1017 lines
22 KiB
Plaintext
1017 lines
22 KiB
Plaintext
1menu:File
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item:test cmask output
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itemmethod: kedit in1
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in:in1
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informat:colormask
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item:New sequence <meta N>
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itemmethod:echo "$Type$Name" > out1
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itemmeta:n
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itemhelp:new_sequence.help
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arg:Name
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argtype:text
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arglabel:New Sequence name?
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argtext:New
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arg:Type
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argtype:choice_list
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arglabel:Type?
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argchoice:DNA/RNA:#
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argchoice:Amino Acid:%
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argchoice:Text:\"
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argchoice:Mask:@
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out:out1
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outformat:flat
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item:Import Foreign Format
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itemmethod:cp $INPUTFILE OUTFILE.tmp;readseq OUTFILE.tmp -a -f2 > OUTPUTFILE;/bin/rm -f OUTFILE.tmp
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itemhelp:readseq.help
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arg:INPUTFILE
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argtype:text
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arglabel:Name of foreign file?
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out:OUTPUTFILE
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outformat:genbank
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item:Export Foreign Format
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itemmethod:readseq INPUTFILE -a -f$FORMAT > $OUTPUTFILE
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itemhelp:readseq.help
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arg:FORMAT
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argtype:choice_list
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argchoice:FASTA:8
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argchoice:NEXUS:17
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argchoice:Phylip v3.3:12
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argchoice:IG/Stanford:1
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argchoice:GenBank:2
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argchoice:NBRF:3
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argchoice:EMBL:4
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argchoice:GCG:5
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argchoice:DNA Strider:6
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argchoice:Fitch:7
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argchoice:Pearson:8
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argchoice:Zuker:9
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argchoice:Olsen:10
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argchoice:Phylip v3.2:11
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argchoice:Phylip v3.3:12
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argchoice:Plain text:13
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arg:OUTPUTFILE
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argtype:text
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arglabel:Save as?
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in:INPUTFILE
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informat:genbank
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item:Save Selection
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itemmethod: cat $SAVE_FUNC > $Name
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itemhelp:save_selection.help
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arg:SAVE_FUNC
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argtype:chooser
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arglabel:File format
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argchoice:Flat:in1
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argchoice:Genbank:in2
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argchoice:GDE/HGL:in3
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arg:Name
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argtype:text
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arglabel:File name?
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in:in1
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informat:flat
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in:in2
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informat:genbank
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in:in3
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informat:gde
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item:Print Selection
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itemmethod:(PrintStrat in1 $SCALE > in1.tmp; $CMD -P$PRINTER in1.tmp; /bin/rm -f in1 in1.tmp)&
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itemhelp:print_alignment.help
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arg:SCALE
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argtype:slider
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arglabel:Reduce printout by?
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argmin:1
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argmax:20
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argvalue:1
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arg:CMD
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argtype:chooser
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argchoice:Lpr:lpr
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argchoice:Enscript Gaudy:enscript -G -q
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argchoice:Enscript Two column:enscript -2rG
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arg:PRINTER
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argtype:text
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arglabel:Which printer?
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argtext:lp
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in:in1
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informat:gde
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insave:
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menu:Edit
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item:Sort
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itemmethod:(heapsortHGL in1 $PRIM_KEY $SEC_KEY > in1.tmp ; gde in1.tmp;/bin/rm -f in1*)&
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itemhelp:heapsortHGL.help
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arg:PRIM_KEY
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argtype:choice_list
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argchoice:Group:group-ID
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argchoice:type:type
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argchoice:name:name
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argchoice:Sequence ID:sequence-ID
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argchoice:creator:creator
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argchoice:offset:offset
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arglabel:Primary sort field?
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arg:SEC_KEY
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argtype:choice_list
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argchoice:None:
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argchoice:Group:group-ID
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argchoice:type:type
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argchoice:name:name
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argchoice:Sequence ID:sequence-ID
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argchoice:creator:creator
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argchoice:offset:offset
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arglabel:Secondary sort field?
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in:in1
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informat:gde
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insave:
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item:extract
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itemmethod:(gde in1;/bin/rm -f in1)&
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in:in1
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informat:gde
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inmask:
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insave:
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menu:DNA/RNA
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item:Translate...
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itemmethod:Translate -tbl $TBL -frame $FRAME -min_frame $MNFRM $LTRCODE in1 > out1
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arg:FRAME
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argtype:chooser
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arglabel:Which reading frame?
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argchoice:First:1
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argchoice:Second:2
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argchoice:Third:3
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argchoice:All six:6
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arg:MNFRM
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arglabel:Minimum length of AA sequence to translate?
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argtype:slider
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argmin:0
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argmax:100
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argvalue:20
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arg:LTRCODE
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argtype:chooser
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arglabel:Translate to:
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argchoice:Single letter codes:
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argchoice:Triple letter codes:-3
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arg:TBL
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arglabel:Codon table?
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argtype:chooser
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argchoice:universal:1
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argchoice:mycoplasma:2
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argchoice:yeast:3
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argchoice:Vert. mito.:4
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in:in1
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informat:gde
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out:out1
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outformat:gde
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item:Dot plot
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itemmethod:(DotPlotTool in1 ; /bin/rm -f in1)&
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itemhelp:DotPlotTool.help
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in:in1
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informat:gde
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insave:
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item:Clustal alignment
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itemmethod:(tr '%#' '>'<in1>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* )&
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itemhelp:clustal_help
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arg:KTUP
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argtype:slider
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arglabel:K-tuple size for pairwise search
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argmin:1
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argmax:10
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argvalue:2
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arg:WIN
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argtype:slider
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arglabel:Window size
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argmin:1
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argmax:10
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argvalue:4
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arg:Trans
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argtype:chooser
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arglabel:Transitions weighted?
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argchoice:Yes:/TRANSIT
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argchoice:No:
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arg:FIXED
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argtype:slider
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arglabel:Fixed gap penalty
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argmin:1
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argmax:100
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argvalue:10
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arg:FLOAT
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arglabel:Floating gap penalty
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argtype:slider
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argmin:1
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argmax:100
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argvalue:10
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arg:REPORT
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argtype:chooser
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arglabel:View assembly report?
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argchoice:No:
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argchoice:Yes:kedit in1.rpt&
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in:in1
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informat:flat
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insave:
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item:Variable Positions
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itemmethod:varpos $REV < in1 > out1
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arg:REV
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argtype:chooser
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arglabel:Highlight (darken)
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argchoice:Conserved positions:
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argchoice:variable positions:-rev
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in:in1
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informat:flat
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out:out1
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outformat:colormask
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item:Phrap
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itemmethod:readseq in1 -a -f8 > OUTPUTFILE;/bin/rm -f OUTFILE.tmp; phrap OUTPUTFILE; readseq -a -f2 OUTPUTFILE.contigs > out1;/bin/rm -rf OUTPUT*;
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in:in1
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informat:genbank
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out:out1
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outformat:genbank
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item:SNAP
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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*;
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in:in1
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informat:flat
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out:out1
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outformat:text
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item:Find all <meta-f>
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itemmethod:findall $SEARCH $PRCNT $CASE $UT -match $MAT -mismatch $MIS < in1 > out1;
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itemhelp:findall.help
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itemmeta:f
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arg:SEARCH
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argtype:text
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arglabel:Search String
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arg:PRCNT
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argtype:slider
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arglabel:Percent mismatch
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argmin:0
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argmax:75
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argvalue:10
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arg:CASE
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argtype:chooser
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arglabel:Case
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argchoice:Upper equals lower:
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argchoice:Upper not equal lower:-case
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arg:UT
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argtype:chooser
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arglabel:U equal T?
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argchoice:Yes:-u=t
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argchoice:No:
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argvalue:0
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arg:MAT
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arglabel:Match color
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argtype:choice_list
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argchoice:yellow:1
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argchoice:violet:2
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argchoice:red:3
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argchoice:aqua:4
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argchoice:green:5
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argchoice:blue:6
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argchoice:grey:11
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argchoice:black:8
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argvalue:2
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arg:MIS
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argtype:choice_list
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arglabel:Mismatch color
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argchoice:yellow:1
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argchoice:violet:2
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argchoice:red:3
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argchoice:aqua:4
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argchoice:green:5
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argchoice:blue:6
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argchoice:grey:11
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argchoice:black:8
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argvalue:7
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in:in1
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informat:flat
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out:out1
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outformat:colormask
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item:Sequence Consensus
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itemmethod:(MakeCons in1 $METHOD $MASK > out1)
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itemhelp:MakeCons.help
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arg:METHOD
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arglabel:Method
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argtype:chooser
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argchoice:IUPAC:-iupac
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argchoice:Majority:-majority $PERCENT
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arg:MASK
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argtype:chooser
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arglabel:Create a new:
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argchoice:Sequence:
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argchoice:Selection Mask: | Consto01mask
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arg:PERCENT
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arglabel:Minimum Percentage for Majority
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argtype:slider
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argmin:50
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argmax:100
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argvalue:75
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in:in1
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informat:gde
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out:out1
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outformat:gde
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#Menu for DNA/RNA
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item:blastn
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itemmethod:(sed "s/[#%]/>/" <in1 > 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*)&
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in:in1
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informat:flat
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insave:
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arg:BLASTDBDNA
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argtype:choice_list
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arglabel:Which Database
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argchoice:HIV-1 Seq. Db.:/usr/local/bio/db/DNA/hiv17-08-01.fasta2
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argchoice:NEW:/usr/local/bio/db/newblast.fasta
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argchoice:TEST:/usr/local/bio/db/test_na_db
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argchoice:testDB:/usr/local/bio/db/test_na_db
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argchoice:HIV-1 Subtype:/usr/local/bio/db/DNA/subcomplete.fasta
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argchoice:HIV-1 HXB2 Numbering:/usr/local/bio/db/HXB2.fasta
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argchoice:HCV Numbering:/usr/local/bio/db/HCV.fasta
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arg:WORDLEN
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argtype:slider
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arglabel:Word Size
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argmin:4
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argmax:18
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argvalue:12
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arg:MATCH
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argtype:slider
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arglabel:Match Score
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argmin:1
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argmax:10
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argvalue:5
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arg:MMSCORE
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argtype:slider
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arglabel:Mismatch Score
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argmin:-10
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argmax:-1
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argvalue:-5
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item:blastx
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itemmethod:(sed "s/[#%]/>/" <in1 > in1.f; /usr/local/bio/blast/blastall -p blastx -d $BLASTDB -i in1.f -W $WORDLEN -M PAM30 > in1.tmp; /usr/openwin/bin/kedit in1.tmp; rm in1*)&
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in:in1
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informat:flat
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insave:
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arg:BLASTDB
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argtype:choice_list
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arglabel:Which Database
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argchoice:HIV Proteins:/usr/local/bio/db/hiv17-08-01.PROT.fasta
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argchoice:genpept:$GDE_HELP_DIR/BLAST/genpept
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arg:WORDLEN
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argtype:slider
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arglabel:Word Size
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argmin:1
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argmax:5
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argvalue:3
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arg:Matrix
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arglabel:Substitution Matrix:
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argtype:choice_list
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argchoice:PAM30:PAM30
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argchoice:PAM70:PAM70
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arg:CODE
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argtype:choice_list
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arglabel:Genetic Code
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argchoice:Standard or Universal:0
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argchoice:Vertebrate Mitochondrial:1
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argchoice:Yeast Mitochondrial:2
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argchoice:Mold Mitochondrial and Mycoplasma:3
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argchoice:Invertebrate Mitochondrial:4
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argchoice:Ciliate Macronuclear:5
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argchoice:Protozoan Mitochondrial:6
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argchoice:Plant Mitochondrial:7
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argchoice:Echinodermate Mitochondrial:8
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item:------------------------
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item:Add a new DNA blast db
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itemmethod:xterm -e formatdb -i $sourcefile -p F -o T; /usr/local/bio/GDE/installBLASTDB.pl $sourcefile $menuname;
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arg:sourcefile
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argtype:text
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arglabel: enter the file name
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arg:menuname
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argtype:text
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arglabel: enter the name of the DB
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menu:HIV Seq. Db.
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item:Ref. Seq. for Drug Resistance
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itemmethod:cp $INPUTFILE OUTFILE.tmp;readseq OUTFILE.tmp -a -f2 > OUTPUTFILE;/bin/rm -f OUTFILE.tmp
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itemhelp:readseq.help
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arg:INPUTFILE
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argtype:chooser
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arglabel:Sequence
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argchoice:Prot function:/database/AA/protease.mutations.fasta
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argchoice:rt function:/database/AA/rtmutations.fasta
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argchoice:pNL4-3 CG :/database/DR/pNL4-3.CG.fasta
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argchoice:pNL4-3 protease :/database/DR/pNL4-3.prot$format.fasta
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argchoice:pNL4-3 RT :/database/DR/pNL4-3.RT$format.fasta
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argchoice:HXB2 CG :/database/DR/HXB2.fasta
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argchoice:HXB2 protease :/database/DR/HXB2.prot$format.fasta
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argchoice:HXB2 RT :/database/DR/HXB2.RT$format.fasta
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argchoice:data1.fasta:/database/DNA/data1.fasta
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arg:format
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argtype:chooser
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arglabel:Format
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argchoice:DNA:
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argchoice:AA:AA
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out:OUTPUTFILE
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outformat:genbank
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item:HIV-1 Subtype Db.
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itemmethod:cp $INPUTFILE OUTFILE.tmp;readseq OUTFILE.tmp -a -f2 > OUTPUTFILE;/bin/rm -f OUTFILE.tmp
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itemhelp:readseq.help
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arg:INPUTFILE
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argtype:choice_list
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arglabel:HIV-1 Subtype genome regions
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argchoice:CG:/usr/local/bio/db/DNA/subtyperef/subcomplete.fasta
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argchoice:sub5ltr.fasta:/usr/local/bio/db/DNA/subtyperef/sub5ltr.fasta
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argchoice:sub5ltrU3.fasta:/usr/local/bio/db/DNA/subtyperef/sub5ltrU3.fasta
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argchoice:sub5ltrU5.fasta:/usr/local/bio/db/DNA/subtyperef/sub5ltrU5.fasta
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argchoice:subenv.fasta:/usr/local/bio/db/DNA/subtyperef/subenv.fasta
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argchoice:subenv-gp120.fasta:/usr/local/bio/db/DNA/subtyperef/subenv-gp120.fasta
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argchoice:subenv-gp41.fasta:/usr/local/bio/db/DNA/subtyperef/subenv-gp41.fasta
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argchoice:subenvv3.fasta:/usr/local/bio/db/DNA/subtyperef/subenvv3.fasta
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argchoice:subgag.fasta:/usr/local/bio/db/DNA/subtyperef/subgag.fasta
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argchoice:subgag-p17.fasta:/usr/local/bio/db/DNA/subtyperef/subgag-p17.fasta
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argchoice:subgag-p24.fasta:/usr/local/bio/db/DNA/subtyperef/subgag-p24.fasta
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argchoice:subgag-pol.fasta:/usr/local/bio/db/DNA/subtyperef/subgag-pol.fasta
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argchoice:subpol.fasta:/usr/local/bio/db/DNA/subtyperef/subpol.fasta
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argchoice:subpol-p15RNAase.fasta:/usr/local/bio/db/DNA/subtyperef/subpol-p15RNAase.fasta
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argchoice:subpol-p31integrase.fasta:/usr/local/bio/db/DNA/subtyperef/subpol-p31integrase.fasta
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argchoice:subpol-p51RT.fasta:/usr/local/bio/db/DNA/subtyperef/subpol-p51RT.fasta
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argchoice:subpol-protease.fasta:/usr/local/bio/db/DNA/subtyperef/subpol-protease.fasta
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argchoice:subrevCDS.fasta:/usr/local/bio/db/DNA/subtyperef/subrevCDS.fasta
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argchoice:subrevexon1.fasta:/usr/local/bio/db/DNA/subtyperef/subrevexon1.fasta
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argchoice:subrevexon2.fasta:/usr/local/bio/db/DNA/subtyperef/subrevexon2.fasta
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argchoice:subrevintron.fasta:/usr/local/bio/db/DNA/subtyperef/subrevintron.fasta
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argchoice:subTAR.fasta:/usr/local/bio/db/DNA/subtyperef/subTAR.fasta
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argchoice:subtatCDS.fasta:/usr/local/bio/db/DNA/subtyperef/subtatCDS.fasta
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|
argchoice:subtatexon1.fasta:/usr/local/bio/db/DNA/subtyperef/subtatexon1.fasta
|
|
argchoice:subtatexon2.fasta:/usr/local/bio/db/DNA/subtyperef/subtatexon2.fasta
|
|
argchoice:subtatintron.fasta:/usr/local/bio/db/DNA/subtyperef/subtatintron.fasta
|
|
argchoice:subvif.fasta:/usr/local/bio/db/DNA/subtyperef/subvif.fasta
|
|
argchoice:subvpr.fasta:/usr/local/bio/db/DNA/subtyperef/subvpr.fasta
|
|
argchoice:subvpu.fasta:/usr/local/bio/db/DNA/subtyperef/subvpu.fasta
|
|
argchoice:subnef.fasta:/usr/local/bio/db/DNA/subtyperef/subnef.fasta
|
|
|
|
out:OUTPUTFILE
|
|
outformat:genbank
|
|
|
|
|
|
item:HIV-1 Subtype reduz.
|
|
itemmethod:cp $INPUTFILE OUTFILE.tmp;readseq OUTFILE.tmp -a -f2 > OUTPUTFILE;/bin/rm -f OUTFILE.tmp
|
|
itemhelp:readseq.help
|
|
|
|
arg:INPUTFILE
|
|
argtype:choice_list
|
|
arglabel:HIV-1 Subtype genome regions
|
|
argchoice:HIV Subtype C CG:/database/DNA/sub-reference/subC.CG.fasta
|
|
argchoice:HIV-1 GAG sub:/database/DNA/sub-reference/gagsub-reference.fasta
|
|
argchoice:HIV-1 POL sub:/database/DNA/sub-reference/polsub-reference.fasta
|
|
argchoice:HIV-1 VIF sub:/database/DNA/sub-reference/vifsub-reference.fasta
|
|
argchoice:HIV-1 VPR sub:/database/DNA/sub-reference/vprsub-reference.fasta
|
|
argchoice:HIV-1 TAT sub:/database/DNA/sub-reference/tatsub-reference.fasta
|
|
argchoice:HIV-1 REV sub:/database/DNA/sub-reference/revsub-reference.fasta
|
|
argchoice:HIV-1 VPU sub:/database/DNA/sub-reference/vpusub-reference.fasta
|
|
argchoice:HIV-1 ENV sub:/database/DNA/sub-reference/envsub-reference.fasta
|
|
argchoice:HIV-1 NEF sub:/database/DNA/sub-reference/nefsub-reference.fasta
|
|
|
|
out:OUTPUTFILE
|
|
outformat:genbank
|
|
|
|
item:HIV-1 Subtype B & C Gen. regions
|
|
itemmethod:cp $INPUTFILE OUTFILE.tmp;readseq OUTFILE.tmp -a -f2 > OUTPUTFILE;/bin/rm -f OUTFILE.tmp
|
|
itemhelp:readseq.help
|
|
|
|
arg:INPUTFILE
|
|
argtype:choice_list
|
|
arglabel:HIV-1 Subtype genome regions
|
|
argchoice:HIV Subtype C CG:/database/DNA/subB/$format.fasta
|
|
argchoice:HIV-1 GAG sub:/database/DNA/subB/$format.gag$type.fasta
|
|
argchoice:HIV-1 POL sub:/database/DNA/subB/$format.pol$type.fasta
|
|
argchoice:HIV-1 PROTEASE sub:/database/DNA/subB/$format.pol-prot$type.fasta
|
|
argchoice:HIV-1 RT sub:/database/DNA/subB/$format.pol-RT$type.fasta
|
|
argchoice:HIV-1 INTEGRASE sub:/database/DNA/subB/$format.pol-INT$type.fasta
|
|
argchoice:HIV-1 VIF sub:/database/DNA/subB/$format.vif$type.fasta
|
|
argchoice:HIV-1 VPR sub:/database/DNA/subB/$format.vpr$type.fasta
|
|
argchoice:HIV-1 TAT sub:/database/DNA/subB/$format.tat$type.fasta
|
|
argchoice:HIV-1 REV sub:/database/DNA/subB/$format.rev$type.fasta
|
|
argchoice:HIV-1 VPU sub:/database/DNA/subB/$format.vpu$type.fasta
|
|
argchoice:HIV-1 ENV sub:/database/DNA/subB/$format.env$type.fasta
|
|
argchoice:HIV-1 NEF sub:/database/DNA/subB/$format.nef$type.fasta
|
|
|
|
arg:format
|
|
argtype:chooser
|
|
arglabel:Format
|
|
argchoice:Subtype B:subB
|
|
argchoice:Subtype C:subC
|
|
|
|
arg:type
|
|
argtype:chooser
|
|
arglabel:type
|
|
argchoice:DNA:
|
|
argchoice:AA:AA
|
|
|
|
out:OUTPUTFILE
|
|
outformat:genbank
|
|
|
|
|
|
item:Find Beggining of Genome regions
|
|
itemmethod:findall $SEARCH $PRCNT $CASE $UT -match $MAT -mismatch $MIS < in1 > out1;
|
|
itemhelp:findall.help
|
|
itemmeta:f
|
|
|
|
arg:SEARCH
|
|
argtype:choice_list
|
|
argchoice:Protease:ATCACTCTTTGG
|
|
argchoice:Protease:ATC
|
|
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:hivHXB2 genome regions aln
|
|
itemmethod:cp $INPUTFILE OUTFILE.tmp;readseq OUTFILE.tmp -a -f2 > OUTPUTFILE;/bin/rm -f OUTFILE.tmp
|
|
itemhelp:readseq.help
|
|
|
|
arg:INPUTFILE
|
|
argtype:chooser
|
|
arglabel:HXB2 Reference Seq
|
|
argchoice:CG:/database/DNA/hivHXB2regions.fasta
|
|
|
|
out:OUTPUTFILE
|
|
outformat:genbank
|
|
|
|
menu:Protein
|
|
|
|
|
|
item:Clustal Protein Alignment
|
|
itemmethod:(tr '%#' '>'<in1>clus_in;clustalw -output=GDE -infile=clus_in -align > in1.rpt;sed "s/>DL;/#/g" < clus_in.gde> in1;$REPORT gde clus_in.gde;/bin/rm -f clus_in* in1* )&
|
|
|
|
|
|
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:kedit in1.rpt&
|
|
|
|
in:in1
|
|
informat:flat
|
|
insave:
|
|
|
|
|
|
#Menu for Protein
|
|
|
|
item:blastp
|
|
itemmethod:(sed "s/[#%]/>/" <in1 > in1.f; cp /usr/local/bio/db/PAM30; /usr/local/bio/blast/blastall -p blastp -d $BLASTDB -i in1.f -W $WORDLEN -M $Matrix > in1.tmp; /usr/openwin/bin/kedit in1.tmp; rm in1* PAM30)&
|
|
|
|
|
|
in:in1
|
|
informat:flat
|
|
insave:
|
|
|
|
arg:BLASTDB
|
|
argtype:choice_list
|
|
arglabel:Which Database
|
|
argchoice:HIV Proteins Tulio:/usr/local/bio/db/HIV-PROTEINS-tulio.fasta
|
|
argchoice:HIV Proteins:/usr/local/bio/db/hiv17-08-01.PROT.fasta
|
|
argchoice:HIV-1 Structures at PDB:/usr/local/bio/db/Prot.3d.fasta
|
|
argchoice:local:$GDE_HELP_DIR/BLAST/local_db
|
|
|
|
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 > 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 DNA blast db
|
|
itemmethod:xterm -e formatdb -i $sourcefile -p T -o T; /usr/local/bio/GDE/installBLASTDBPROT.pl $sourcefile $menuname;
|
|
|
|
arg:sourcefile
|
|
argtype:text
|
|
arglabel: enter the file name
|
|
|
|
arg:menuname
|
|
argtype:text
|
|
arglabel: enter the name of the DB
|
|
|
|
menu:Phylogeny
|
|
|
|
|
|
item:Phylip help
|
|
itemmethod:(netscape /usr/local/bio/phylip/doc/$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:
|
|
|
|
|
|
|
|
|
|
|
|
menu:On-Line Res.
|
|
item:test
|
|
itemmethod:netscape http://test.com
|
|
item:test
|
|
itemmethod:netscape http://test.com
|
|
item:test
|
|
itemmethod:netscape http://test.com
|
|
|
|
item:add a new website
|
|
itemmethod:xterm -e /usr/local/biotools/GDE/newURL.pl $name $url
|
|
|
|
arg:name
|
|
argtype:text
|
|
arglabel:Enter the site name
|
|
|
|
arg:url
|
|
argtype:text
|
|
arglabel:Enter the URL (including http://)
|