usr/bin/X11/xterm -e consense; +menu:Email -arg:PROG -arglabel:Which method? -argtype:chooser -argchoice:Bootstrap: /usr/bin/X11/xterm -e seqboot; -argchoice:No Bootstrap: +item:BLASTN +itemmethod:(echo BLASTPROGRAM blastn > in1.tmp; echo DATALIB $DBASE >> in1.tmp; echo MATCH $MSCORE >> in1.tmp; echo BEGIN >> in1.tmp; sed "s/-//g" < in1 | tr '@%#' '>' >> in1.tmp; Mail BLAST@GENBANK.BIO.NET < in1.tmp; rm in1 in1.tmp) & -arg:PREEDIT +arg:DBASE +argtype:choice_list +arglabel:Which Database? +argchoice:GenBank Qtrly & Updates:GenBank +argchoice:EMBL:embl + +arg:MSCORE +argtype:slider +arglabel:Match Score +argmin:3 +argmax:7 +argvalue:5 + +in:in1 +informat:flat +insave: + +item:BLASTP +itemmethod:(echo BLASTPROGRAM blastp >in1.tmp; echo DATALIB $DBASE >> in1.tmp; echo BEGIN >> in1.tmp; sed "s/-//g" < in1 | tr '@%#' '>' >> in1.tmp; Mail BLAST@GENBANK.BIO.NET < in1.tmp; rm in1 in1.tmp) & + +arg:DBASE +argtype:choice_list +arglabel:Which Database? +argchoice:Swiss-Prot:swiss-prot +argchoice:PIR:pir + +in:in1 +informat:flat +insave: + +item:Fasta-(DNA) +itemmethod:(echo DATALIB $DBASE > in1.tmp; echo KTUP $KPL >> in1.tmp; echo SCORES $TOP >> in1.tmp; echo ALIGNMENTS $ALNG >> in1.tmp; echo BEGIN >> in1.tmp; sed "s/-//g" < in1 | tr '@%#' '>' >> in1.tmp;Mail SEARCH@GENBANK.BIO.NET < in1.tmp; rm in1 in1.tmp) & + +arg:DBASE +argtype:choice_list +arglabel:Which GenBank Database? +argchoice:Qrtly & Updates:GenBank/all +argchoice:Updates:GenBank/new +argchoice:Primate:GenBank/primate +argchoice:Rodent:GenBank/rodent +argchoice:Other-Mammalian:GenBank/other_mammalian +argchoice:Other-Vertebrate:GenBank/other_vertebrate +argchoice:Invertebrate:GenBank/invertebrate +argchoice:Plant:GenBank/plant +argchoice:Organelle:GenBank/organelle +argchoice:Bacterial:GenBank/bacterial +argchoice:Structural-RNA:GenBank/structural_rna +argchoice:Viral:GenBank/viral +argchoice:Phage:GenBank/phage +argchoice:Synthetic:GenBank/synthetic +argchoice:Unannotated:GenBank/unannotated + +arg:KPL +argtype:slider +arglabel:K-tuple window +argmin:3 +argmax:6 +argvalue:4 + +arg:TOP +argtype:slider +arglabel:Scores Displayed? +argmin:1 +argmax:200 +argvalue:100 + +arg:ALNG +argtype:slider +arglabel:# Alignments Displayed? +argmin:1 +argmax:200 +argvalue:20 + +in:in1 +informat:flat +insave: + +item:Fasta-(PROTEIN) +itemmethod:(echo DATALIB $DBASE > in1.tmp; echo KTUP $TPL >> in1.tmp; echo SCORES $SCRS >> in1.tmp; echo ALIGNMENTS $ALNMNTS >> in1.tmp; echo BEGIN >> in1.tmp; sed "s/-//g" < in1 | tr '@%#$' '>' >> in1.tmp; Mail SEARCH@GENBANK.BIO.NET < in1.tmp; rm in1 in1.tmp) & + +arg:DBASE +argtype:choice_list +arglabel:Which Protein Database? +argchoice:Trans GenBank Qrtly:GenPept/all +argchoice:Trans GenBank Daily:GenPept/new +argchoice:Swiss-Protein:SWISS-PROT/all + +arg:TPL +argtype:slider +arglabel:K-TUP window +argmin:1 +argmax:2 +argvalue:1 + +arg:SCRS +argtype:slider +arglabel:# Scores Displayed? +argmin:1 +argmax:200 +argvalue:100 + +arg:ALNMNTS +argtype:slider +arglabel:# Alignments Displayed? +argmin:1 +argmax:200 +argvalue:20 + +in:in1 +informat:flat +insave: + +item:GeneID +itemmethod:($REPRINT > in1.tmp; echo Genomic Sequence >> in1.tmp; sed "s/-//g" < in1 | tr '@%#' '>' >> in1.tmp; Mail geneid@darwin.bu.edu < in1.tmp; rm in1 in1.tmp) & + +arg:REPRINT argtype:chooser -arglabel:Edit input before running? +arglabel:Do you want a GENEID reprint? +argchoice:YES:echo "Preprint Request" >> in1.tmp +argchoice:NO + +in:in1 +informat:flat +insave: + +item:Sequence Retrieval +itemmethod:(echo $REGEXP > in1.tmp; Mail RETRIEVE@GENBANK.BIO.NET < in1.tmp; rm in1.tmp) & + +arg:REGEXP +argtype:text +arglabel:Accession # or LOCUS name of sequence to retrieve + +item:Grail +itemmethod:(echo Sequences $TOTALSEQS $ID > in1.tmp; sed "s/-//g" < in1 | tr '@%#' '>' >> in1.tmp; Mail grail@ornl.gov in1.tmp; echo $NAME >> in1.tmp; echo $ADDRESS >> in1.tmp; echo $PHONE >> in1.tmp; echo $EMAIL >> in1.tmp; Mail grail@ornl.gov < in1.tmp; rm in1.tmp) + +arg:NAME +argtype:text +arglabel:Your Name + +arg:ADDRESS +argtype:text +arglabel:Your Address + +arg:PHONE +argtype:text +arglabel:Your Phone Number + +arg:EMAIL +argtype:text +arglabel:Your E-Mail Address + + +# +# dgg added new readseq formats, 29 dec 92 +# + +item:Export Foreign Format +itemmethod:readseq in1 -pipe -all -form=$FORMAT > $OUTPUTFILE +itemhelp:readseq.help + +arg:FORMAT +argtype:choice_list +argchoice:GenBank:genbank +argchoice:IG/Stanford:ig +argchoice:NBRF:nbrf +argchoice:EMBL:embl +argchoice:GCG:gcg +argchoice:DNA Strider:strider +argchoice:Fitch:fitch +argchoice:Pearson/Fasta:pearson +argchoice:Zuker:zuker +argchoice:Olsen:olsen +argchoice:Phylip:phylip +#argchoice:Phylip v3.2:phylip3.2 +argchoice:Plain text:raw +argchoice:ASN.1:asn +argchoice:PIR:pir +argchoice:MSF:msf +argchoice:PAUP:paup +argchoice:Pretty:pretty -nametop -nameleft=3 -numright -nameright -numtop + +arg:OUTPUTFILE +argtype:text +arglabel:Save as? + +in:in1 +informat:genbank + + +# +#dgg addition for new readseq, 24 dec 92 +# + +item:Pretty Print +itemmethod:readseq in1 -p -a -f=pretty $NAMELEFT $NAMERIGHT $NUMTOP $NUMBOT $NUMLEFT $NUMRIGHT -col=$COLS -width=$WIDTH $MATCH $GAPC > in1.pretty; (textedit in1.pretty; /bin/rm -f in1 in1.pretty)& +itemhelp:readseq.help + +#nametop is bad !? + +in:in1 +informat:genbank + +arg:NAMETOP +argtype:chooser +arglabel:Names at top ? argchoice:No: -argchoice:Yes:kedit infile; - -in:in1 -informat:genbank -inmask: -insave: +argchoice:Yes:-nametop + +arg:NAMELEFT +argtype:chooser +arglabel:Names at left ? +argchoice:No: +argchoice:Yes:-nameleft + +arg:NAMERIGHT +argtype:chooser +arglabel:Names at right? +argchoice:Yes:-nameright +argchoice:No: + +arg:NUMTOP +argtype:chooser +arglabel:Numbers at top ? +argchoice:Yes:-numtop +argchoice:No: + +arg:NUMBOT +argtype:chooser +arglabel:Numbers at tail ? +argchoice:No: +argchoice:Yes:-numbot + +arg:NUMLEFT +argtype:chooser +arglabel:Numbers at left ? +argchoice:Yes:-numleft +argchoice:No: + +arg:NUMRIGHT +argtype:chooser +arglabel:Numbers at right? +argchoice:Yes:-numright +argchoice:No: + +arg:MATCH +argtype:chooser +arglabel:Use match '.' for 2..n species? +argchoice:No: +argchoice:Yes:-match + +arg:GAPC +argtype:chooser +arglabel:Count gap symbols? +argchoice:No: +argchoice:Yes:-gap + +arg:WIDTH +argtype:slider +arglabel:Sequence width? +argmin:10 +argmax:200 +argvalue:50 + +arg:COLS +argtype:slider +arglabel:Column spacers? +argmin:0 +argmax:50 +argvalue:10 + + +### pretty print insert end +# + +item:Wally's test function +itemmethod:run__wally $ONE $TWO $THREE < $FILE + +arg:ONE +argtype:chooser +arglabel:How? +argchoice:Fast:-fast +argchoice:Slow:-slow + +arg:TWO +argtype:slider +argmin:0 +argmax:100 +argvalue:50 +arglabel:how many? + +arg:THREE +argtype:choice_list +arglabel:Which one? +argchoice:Fast:-fast +argchoice:Slow:-slow + +arg:FILE +argtype:text +arglabel:Which file diff --git a/CORE/.GDEmenus.linux b/CORE/.GDEmenus.linux new file mode 100644 index 0000000..76ae008 --- /dev/null +++ b/CORE/.GDEmenus.linux @@ -0,0 +1,746 @@ +1menu:File + +item:test cmask output +itemmethod: kedit in1 + +in:in1 +informat:colormask + +item:New sequence +itemmethod:echo "$Type$Name" > out1 +itemmeta:n +itemhelp:new_sequence.help + +arg:Name +argtype:text +arglabel:New Sequence name? +argtext:New + +arg:Type +argtype:choice_list +arglabel:Type? +argchoice:DNA/RNA:# +argchoice:Amino Acid:% +argchoice:Text:\" +argchoice:Mask:@ + +out:out1 +outformat:flat + +item:Import Foreign Format +itemmethod:cp $INPUTFILE OUTFILE.tmp;readseq OUTFILE.tmp -a -f2 > OUTPUTFILE;/bin/rm -f OUTFILE.tmp +itemhelp:readseq.help + +arg:INPUTFILE +argtype:text +arglabel:Name of foreign file? + +out:OUTPUTFILE +outformat:genbank + +item:Export Foreign Format +itemmethod:readseq INPUTFILE -a -f$FORMAT > $OUTPUTFILE +itemhelp:readseq.help + +arg:FORMAT +argtype:choice_list +argchoice:FASTA:8 +argchoice:NEXUS:17 +argchoice:Phylip v3.3:12 +argchoice:IG/Stanford:1 +argchoice:GenBank:2 +argchoice:NBRF:3 +argchoice:EMBL:4 +argchoice:GCG:5 +argchoice:DNA Strider:6 +argchoice:Fitch:7 +argchoice:Pearson:8 +argchoice:Zuker:9 +argchoice:Olsen:10 +argchoice:Phylip v3.2:11 +argchoice:Phylip v3.3:12 +argchoice:Plain text:13 + +arg:OUTPUTFILE +argtype:text +arglabel:Save as? + +in:INPUTFILE +informat:genbank + + +item:Save Selection +itemmethod: cat $SAVE_FUNC > $Name +itemhelp:save_selection.help + +arg:SAVE_FUNC +argtype:chooser +arglabel:File format +argchoice:Flat:in1 +argchoice:Genbank:in2 +argchoice:GDE/HGL:in3 + +arg:Name +argtype:text +arglabel:File name? + +in:in1 +informat:flat + +in:in2 +informat:genbank + +in:in3 +informat:gde + +item:Print Selection +itemmethod:(PrintStrat in1 $SCALE > in1.tmp; $CMD -P$PRINTER in1.tmp; /bin/rm -f in1 in1.tmp)& +itemhelp:print_alignment.help + +arg:SCALE +argtype:slider +arglabel:Reduce printout by? +argmin:1 +argmax:20 +argvalue:1 + +arg:CMD +argtype:chooser +argchoice:Lpr:lpr +argchoice:Enscript Gaudy:enscript -G -q +argchoice:Enscript Two column:enscript -2rG + +arg:PRINTER +argtype:text +arglabel:Which printer? +argtext:lp + +in:in1 +informat:gde +insave: + +menu:Edit + +item:Sort +itemmethod:(heapsortHGL in1 $PRIM_KEY $SEC_KEY > in1.tmp ; gde in1.tmp;/bin/rm -f in1*)& +itemhelp:heapsortHGL.help + +arg:PRIM_KEY +argtype:choice_list +argchoice:Group:group-ID +argchoice:type:type +argchoice:name:name +argchoice:Sequence ID:sequence-ID +argchoice:creator:creator +argchoice:offset:offset +arglabel:Primary sort field? + +arg:SEC_KEY +argtype:choice_list +argchoice:None: +argchoice:Group:group-ID +argchoice:type:type +argchoice:name:name +argchoice:Sequence ID:sequence-ID +argchoice:creator:creator +argchoice:offset:offset +arglabel:Secondary sort field? + +in:in1 +informat:gde +insave: + +item:extract +itemmethod:(gde in1;/bin/rm -f in1)& + +in:in1 +informat:gde +inmask: +insave: + +menu:DNA/RNA + +item:Translate... +itemmethod:Translate -tbl $TBL -frame $FRAME -min_frame $MNFRM $LTRCODE in1 > out1 + +arg:FRAME +argtype:chooser +arglabel:Which reading frame? +argchoice:First:1 +argchoice:Second:2 +argchoice:Third:3 +argchoice:All six:6 + +arg:MNFRM +arglabel:Minimum length of AA sequence to translate? +argtype:slider +argmin:0 +argmax:100 +argvalue:20 + +arg:LTRCODE +argtype:chooser +arglabel:Translate to: +argchoice:Single letter codes: +argchoice:Triple letter codes:-3 + +arg:TBL +arglabel:Codon table? +argtype:chooser +argchoice:universal:1 +argchoice:mycoplasma:2 +argchoice:yeast:3 +argchoice:Vert. mito.:4 +in:in1 +informat:gde + +out:out1 +outformat:gde + +item:Dot plot +itemmethod:(DotPlotTool in1 ; /bin/rm -f in1)& +itemhelp:DotPlotTool.help + +in:in1 +informat:gde +insave: + +item:Clustal alignment +itemmethod:(tr '%#' '>'clus_in;clustalw -quicktree -output=PIR -infile=clus_in -align > in1.rpt;sed "s/>DL;/#/g" < clus_in.pir> in1;$REPORT gde in1;/bin/rm -f clus_in* in1* )& + +itemhelp:clustal_help + +arg:KTUP +argtype:slider +arglabel:K-tuple size for pairwise search +argmin:1 +argmax:10 +argvalue:2 + +arg:WIN +argtype:slider +arglabel:Window size +argmin:1 +argmax:10 +argvalue:4 + +arg:Trans +argtype:chooser +arglabel:Transitions weighted? +argchoice:Yes:/TRANSIT +argchoice:No: + +arg:FIXED +argtype:slider +arglabel:Fixed gap penalty +argmin:1 +argmax:100 +argvalue:10 + +arg:FLOAT +arglabel:Floating gap penalty +argtype:slider +argmin:1 +argmax:100 +argvalue:10 + +arg:REPORT +argtype:chooser +arglabel:View assembly report? +argchoice:No: +argchoice:Yes:kedit in1.rpt& + + +in:in1 +informat:flat +insave: + +item:Variable Positions +itemmethod:varpos $REV < in1 > out1 + +arg:REV +argtype:chooser +arglabel:Highlight (darken) +argchoice:Conserved positions: +argchoice:variable positions:-rev + +in:in1 +informat:flat + +out:out1 +outformat:colormask + +item:Phrap +itemmethod:readseq in1 -a -f8 > OUTPUTFILE;/bin/rm -f OUTFILE.tmp; phrap OUTPUTFILE; readseq -a -f2 OUTPUTFILE.contigs > out1;/bin/rm -rf OUTPUT*; + +in:in1 +informat:genbank + +out:out1 +outformat:genbank + +item:SNAP +itemmethod: cat in1 > infile;/usr/local/bio/GDE/bin/fasta2snap.pl > outfile; /usr/bin/X11/xterm -e /home/tulio/bio/SNAP/SNAP.pl outfile; kedit backg*; kedit summ*; sheeltool /home/tulio/bio/codons-xyplot.pl codons.*; kedit codon.data; /bin/rm -rf back* codon* summ*; + +in:in1 +informat:flat +out:out1 +outformat:text + + + + +item:Find all +itemmethod:findall $SEARCH $PRCNT $CASE $UT -match $MAT -mismatch $MIS < in1 > out1; +itemhelp:findall.help +itemmeta:f + +arg:SEARCH +argtype:text +arglabel:Search String + +arg:PRCNT +argtype:slider +arglabel:Percent mismatch +argmin:0 +argmax:75 +argvalue:10 + +arg:CASE +argtype:chooser +arglabel:Case +argchoice:Upper equals lower: +argchoice:Upper not equal lower:-case + +arg:UT +argtype:chooser +arglabel:U equal T? +argchoice:Yes:-u=t +argchoice:No: +argvalue:0 + +arg:MAT +arglabel:Match color +argtype:choice_list +argchoice:yellow:1 +argchoice:violet:2 +argchoice:red:3 +argchoice:aqua:4 +argchoice:green:5 +argchoice:blue:6 +argchoice:grey:11 +argchoice:black:8 +argvalue:2 + +arg:MIS +argtype:choice_list +arglabel:Mismatch color +argchoice:yellow:1 +argchoice:violet:2 +argchoice:red:3 +argchoice:aqua:4 +argchoice:green:5 +argchoice:blue:6 +argchoice:grey:11 +argchoice:black:8 +argvalue:7 + +in:in1 +informat:flat + +out:out1 +outformat:colormask + +item:Sequence Consensus +itemmethod:(MakeCons in1 $METHOD $MASK > out1) +itemhelp:MakeCons.help + +arg:METHOD +arglabel:Method +argtype:chooser +argchoice:IUPAC:-iupac +argchoice:Majority:-majority $PERCENT + +arg:MASK +argtype:chooser +arglabel:Create a new: +argchoice:Sequence: +argchoice:Selection Mask: | Consto01mask + +arg:PERCENT +arglabel:Minimum Percentage for Majority +argtype:slider +argmin:50 +argmax:100 +argvalue:75 + +in:in1 +informat:gde + +out:out1 +outformat:gde + + +#Menu for DNA/RNA + +item:blastn +itemmethod:(sed "s/[#%]/>/" in1.f; /usr/local/bio/blast/blastall -p blastn -d $BLASTDBDNA -i in1.f -W $WORDLEN -M $MATCH > in1.tmp; kedit in1.tmp; rm in1*)& + +in:in1 +informat:flat +insave: + +arg:BLASTDBDNA +argtype:choice_list +arglabel:Which Database +argchoice:HIV-1 Seq. Db.:/usr/local/bio/db/DNA/hiv17-08-01.fasta2 +arg:WORDLEN +argtype:slider +arglabel:Word Size +argmin:4 +argmax:18 +argvalue:12 + +arg:MATCH +argtype:slider +arglabel:Match Score +argmin:1 +argmax:10 +argvalue:5 + +arg:MMSCORE +argtype:slider +arglabel:Mismatch Score +argmin:-10 +argmax:-1 +argvalue:-5 + +item:blastx +itemmethod:(sed "s/[#%]/>/" in1.f; /usr/local/bio/blast/blastall -p blastx -d $BLASTDB -i in1.f -W $WORDLEN -M PAM30 > in1.tmp; /usr/openwin/bin/kedit in1.tmp; rm in1*)& + + + +in:in1 +informat:flat +insave: + +arg:BLASTDBDNA +argtype:choice_list +arglabel:Which Database +argchoice:HIV Proteins:/usr/local/bio/db/hiv17-08-01.PROT.fasta +argchoice:genpept:$GDE_HELP_DIR/BLAST/genpept + +arg:WORDLEN +argtype:slider +arglabel:Word Size +argmin:1 +argmax:5 +argvalue:3 + +arg:Matrix +arglabel:Substitution Matrix: +argtype:choice_list +argchoice:PAM30:PAM30 +argchoice:PAM70:PAM70 + +arg:CODE +argtype:choice_list +arglabel:Genetic Code + +argchoice:Standard or Universal:0 +argchoice:Vertebrate Mitochondrial:1 +argchoice:Yeast Mitochondrial:2 +argchoice:Mold Mitochondrial and Mycoplasma:3 +argchoice:Invertebrate Mitochondrial:4 +argchoice:Ciliate Macronuclear:5 +argchoice:Protozoan Mitochondrial:6 +argchoice:Plant Mitochondrial:7 +argchoice:Echinodermate Mitochondrial:8 + +item:------------------------ + +item:Add a new DNA blast db +itemmethod:xterm -e formatdb -i $sourcefile -p F -o T; /usr/local/bio/GDE/bin/installBLASTDB.pl $sourcefile $menuname; + +arg:sourcefile +argtype:text +arglabel: enter the file name + +arg:menuname +argtype:text +arglabel: enter the name of the DB + + +#Sequence dataset +menu:seq. datasets + + +item:------------- +item:add a new dataset +itemmethod:mkdir db; cp $file db/ ;xterm -e /usr/local/bio/GDE/newDATASET.pl $name $file + +arg:name +argtype:text +arglabel:Enter the dataset name ? + +arg:file +argtype:text +arglabel:Enter the dataset file (in FASTA) ? + + +#Menu for Protein +menu:protein +item:blastp +itemmethod:(sed "s/[#%]/>/" in1.f; cp /usr/local/bio/db/PAM30; /usr/local/bio/blast/blastall -p blastp -d $BLASTDBPROT -i in1.f -W $WORDLEN -M $Matrix > in1.tmp; /usr/openwin/bin/kedit in1.tmp; rm in1* PAM30)& + + +in:in1 +informat:flat +insave: + +arg:BLASTDBPROT +argtype:choice_list +arglabel:Which Database +argchoice:HIV Proteins:/usr/local/bio/db/hiv17-08-01.PROT.fasta + +arg:Matrix +barglabel:Substitution Matrix: +argtype:choice_list +argchoice:PAM30:PAM30 +argchoice:PAM70:PAM70 + +arg:WORDLEN +argtype:slider +arglabel:Word Size +argmin:1 +argmax:5 +argvalue:3 + +item:tblastn +itemmethod:(sed "s/[#%]/>/" in1.f; cp /usr/local/bio/db/PAM??? .; tblastn $BLASTDB in1.f W=$WORDLEN M=$Matrix C=$CODE > in1.tmp; kedit in1.tmp; rm in1* PAM???)& + +in:in1 +informat:flat +insave: + +arg:BLASTDB +argtype:choice_list +arglabel:Which Database +argchoice:genbank:$GDE_HELP_DIR/BLAST/genbank +argchoice:genbank update:$GDE_HELP_DIR/BLAST/genupdate + +arg:Matrix +arglabel:Substitution Matrix: +argtype:choice_list +argchoice:PAM30:PAM30 +argchoice:PAM70:PAM70 + +arg:WORDLEN +argtype:slider +arglabel:Word Size +argmin:4 +argmax:18 +argvalue:12 + +arg:CODE +argtype:choice_list +arglabel:Genetic Code +argchoice:Standard or Universal:0 +argchoice:Vertebrate Mitochondrial:1 +argchoice:Yeast Mitochondrial:2 +argchoice:Mold Mitochondrial and Mycoplasma:3 +argchoice:Invertebrate Mitochondrial:4 +argchoice:Ciliate Macronuclear:5 +argchoice:Protozoan Mitochondrial:6 +argchoice:Plant Mitochondrial:7 +argchoice:Echinodermate Mitochondrial:8 + + +item:Map View +itemmethod:(mapview in1 -pbl $PBL -npp $NPP; /bin/rm -f in1)& +itemhelp:mapview.help + +in:in1 +informat:gde +insave: + +arg:PBL +arglabel:Pixel Between Lines +argtype:slider +argvalue:10 +argmin:1 +argmax:15 + +arg:NPP +arglabel:Nucleotides Per Pixel +argtype:slider +argvalue:1 +argmin:1 +argmax:20 + +arg:LWIDTH +arglabel:Line Thickness +argtype:slider +argvalue:2 +argmin:1 +argmax:5 + +item:-------------------------- +item:Add a new Protein blast db +itemmethod:xterm -e formatdb -i $sourcefile -p T -o T; /usr/local/bio/GDE/bin/installBLASTDBPROT.pl $sourcefile $menuname; + +arg:sourcefile +argtype:text +arglabel: Enter the file (in FASTA) + +arg:menuname +argtype:text +arglabel: Enter the name of the DB + +#Phylogenetic Menu + +menu:Phylogeny + +item:Phylip help +itemmethod:(netscape /usr/local/bio/phylip/doc/$FILE)& + +arg:FILE +argtype:choice_list +arglabel:Which program? +argchoice:clique:clique.html +argchoice:consense:consense.html +argchoice:contchar:contchar.html +argchoice:contml:contml.html +argchoice:contrast:contrast.html +argchoice:discrete:discrete.html +argchoice:distance:distance.html +argchoice:dnaboot:dnaboot.html +argchoice:dnacomp:dnacomp.html +argchoice:dnadist:dnadist.html +argchoice:dnainvar:dnainvar.html +argchoice:dnaml:dnaml.html +argchoice:dnamlk:dnamlk.html +argchoice:dnamove:dnamove.html +argchoice:dnapars:dnapars.html +argchoice:dnapenny:dnapenny.html +argchoice:dollop:dollop.html +argchoice:dolmove:dolmove.html +argchoice:dolpenny:dolpenny.html +argchoice:draw:draw.html +argchoice:drawgram:drawgram.html +argchoice:drawtree:drawtree.html +argchoice:factor:factor.html +argchoice:fitch:fitch.html +argchoice:gendist:gendist.html +argchoice:kitsch:kitsch.html +argchoice:main:main.html +argchoice:mix:mix.html +argchoice:move:move.html +argchoice:neighbor:neighbor.html +argchoice:penny:penny.html +argchoice:protpars:protpars.html +argchoice:read.me.general:read.me.general.html +argchoice:restml:restml.html +argchoice:seqboot:seqboot.html +argchoice:sequence:sequence.html + + + +item:Phylip 3.5 +itemmethod:(rm -f outfile ; readseq -a -f12 in1 | sed "s/ YF//1" > infile;$PREEDIT /usr/bin/X11/xterm -e $PROGRAM;kedit outfile; treetool outtree; rm in1 )& + +arg:PROGRAM +argtype:choice_list +arglabel:Which program to run? +argchoice:DNAPARS:dnapars +argchoice:DNABOOT:dnaboot +argchoice:DNAPENNY:dnapenny +argchoice:DNAML:dnaml +argchoice:DNAMLK:dnamlk +argchoice:DNACOMP:dnacomp +argchoice:DNAMOVE:dnamove +argchoice:DNAINVAR:dnainvar +argchoice:PROTPARS:protpars + +arg:PREEDIT +argtype:chooser +arglabel:Edit input before running? +argchoice:No: +argchoice:Yes:kedit infile; + +in:in1 +informat:genbank +inmask: +insave: + + + +item:Phylip DNA Distance methods +itemmethod:(readseq -a -f12 in1 | sed "s/ YF//1" > infile ;$PROG mv -f outfile infile; /usr/bin/X11/xterm -e dnadist;mv -f outfile infile; cp infile $DNA; /usr/bin/X11/xterm -e neighbor; cp outtree intree; cp outfile $NEI; $PROGRAM kedit outfile; cp outtree $TREE; treetool outtree; /bin/rm -f in1 infile outfile intree outtree)& + +arg:EXPLAIN +argtype:text +arglabel:To produce a bootstraped tree choose DNADIST+NEIGHOR+CONSENSE + + +arg:PROGRAM +arglabel:Which method? +argtype:chooser +argchoice:DNADIST+NEIGHBOR: +argchoice:DNADIST+NEIGHOR+CONSENSE: /usr/bin/X11/xterm -e consense; + +arg:PROG +arglabel:Run ? +argtype:chooser +argchoice:Run without Bootstrap: +argchoice:Run with Bootstrap: /usr/bin/X11/xterm -e seqboot; + +arg:DNA +argtype:text +arglabel:Name of DNADIST outfile? + +arg:NEI +argtype:text +arglabel:Name of NEIGHBOR outfile? + +arg:TREE +argtype:text +arglabel:Name of TREEFILE ? + +arg:PREEDIT +argtype:chooser +arglabel:Edit input before running? +argchoice:No: +argchoice:Yes:kedit infile; + +in:in1 +informat:genbank +inmask: +insave: + +item:Phylip PROTEIN Distance methods +itemmethod:(readseq -a -f12 in1 > infile ;$PROG mv -f outfile infile; /usr/bin/X11/xterm -e protdist;mv -f outfile infile; /usr/bin/X11/xterm -e neighbor; cp outtree intree; $PROGRAM kedit outfile;treetool outtree;/bin/rm -f in1 infile outfile)& + +arg:PROGRAM +arglabel:Which method? +argtype:chooser +argchoice:PROTDIST+NEIGHBOR: +argchoice:PROTDIST+NEIGHOR+CONSENSE: /usr/bin/X11/xterm -e consense; + +arg:PROG +arglabel:Which method? +argtype:chooser +argchoice:Bootstrap: /usr/bin/X11/xterm -e seqboot; +argchoice:No Bootstrap: + +arg:PREEDIT +argtype:chooser +arglabel:Edit input before running? +argchoice:No: +argchoice:Yes:kedit infile; + +in:in1 +informat:genbank +inmask: +insave: + diff --git a/CORE/.GDEmenus.sunos b/CORE/.GDEmenus.sunos new file mode 100644 index 0000000..40d513f --- /dev/null +++ b/CORE/.GDEmenus.sunos @@ -0,0 +1,1236 @@ +menu:File + +item:test cmask output +itemmethod: textedit in1 + +in:in1 +informat:colormask + +item:New sequence +itemmethod:echo "$Type$Name" > out1 +itemmeta:n +itemhelp:new_sequence.help + +arg:Name +argtype:text +arglabel:New Sequence name? +argtext:New + +arg:Type +argtype:choice_list +arglabel:Type? +argchoice:DNA/RNA:# +argchoice:Amino Acid:% +argchoice:Text:\" +argchoice:Mask:@ + +out:out1 +outformat:flat + +item:Import Foreign Format +itemmethod:cp $INPUTFILE OUTFILE.tmp;readseq OUTFILE.tmp -a -f2 > OUTPUTFILE;/bin/rm -f OUTFILE.tmp +itemhelp:readseq.help + +arg:INPUTFILE +argtype:text +arglabel:Name of foreign file? + +out:OUTPUTFILE +outformat:genbank + +item:Export Foreign Format +itemmethod:readseq INPUTFILE -a -f$FORMAT > $OUTPUTFILE +itemhelp:readseq.help + +arg:FORMAT +argtype:choice_list +argchoice:IG/Stanford:1 +argchoice:GenBank:2 +argchoice:NBRF:3 +argchoice:EMBL:4 +argchoice:GCG:5 +argchoice:DNA Strider:6 +argchoice:Fitch:7 +argchoice:Pearson:8 +argchoice:Zuker:9 +argchoice:Olsen:10 +argchoice:Phylip v3.2:11 +argchoice:Phylip v3.3:12 +argchoice:Plain text:13 + +arg:OUTPUTFILE +argtype:text +arglabel:Save as? + +in:INPUTFILE +informat:genbank + + +item:Save Selection +itemmethod: cat $SAVE_FUNC > $Name +itemhelp:save_selection.help + +arg:SAVE_FUNC +argtype:chooser +arglabel:File format +argchoice:Flat:in1 +argchoice:Genbank:in2 +argchoice:GDE/HGL:in3 + +arg:Name +argtype:text +arglabel:File name? + +in:in1 +informat:flat + +in:in2 +informat:genbank + +in:in3 +informat:gde + +item:Print Selection +itemmethod:(PrintStrat in1 $SCALE > in1.tmp; $CMD -P$PRINTER in1.tmp; /bin/rm -f in1 in1.tmp)& +itemhelp:print_alignment.help + +arg:SCALE +argtype:slider +arglabel:Reduce printout by? +argmin:1 +argmax:20 +argvalue:1 + +arg:CMD +argtype:chooser +argchoice:Lpr:lpr +argchoice:Enscript Gaudy:enscript -G -q +argchoice:Enscript Two column:enscript -2rG + +arg:PRINTER +argtype:text +arglabel:Which printer? +argtext:lp + +in:in1 +informat:gde +insave: + +menu:Edit + +item:Sort +itemmethod:(heapsortHGL in1 $PRIM_KEY $SEC_KEY > in1.tmp ; gde in1.tmp;/bin/rm -f in1*)& +itemhelp:heapsortHGL.help + +arg:PRIM_KEY +argtype:choice_list +argchoice:Group:group-ID +argchoice:type:type +argchoice:name:name +argchoice:Sequence ID:sequence-ID +argchoice:creator:creator +argchoice:offset:offset +arglabel:Primary sort field? + +arg:SEC_KEY +argtype:choice_list +argchoice:None: +argchoice:Group:group-ID +argchoice:type:type +argchoice:name:name +argchoice:Sequence ID:sequence-ID +argchoice:creator:creator +argchoice:offset:offset +arglabel:Secondary sort field? + +in:in1 +informat:gde +insave: + +item:extract +itemmethod:(gde in1;/bin/rm -f in1)& + +in:in1 +informat:gde +inmask: +insave: + +menu:DNA/RNA + +item:Translate... +itemmethod:Translate -tbl $TBL -frame $FRAME -min_frame $MNFRM $LTRCODE in1 > out1 + +arg:FRAME +argtype:chooser +arglabel:Which reading frame? +argchoice:First:1 +argchoice:Second:2 +argchoice:Third:3 +argchoice:All six:6 + +arg:MNFRM +arglabel:Minimum length of AA sequence to translate? +argtype:slider +argmin:0 +argmax:100 +argvalue:20 + +arg:LTRCODE +argtype:chooser +arglabel:Translate to: +argchoice:Single letter codes: +argchoice:Triple letter codes:-3 + +arg:TBL +arglabel:Codon table? +argtype:chooser +argchoice:universal:1 +argchoice:mycoplasma:2 +argchoice:yeast:3 +argchoice:Vert. mito.:4 +in:in1 +informat:gde + +out:out1 +outformat:gde + +item:Dot plot +itemmethod:(DotPlotTool in1 ; /bin/rm -f in1)& +itemhelp:DotPlotTool.help + +in:in1 +informat:gde +insave: + +item:Clustal alignment +itemmethod:(tr '%#' '>'clus_in;clustalv /output=PIR /infile=clus_in /align /ktup=$KTUP /window=$WIN $Trans /fixedgap=$FIXED /floatgap=$FLOAT > in1.rpt;sed "s/>DL;/#/g" < clus_in.pir> in1;$REPORT gde in1; /bin/rm -f clus_in* in1* )& + +itemhelp:clustal_help + +arg:KTUP +argtype:slider +arglabel:K-tuple size for pairwise search +argmin:1 +argmax:10 +argvalue:2 + +arg:WIN +argtype:slider +arglabel:Window size +argmin:1 +argmax:10 +argvalue:4 + +arg:Trans +argtype:chooser +arglabel:Transitions weighted? +argchoice:Yes:/TRANSIT +argchoice:No: + +arg:FIXED +argtype:slider +arglabel:Fixed gap penalty +argmin:1 +argmax:100 +argvalue:10 + +arg:FLOAT +arglabel:Floating gap penalty +argtype:slider +argmin:1 +argmax:100 +argvalue:10 + +arg:REPORT +argtype:chooser +arglabel:View assembly report? +argchoice:No: +argchoice:Yes:textedit in1.rpt& + + +in:in1 +informat:flat +insave: + +item:Variable Positions +itemmethod:varpos $REV < in1 > out1 + +arg:REV +argtype:chooser +arglabel:Highlight (darken) +argchoice:Conserved positions: +argchoice:variable positions:-rev + +in:in1 +informat:flat + +out:out1 +outformat:colormask + + +item:Find all +itemmethod:findall $SEARCH $PRCNT $CASE $UT -match $MAT -mismatch $MIS < in1 > out1; +itemhelp:findall.help +itemmeta:f + +arg:SEARCH +argtype:text +arglabel:Search String + +arg:PRCNT +argtype:slider +arglabel:Percent mismatch +argmin:0 +argmax:75 +argvalue:10 + +arg:CASE +argtype:chooser +arglabel:Case +argchoice:Upper equals lower: +argchoice:Upper not equal lower:-case + +arg:UT +argtype:chooser +arglabel:U equal T? +argchoice:Yes:-u=t +argchoice:No: +argvalue:0 + +arg:MAT +arglabel:Match color +argtype:choice_list +argchoice:yellow:1 +argchoice:violet:2 +argchoice:red:3 +argchoice:aqua:4 +argchoice:green:5 +argchoice:blue:6 +argchoice:grey:11 +argchoice:black:8 +argvalue:2 + +arg:MIS +argtype:choice_list +arglabel:Mismatch color +argchoice:yellow:1 +argchoice:violet:2 +argchoice:red:3 +argchoice:aqua:4 +argchoice:green:5 +argchoice:blue:6 +argchoice:grey:11 +argchoice:black:8 +argvalue:7 + +in:in1 +informat:flat + +out:out1 +outformat:colormask + +item:Sequence Consensus +itemmethod:(MakeCons in1 $METHOD $MASK > out1) +itemhelp:MakeCons.help + +arg:METHOD +arglabel:Method +argtype:chooser +argchoice:IUPAC:-iupac +argchoice:Majority:-majority $PERCENT + +arg:MASK +argtype:chooser +arglabel:Create a new: +argchoice:Sequence: +argchoice:Selection Mask: | Consto01mask + +arg:PERCENT +arglabel:Minimum Percentage for Majority +argtype:slider +argmin:50 +argmax:100 +argvalue:75 + +in:in1 +informat:gde + +out:out1 +outformat:gde + + +item:MFOLD +itemmethod:(tr 'a-z' 'A-Z' < seqGB > .GDE.tmp.caps; ZUKERGDE.sh .GDE.tmp.caps $CT $GDE_HELP_DIR/ZUKER/ > out1 && $METHOD < out1; Zuk_to_gen < $CT >file.gen; gde file.gen& textedit RegionTable; /bin/rm -f RegionTable out1 seqGB* .GDE.tmp.caps)& +itemhelp:MFOLD.help + +in:seqGB +informat:genbank +insave: + +arg:METHOD +argtype:chooser +arglabel:RNA type +argchoice:Fold Linear RNA:lrna +argchoice:Fold Circular RNA:crna + +arg:CT +argtype:text +arglabel:Pairing(ct) File Name +argtext:mfold_out + + +item:Draw Secondary structure +itemmethod:(LoopTool $TEMPLATE in1 ; /bin/rm -f in1) & +itemhelp:LoopTool.help + +arg:TEMPLATE +argtype:chooser +arglabel:Use template file ./loop.temp? +argchoice:No: +argchoice:Yes:-t loop.temp + +in:in1 +informat:genbank +insave: + +item:Highlight helix +itemmethod:readseq -a -f8 in1 | sed "s/>HELIX/\"HELIX/" > in1.flat; sho_helix < in1.flat > out1;rm in1.flat +itemhelp:sho_helix.help + +in:in1 +informat:genbank + +out:out1 +outformat:colormask + + +#Menu for DNA/RNA + +item:blastn +itemmethod:(sed "s/[#%]/>/" in1.f; blastn $BLASTDB in1.f W=$WORDLEN M=$MATCH N=$MMSCORE > in1.tmp; textedit in1.tmp; rm in1*)& + +in:in1 +informat:flat +insave: + +arg:BLASTDB +argtype:choice_list +arglabel:Which Database +argchoice:genbank:$GDE_HELP_DIR/BLAST/genbank +argchoice:genbank update:$GDE_HELP_DIR/BLAST/genupdate + +arg:WORDLEN +argtype:slider +arglabel:Word Size +argmin:4 +argmax:18 +argvalue:12 + +arg:MATCH +argtype:slider +arglabel:Match Score +argmin:1 +argmax:10 +argvalue:5 + +arg:MMSCORE +argtype:slider +arglabel:Mismatch Score +argmin:-10 +argmax:-1 +argvalue:-5 + +item:blastx +itemmethod:(sed "s/[#%]/>/" in1.f; cp $GDE_HELP_DIR/BLAST/PAM??? .; blastx $BLASTDB in1.f W=$WORDLEN M=$Matrix C=$CODE> in1.tmp; textedit in1.tmp; rm in1* PAM???)& + +in:in1 +informat:flat +insave: + +arg:BLASTDB +argtype:choice_list +arglabel:Which Database +argchoice:pir1:$GDE_HELP_DIR/BLAST/pir +argchoice:genpept:$GDE_HELP_DIR/BLAST/genpept + +arg:WORDLEN +argtype:slider +arglabel:Word Size +argmin:1 +argmax:5 +argvalue:3 + +arg:Matrix +arglabel:Substitution Matrix: +argtype:choice_list +argchoice:PAM120:PAM120 +argchoice:PAM250:PAM250 + +arg:CODE +argtype:choice_list +arglabel:Genetic Code +argchoice:Standard or Universal:0 +argchoice:Vertebrate Mitochondrial:1 +argchoice:Yeast Mitochondrial:2 +argchoice:Mold Mitochondrial and Mycoplasma:3 +argchoice:Invertebrate Mitochondrial:4 +argchoice:Ciliate Macronuclear:5 +argchoice:Protozoan Mitochondrial:6 +argchoice:Plant Mitochondrial:7 +argchoice:Echinodermate Mitochondrial:8 + + +item:FASTA (DNA/RNA) +itemmethod:(sed "s/[#%]/>/"in1.fasta;fasta -Q -d $NUMOFALN $MATRIX in1.fasta $DBASE > in1.out; textedit in1.out;\rm in1*) & +itemhelp:FASTA.help + +in:in1 +informat:flat + +arg:DBASE +argtype:choice_list +arglabel:Database +argchoice:GenBank Primate:$GDE_HELP_DIR/FASTA/GENBANK/gbpri.seq\ 1 +argchoice:GenBank Rodent:$GDE_HELP_DIR/FASTA/GENBANK/gbrod.seq\ 1 +argchoice:GenBank all Mammal:$GDE_HELP_DIR/FASTA/GENBANK/gbmam.seq\ 1 +argchoice:GenBank verteBrates:$GDE_HELP_DIR/FASTA/GENBANK/gbvrt.seq\ 1 +argchoice:GenBank Inverts:$GDE_HELP_DIR/FASTA/GENBANK/gbinv.seq\ 1 +argchoice:GenBank pLants:$GDE_HELP_DIR/FASTA/GENBANK/gbpln.seq\ 1 +argchoice:GenBank Struct RNA:$GDE_HELP_DIR/FASTA/GENBANK/gbrna.seq\ 1 +argchoice:GenBank euk. Organelles:$GDE_HELP_DIR/FASTA/GENBANK/gborg.seq\ 1 +argchoice:GenBank phaGe:$GDE_HELP_DIR/FASTA/GENBANK/gbphg.seq\ 1 +argchoice:GenBank bacTeria:$GDE_HELP_DIR/FASTA/GENBANK/gbbct.seq\ 1 +argchoice:GenBank sYnthetic:$GDE_HELP_DIR/FASTA/GENBANK/gbsyn.seq\ 1 +argchoice:GenBank Viral:$GDE_HELP_DIR/FASTA/GENBANK/gbvrl.seq\ 1 +argchoice:GenBank Unannotated:$GDE_HELP_DIR/FASTA/GENBANK/gbuna.seq\ 1 + +arg:NUMOFALN +argtype:slider +arglabel:Number of Alignment to Report +argmin:1 +argmax:100 +argvalue:20 + +arg:MATRIX +arglabel:Which SMATRIX +argtype:choice_list +argchoice:Default: +argchoice:altdiag.mat:-s $GDE_HELP_DIR/FASTA/MATRIX/altdiag.mat +argchoice:altprot.mat:-s $GDE_HELP_DIR/FASTA/MATRIX/altprot.mat +argchoice:dna.mat:-s $GDE_HELP_DIR/FASTA/MATRIX/dna.mat +argchoice:prot.mat:-s $GDE_HELP_DIR/FASTA/MATRIX/prot.mat + +menu:Protein + +item:Clustal Protein Alignment +itemmethod:(tr '%#"' '>' clus_in;clustalv /output=PIR /infile=clus_in /align /ktup=$KTUP /window=$WIN $Matrx /fixedgap=$FIXED /floatgap=$FLOAT > in1.rpt;sed "s/>P1;/%/g" < clus_in.pir > in1;$REPORT gde in1;/bin/rm -f in1* clus_in* )& +itemhelp:clustal_help + +arg:KTUP +argtype:slider +arglabel:K-tuple size for pairwise search +argmin:1 +argmax:10 +argvalue:2 + +arg:WIN +argtype:slider +arglabel:Window size +argmin:1 +argmax:10 +argvalue:4 + +arg:Matrx +argtype:chooser +arglabel:Weighting matrix +argchoice:PAM 250:PAM250 +argchoice:PAM 100:PAM100 +argchoice:Identity:ID + +arg:FIXED +argtype:slider +arglabel:Fixed gap penalty +argmin:1 +argmax:100 +argvalue:10 + +arg:FLOAT +arglabel:Floating gap penalty +argtype:slider +argmin:1 +argmax:100 +argvalue:10 + +arg:REPORT +argtype:chooser +arglabel:View assembly report? +argchoice:No: +argchoice:Yes:textedit in1.rpt& + +in:in1 +informat:flat +insave: + +#Menu for Protein + +item:blastp +itemmethod:(sed "s/[#%]/>/" in1.f; cp $GDE_HELP_DIR/BLAST/PAM??? .; blastp $BLASTDB in1.f W=$WORDLEN M=$Matrix > in1.tmp;textedit in1.tmp; rm in1* PAM???)& + +in:in1 +informat:flat +insave: + +arg:BLASTDB +argtype:choice_list +arglabel:Which Database +argchoice:pir:$GDE_HELP_DIR/BLAST/pir +argchoice:genpept:$GDE_HELP_DIR/BLAST/genpept +argchoice:local:$GDE_HELP_DIR/BLAST/local_db + +arg:Matrix +arglabel:Substitution Matrix: +argtype:choice_list +argchoice:PAM120:PAM120 +argchoice:PAM250:PAM250 + +arg:WORDLEN +argtype:slider +arglabel:Word Size +argmin:1 +argmax:5 +argvalue:3 + +item:tblastn +itemmethod:(sed "s/[#%]/>/" in1.f; cp $GDE_HELP_DIR/BLAST/PAM??? .; tblastn $BLASTDB in1.f W=$WORDLEN M=$Matrix C=$CODE > in1.tmp; textedit in1.tmp; rm in1* PAM???)& + +in:in1 +informat:flat +insave: + +arg:BLASTDB +argtype:choice_list +arglabel:Which Database +argchoice:genbank:$GDE_HELP_DIR/BLAST/genbank +argchoice:genbank update:$GDE_HELP_DIR/BLAST/genupdate + +arg:Matrix +arglabel:Substitution Matrix: +argtype:choice_list +argchoice:PAM120:PAM120 +argchoice:PAM250:PAM250 + +arg:WORDLEN +argtype:slider +arglabel:Word Size +argmin:4 +argmax:18 +argvalue:12 + +arg:CODE +argtype:choice_list +arglabel:Genetic Code +argchoice:Standard or Universal:0 +argchoice:Vertebrate Mitochondrial:1 +argchoice:Yeast Mitochondrial:2 +argchoice:Mold Mitochondrial and Mycoplasma:3 +argchoice:Invertebrate Mitochondrial:4 +argchoice:Ciliate Macronuclear:5 +argchoice:Protozoan Mitochondrial:6 +argchoice:Plant Mitochondrial:7 +argchoice:Echinodermate Mitochondrial:8 + +item:blast3 +itemmethod:(sed "s/[#%]/>/" in1.f; cp $GDE_HELP_DIR/BLAST/PAM??? .; blast3 $BLASTDB in1.f W=$WORDLEN M=$Matrix > in1.tmp;textedit in1.tmp; rm in1* PAM???)& + +in:in1 +informat:flat +insave: + +arg:BLASTDB +argtype:choice_list +arglabel:Which Database +argchoice:pir1:$GDE_HELP_DIR/BLAST/pir +argchoice:genpept:$GDE_HELP_DIR/BLAST/genpept + +arg:Matrix +arglabel:Substitution Matrix: +argtype:choice_list +argchoice:PAM120:PAM120 +argchoice:PAM250:PAM250 + +arg:WORDLEN +argtype:slider +arglabel:Word Size +argmin:1 +argmax:5 +argvalue:3 + +item:FASTA (Protein) +itemmethod:(sed "s/[#%]/>/"in1.fasta;fasta -Q -d $NUMOFALN $MATRIX in1.fasta $DBASE > in1.out; textedit in1.out;\rm in1*) & +itemhelp:FASTA.help + +in:in1 +informat:flat + +arg:DBASE +argtype:choice_list +arglabel:Database +argchoice:NBRF PIR1:$GDE_HELP_DIR/FASTA/PIR/pir1.dat\ 2 +argchoice:NBRF PIR2:$GDE_HELP_DIR/FASTA/PIR/pir2.dat\ 2 +argchoice:NBRF PIR3:$GDE_HELP_DIR/FASTA/PIR/pir3.dat\ 2 + + +arg:NUMOFALN +argtype:slider +arglabel:Number of Alignment to Report +argmin:1 +argmax:100 +argvalue:20 + +arg:MATRIX +arglabel:Which SMATRIX +argtype:choice_list +argchoice:Default: +argchoice:Minimum mutation matrix:-s $GDE_HELP_DIR/FASTA/MATRIX/codaa.mat +argchoice:Identity matrix:-s $GDE_HELP_DIR/FASTA/MATRIX/idnaa.mat +argchoice:Identity matrix for mismatches:-s $GDE_HELP_DIR/FASTA/MATRIX/idpaa.mat +argchoice:PAM250:-s $GDE_HELP_DIR/FASTA/MATRIX/pam250.mat +argchoice:PAM120:-s $GDE_HELP_DIR/FASTA/MATRIX/pam120.mat + +menu:Seq management + +item:Assemble Contigs +itemmethod:(sed "s/#/>/"in1.tmp; CAP2 in1.tmp $OVERLAP $PMATCH > out1;/bin/rm -f in1.tmp) +itemhelp:CAP2.help + +arg:OVERLAP +argtype:slider +arglabel:Minimum overlap? +argmin:5 +argmax:100 +argvalue:20 + +arg:PMATCH +argtype:slider +arglabel:Percent match required within overlap +argmin:25 +argmax:100 +argvalue:90 + +in:in1 +informat:flat + +out:out1 +outformat:gde +outoverwrite: + +item:Map View +itemmethod:(mapview in1 -pbl $PBL -npp $NPP; /bin/rm -f in1)& +itemhelp:mapview.help + +in:in1 +informat:gde +insave: + +arg:PBL +arglabel:Pixel Between Lines +argtype:slider +argvalue:10 +argmin:1 +argmax:15 + +arg:NPP +arglabel:Nucleotides Per Pixel +argtype:slider +argvalue:1 +argmin:1 +argmax:20 + +arg:LWIDTH +arglabel:Line Thickness +argtype:slider +argvalue:2 +argmin:1 +argmax:5 + + +item:Restriction sites +itemmethod:(cp $ENZ in1.tmp ; $PRE_EDIT Restriction in1.tmp in1 > out1 ; rm in1.tmp); +itemhelp:Restriction.help + +arg:ENZ +argtype:text +arglabel:Enzyme file +argtext:$GDE_HELP_DIR/DATA_FILES/enzymes + +arg:PRE_EDIT +argtype:chooser +arglabel:Edit enzyme file first? +argchoice:Yes:textedit in1.tmp; +argchoice:No: + +in:in1 +informat:flat + +out:out1 +outformat:colormask + +menu:Phylogeny + +item:DeSoete Tree fit +itemmethod: (readseq -a -f8 in1>in1.flat;count -t $CORR in1.flat> in1.tmp ; lsadt in1.out ; $DISPLAY_FUNC in1.out;/bin/rm -f in1* )& +itemhelp:lsadt.help + +in:in1 +informat:genbank +insave: +inmask: + +arg:CORR +arglabel:Distance correction? +argtype:chooser +argchoice:Olsen:-c=olsen +argchoice:Jukes/Cantor:-c=jukes +argchoice:None:-c=none + +arg:INIT +arglabel:Initial parameter estimate +argtype:choice_list +argchoice:uniformly distributed random numbers:1 +argchoice:error-perturbed data:2 +argchoice:original distance data from input matrix:3 + +arg:SEED +argtype:slider +arglabel:Random number seed +argmin:0 +argmax:65535 +argvalue:12345 + +arg:DISPLAY_FUNC +argtype:chooser +arglabel:View tree using +argchoice:TextEdit:textedit +argchoice:Treetool:treetool < + +item:Phylip help +itemmethod:(textedit $GDE_HELP_DIR/PHYLIP/$FILE)& + +arg:FILE +argtype:choice_list +arglabel:Which program? +argchoice:boot:boot.doc +argchoice:clique:clique.doc +argchoice:consense:consense.doc +argchoice:contchar:contchar.doc +argchoice:contml:contml.doc +argchoice:contrast:contrast.doc +argchoice:discrete:discrete.doc +argchoice:distance:distance.doc +argchoice:dnaboot:dnaboot.doc +argchoice:dnacomp:dnacomp.doc +argchoice:dnadist:dnadist.doc +argchoice:dnainvar:dnainvar.doc +argchoice:dnaml:dnaml.doc +argchoice:dnamlk:dnamlk.doc +argchoice:dnamove:dnamove.doc +argchoice:dnapars:dnapars.doc +argchoice:dnapenny:dnapenny.doc +argchoice:dolboot:dolboot.doc +argchoice:dollop:dollop.doc +argchoice:dolmove:dolmove.doc +argchoice:dolpenny:dolpenny.doc +argchoice:draw:draw.doc +argchoice:drawgram:drawgram.doc +argchoice:drawtree:drawtree.doc +argchoice:factor:factor.doc +argchoice:fitch:fitch.doc +argchoice:gendist:gendist.doc +argchoice:kitsch:kitsch.doc +argchoice:main:main.doc +argchoice:mix:mix.doc +argchoice:move:move.doc +argchoice:neighbor:neighbor.doc +argchoice:penny:penny.doc +argchoice:protpars:protpars.doc +argchoice:read.me.general:read.me.general.doc +argchoice:restml:restml.doc +argchoice:seqboot:seqboot.doc +argchoice:sequence:sequence.doc + + +item:Phylip 3.4 +itemmethod:(rm -f outfile ; readseq -a -f12 in1 | sed "s/ YF//1" > infile;$PREEDIT shelltool $PROGRAM;textedit outfile;rm in1 )& + +arg:PROGRAM +argtype:choice_list +arglabel:Which program to run? +argchoice:DNAPARS:dnapars +argchoice:DNABOOT:dnaboot +argchoice:DNAPENNY:dnapenny +argchoice:DNAML:dnaml +argchoice:DNAMLK:dnamlk +argchoice:DNACOMP:dnacomp +argchoice:DNAMOVE:dnamove +argchoice:DNAINVAR:dnainvar +argchoice:PROTPARS:protpars + +arg:PREEDIT +argtype:chooser +arglabel:Edit input before running? +argchoice:No: +argchoice:Yes:textedit infile; + +in:in1 +informat:genbank +inmask: +insave: + +item:Phylip Distance methods +itemmethod:(readseq -a -f12 in1 | sed "s/ YF//1" > infile ; $PREEDIT shelltool dnadist;mv -f outfile infile;$PROGRAM textedit outfile;/bin/rm -f in1 infile outfile)& + +arg:PROGRAM +arglabel:Which method? +argtype:chooser +argchoice:DNADIST:mv -f infile outfile; +argchoice:Fitch:shelltool fitch; +argchoice:Kitsch:shelltool kitsch; +argchoice:Neighbor:shelltool neighbor; + +arg:PREEDIT +argtype:chooser +arglabel:Edit input before running? +argchoice:No: +argchoice:Yes:textedit infile; + +in:in1 +informat:genbank +inmask: +insave: + +menu:Email + +item:BLASTN +itemmethod:(echo BLASTPROGRAM blastn > in1.tmp; echo DATALIB $DBASE >> in1.tmp; echo MATCH $MSCORE >> in1.tmp; echo BEGIN >> in1.tmp; sed "s/-//g" < in1 | tr '@%#' '>' >> in1.tmp; Mail BLAST@GENBANK.BIO.NET < in1.tmp; rm in1 in1.tmp) & + +arg:DBASE +argtype:choice_list +arglabel:Which Database? +argchoice:GenBank Qtrly & Updates:GenBank +argchoice:EMBL:embl + +arg:MSCORE +argtype:slider +arglabel:Match Score +argmin:3 +argmax:7 +argvalue:5 + +in:in1 +informat:flat +insave: + +item:BLASTP +itemmethod:(echo BLASTPROGRAM blastp >in1.tmp; echo DATALIB $DBASE >> in1.tmp; echo BEGIN >> in1.tmp; sed "s/-//g" < in1 | tr '@%#' '>' >> in1.tmp; Mail BLAST@GENBANK.BIO.NET < in1.tmp; rm in1 in1.tmp) & + +arg:DBASE +argtype:choice_list +arglabel:Which Database? +argchoice:Swiss-Prot:swiss-prot +argchoice:PIR:pir + +in:in1 +informat:flat +insave: + +item:Fasta-(DNA) +itemmethod:(echo DATALIB $DBASE > in1.tmp; echo KTUP $KPL >> in1.tmp; echo SCORES $TOP >> in1.tmp; echo ALIGNMENTS $ALNG >> in1.tmp; echo BEGIN >> in1.tmp; sed "s/-//g" < in1 | tr '@%#' '>' >> in1.tmp;Mail SEARCH@GENBANK.BIO.NET < in1.tmp; rm in1 in1.tmp) & + +arg:DBASE +argtype:choice_list +arglabel:Which GenBank Database? +argchoice:Qrtly & Updates:GenBank/all +argchoice:Updates:GenBank/new +argchoice:Primate:GenBank/primate +argchoice:Rodent:GenBank/rodent +argchoice:Other-Mammalian:GenBank/other_mammalian +argchoice:Other-Vertebrate:GenBank/other_vertebrate +argchoice:Invertebrate:GenBank/invertebrate +argchoice:Plant:GenBank/plant +argchoice:Organelle:GenBank/organelle +argchoice:Bacterial:GenBank/bacterial +argchoice:Structural-RNA:GenBank/structural_rna +argchoice:Viral:GenBank/viral +argchoice:Phage:GenBank/phage +argchoice:Synthetic:GenBank/synthetic +argchoice:Unannotated:GenBank/unannotated + +arg:KPL +argtype:slider +arglabel:K-tuple window +argmin:3 +argmax:6 +argvalue:4 + +arg:TOP +argtype:slider +arglabel:Scores Displayed? +argmin:1 +argmax:200 +argvalue:100 + +arg:ALNG +argtype:slider +arglabel:# Alignments Displayed? +argmin:1 +argmax:200 +argvalue:20 + +in:in1 +informat:flat +insave: + +item:Fasta-(PROTEIN) +itemmethod:(echo DATALIB $DBASE > in1.tmp; echo KTUP $TPL >> in1.tmp; echo SCORES $SCRS >> in1.tmp; echo ALIGNMENTS $ALNMNTS >> in1.tmp; echo BEGIN >> in1.tmp; sed "s/-//g" < in1 | tr '@%#$' '>' >> in1.tmp; Mail SEARCH@GENBANK.BIO.NET < in1.tmp; rm in1 in1.tmp) & + +arg:DBASE +argtype:choice_list +arglabel:Which Protein Database? +argchoice:Trans GenBank Qrtly:GenPept/all +argchoice:Trans GenBank Daily:GenPept/new +argchoice:Swiss-Protein:SWISS-PROT/all + +arg:TPL +argtype:slider +arglabel:K-TUP window +argmin:1 +argmax:2 +argvalue:1 + +arg:SCRS +argtype:slider +arglabel:# Scores Displayed? +argmin:1 +argmax:200 +argvalue:100 + +arg:ALNMNTS +argtype:slider +arglabel:# Alignments Displayed? +argmin:1 +argmax:200 +argvalue:20 + +in:in1 +informat:flat +insave: + +item:GeneID +itemmethod:($REPRINT > in1.tmp; echo Genomic Sequence >> in1.tmp; sed "s/-//g" < in1 | tr '@%#' '>' >> in1.tmp; Mail geneid@darwin.bu.edu < in1.tmp; rm in1 in1.tmp) & + +arg:REPRINT +argtype:chooser +arglabel:Do you want a GENEID reprint? +argchoice:YES:echo "Preprint Request" >> in1.tmp +argchoice:NO + +in:in1 +informat:flat +insave: + +item:Sequence Retrieval +itemmethod:(echo $REGEXP > in1.tmp; Mail RETRIEVE@GENBANK.BIO.NET < in1.tmp; rm in1.tmp) & + +arg:REGEXP +argtype:text +arglabel:Accession # or LOCUS name of sequence to retrieve + +item:Grail +itemmethod:(echo Sequences $TOTALSEQS $ID > in1.tmp; sed "s/-//g" < in1 | tr '@%#' '>' >> in1.tmp; Mail grail@ornl.gov in1.tmp; echo $NAME >> in1.tmp; echo $ADDRESS >> in1.tmp; echo $PHONE >> in1.tmp; echo $EMAIL >> in1.tmp; Mail grail@ornl.gov < in1.tmp; rm in1.tmp) + +arg:NAME +argtype:text +arglabel:Your Name + +arg:ADDRESS +argtype:text +arglabel:Your Address + +arg:PHONE +argtype:text +arglabel:Your Phone Number + +arg:EMAIL +argtype:text +arglabel:Your E-Mail Address + + +# +# dgg added new readseq formats, 29 dec 92 +# + +item:Export Foreign Format +itemmethod:readseq in1 -pipe -all -form=$FORMAT > $OUTPUTFILE +itemhelp:readseq.help + +arg:FORMAT +argtype:choice_list +argchoice:GenBank:genbank +argchoice:IG/Stanford:ig +argchoice:NBRF:nbrf +argchoice:EMBL:embl +argchoice:GCG:gcg +argchoice:DNA Strider:strider +argchoice:Fitch:fitch +argchoice:Pearson/Fasta:pearson +argchoice:Zuker:zuker +argchoice:Olsen:olsen +argchoice:Phylip:phylip +#argchoice:Phylip v3.2:phylip3.2 +argchoice:Plain text:raw +argchoice:ASN.1:asn +argchoice:PIR:pir +argchoice:MSF:msf +argchoice:PAUP:paup +argchoice:Pretty:pretty -nametop -nameleft=3 -numright -nameright -numtop + +arg:OUTPUTFILE +argtype:text +arglabel:Save as? + +in:in1 +informat:genbank + + +# +#dgg addition for new readseq, 24 dec 92 +# + +item:Pretty Print +itemmethod:readseq in1 -p -a -f=pretty $NAMELEFT $NAMERIGHT $NUMTOP $NUMBOT $NUMLEFT $NUMRIGHT -col=$COLS -width=$WIDTH $MATCH $GAPC > in1.pretty; (textedit in1.pretty; /bin/rm -f in1 in1.pretty)& +itemhelp:readseq.help + +#nametop is bad !? + +in:in1 +informat:genbank + +arg:NAMETOP +argtype:chooser +arglabel:Names at top ? +argchoice:No: +argchoice:Yes:-nametop + +arg:NAMELEFT +argtype:chooser +arglabel:Names at left ? +argchoice:No: +argchoice:Yes:-nameleft + +arg:NAMERIGHT +argtype:chooser +arglabel:Names at right? +argchoice:Yes:-nameright +argchoice:No: + +arg:NUMTOP +argtype:chooser +arglabel:Numbers at top ? +argchoice:Yes:-numtop +argchoice:No: + +arg:NUMBOT +argtype:chooser +arglabel:Numbers at tail ? +argchoice:No: +argchoice:Yes:-numbot + +arg:NUMLEFT +argtype:chooser +arglabel:Numbers at left ? +argchoice:Yes:-numleft +argchoice:No: + +arg:NUMRIGHT +argtype:chooser +arglabel:Numbers at right? +argchoice:Yes:-numright +argchoice:No: + +arg:MATCH +argtype:chooser +arglabel:Use match '.' for 2..n species? +argchoice:No: +argchoice:Yes:-match + +arg:GAPC +argtype:chooser +arglabel:Count gap symbols? +argchoice:No: +argchoice:Yes:-gap + +arg:WIDTH +argtype:slider +arglabel:Sequence width? +argmin:10 +argmax:200 +argvalue:50 + +arg:COLS +argtype:slider +arglabel:Column spacers? +argmin:0 +argmax:50 +argvalue:10 + + +### pretty print insert end +# + +item:Wally's test function +itemmethod:run__wally $ONE $TWO $THREE < $FILE + +arg:ONE +argtype:chooser +arglabel:How? +argchoice:Fast:-fast +argchoice:Slow:-slow + +arg:TWO +argtype:slider +argmin:0 +argmax:100 +argvalue:50 +arglabel:how many? + +arg:THREE +argtype:choice_list +arglabel:Which one? +argchoice:Fast:-fast +argchoice:Slow:-slow + +arg:FILE +argtype:text +arglabel:Which file +