2050 lines
47 KiB
Plaintext
Executable File
2050 lines
47 KiB
Plaintext
Executable File
1menu:File
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item:test cmask output
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itemmethod: textedit 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:textedit 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/biotools/GDE/bin/fasta2snap.pl > outfile; /usr/bin/X11/xterm -e /home/tulio/biotools/SNAP/SNAP.pl outfile; textedit backg*; textedit summ*; sheeltool /home/tulio/biotools/codons-xyplot.pl codons.*; textedit 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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item:MFOLD
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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)&
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itemhelp:MFOLD.help
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in:seqGB
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informat:genbank
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insave:
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arg:METHOD
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argtype:chooser
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arglabel:RNA type
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argchoice:Fold Linear RNA:lrna
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argchoice:Fold Circular RNA:crna
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arg:CT
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argtype:text
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arglabel:Pairing(ct) File Name
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argtext:mfold_out
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item:Draw Secondary structure
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itemmethod:(LoopTool $TEMPLATE in1 ; /bin/rm -f in1) &
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itemhelp:LoopTool.help
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arg:TEMPLATE
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argtype:chooser
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arglabel:Use template file ./loop.temp?
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argchoice:No:
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argchoice:Yes:-t loop.temp
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in:in1
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informat:genbank
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insave:
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item:Highlight helix
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itemmethod:readseq -a -f8 in1 | sed "s/>HELIX/\"HELIX/" > in1.flat; sho_helix < in1.flat > out1;rm in1.flat
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itemhelp:sho_helix.help
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in:in1
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informat:genbank
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out:out1
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outformat:colormask
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#Menu for DNA/RNA
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item:codeml
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itemmethod:(readseq -a -f11 in1 | sed "s/ YF//1" > test.phy; /usr/bin/X11/xterm -e codeml $METHOD)&
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arg:METHOD
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arglabel:Which method ?
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argtype:chooser
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argchoice:0:/home/tulio/biotools/paml/method0.ctl
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argchoice:1:/home/tulio/biotools/paml/method1.ctl
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argchoice:2:/home/tulio/biotools/paml/method2.ctl
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argchoice:3:/home/tulio/biotools/paml/method3.ctl
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argchoice:4:/home/tulio/biotools/paml/method4.ctl
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argchoice:5:/home/tulio/biotools/paml/method5.ctl
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argchoice:6:/home/tulio/biotools/paml/method6.ctl
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in:in1
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informat:genbank
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inmask:
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insave:
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item:blastn
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itemmethod:(sed "s/[#%]/>/" <in1 > in1.f; /usr/local/biotools/blast/blastall -p blastn -d $BLASTDB -i in1.f -W $WORDLEN -M $MATCH > in1.tmp; /usr/openwin/bin/textedit 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-1 Seq. Db.:/var/www/cgi-bin/db/hiv17-08-01.fasta2
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argchoice:HIV-1 Subtype:/var/www/cgi-bin/db/subcomplete.fasta
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argchoice:HIV-1 HXB2 Numbering:/var/www/cgi-bin/db/HXB2.fasta
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argchoice:HCV Numbering:/var/www/cgi-bin/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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||
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||
item:blastx
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itemmethod:(sed "s/[#%]/>/" <in1 > in1.f; /usr/local/biotools/blast/blastall -p blastx -d $BLASTDB -i in1.f -W $WORDLEN -M PAM30 > in1.tmp; /usr/openwin/bin/textedit in1.tmp; rm in1*)&
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||
|
||
|
||
|
||
in:in1
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||
informat:flat
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||
insave:
|
||
|
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arg:BLASTDB
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argtype:choice_list
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arglabel:Which Database
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argchoice:HIV Proteins:/var/www/cgi-bin/db/hiv17-08-01.PROT.fasta
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argchoice:genpept:$GDE_HELP_DIR/BLAST/genpept
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||
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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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||
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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
|
||
argtype:choice_list
|
||
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:FASTA (DNA/RNA)
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||
itemmethod:(sed "s/[#%]/>/"<in1 >in1.fasta;fasta -Q -d $NUMOFALN $MATRIX in1.fasta $DBASE > in1.out; textedit in1.out;\rm in1*) &
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||
itemhelp:FASTA.help
|
||
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||
in:in1
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||
informat:flat
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||
|
||
arg:DBASE
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||
argtype:choice_list
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||
arglabel:Database
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||
argchoice:GenBank Primate:$GDE_HELP_DIR/FASTA/GENBANK/gbpri.seq\ 1
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||
argchoice:GenBank Rodent:$GDE_HELP_DIR/FASTA/GENBANK/gbrod.seq\ 1
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||
argchoice:GenBank all Mammal:$GDE_HELP_DIR/FASTA/GENBANK/gbmam.seq\ 1
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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
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||
argchoice:GenBank euk. Organelles:$GDE_HELP_DIR/FASTA/GENBANK/gborg.seq\ 1
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||
argchoice:GenBank phaGe:$GDE_HELP_DIR/FASTA/GENBANK/gbphg.seq\ 1
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||
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:HIV Seq. Db.
|
||
item:Ref. Seq. for Drug Resistance
|
||
itemmethod:cp $INPUTFILE OUTFILE.tmp;readseq OUTFILE.tmp -a -f2 > OUTPUTFILE;/bin/rm -f OUTFILE.tmp
|
||
itemhelp:readseq.help
|
||
|
||
arg:INPUTFILE
|
||
argtype:chooser
|
||
arglabel:Sequence
|
||
argchoice:Prot function:/database/AA/protease.mutations.fasta
|
||
argchoice:rt function:/database/AA/rtmutations.fasta
|
||
argchoice:pNL4-3 CG :/database/DR/pNL4-3.CG.fasta
|
||
argchoice:pNL4-3 protease :/database/DR/pNL4-3.prot$format.fasta
|
||
argchoice:pNL4-3 RT :/database/DR/pNL4-3.RT$format.fasta
|
||
argchoice:HXB2 CG :/database/DR/HXB2.fasta
|
||
argchoice:HXB2 protease :/database/DR/HXB2.prot$format.fasta
|
||
argchoice:HXB2 RT :/database/DR/HXB2.RT$format.fasta
|
||
argchoice:data1.fasta:/database/DNA/data1.fasta
|
||
|
||
|
||
arg:format
|
||
argtype:chooser
|
||
arglabel:Format
|
||
argchoice:DNA:
|
||
argchoice:AA:AA
|
||
|
||
out:OUTPUTFILE
|
||
outformat:genbank
|
||
|
||
item:HIV-1 Subtype Db.
|
||
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:CG:/database/DNA/subtyperef/subcomplete.fasta
|
||
argchoice:sub5ltr.fasta:/database/DNA/subtyperef/sub5ltr.fasta
|
||
argchoice:sub5ltrU3.fasta:/database/DNA/subtyperef/sub5ltrU3.fasta
|
||
argchoice:sub5ltrU5.fasta:/database/DNA/subtyperef/sub5ltrU5.fasta
|
||
argchoice:subenv.fasta:/database/DNA/subtyperef/subenv.fasta
|
||
argchoice:subenv-gp120.fasta:/database/DNA/subtyperef/subenv-gp120.fasta
|
||
argchoice:subenv-gp41.fasta:/database/DNA/subtyperef/subenv-gp41.fasta
|
||
argchoice:subenvv3.fasta:/database/DNA/subtyperef/subenvv3.fasta
|
||
argchoice:subgag.fasta:/database/DNA/subtyperef/subgag.fasta
|
||
argchoice:subgag-p17.fasta:/database/DNA/subtyperef/subgag-p17.fasta
|
||
argchoice:subgag-p24.fasta:/database/DNA/subtyperef/subgag-p24.fasta
|
||
argchoice:subgag-pol.fasta:/database/DNA/subtyperef/subgag-pol.fasta
|
||
argchoice:subpol.fasta:/database/DNA/subtyperef/subpol.fasta
|
||
argchoice:subpol-p15RNAase.fasta:/database/DNA/subtyperef/subpol-p15RNAase.fasta
|
||
argchoice:subpol-p31integrase.fasta:/database/DNA/subtyperef/subpol-p31integrase.fasta
|
||
argchoice:subpol-p51RT.fasta:/database/DNA/subtyperef/subpol-p51RT.fasta
|
||
argchoice:subpol-protease.fasta:/database/DNA/subtyperef/subpol-protease.fasta
|
||
argchoice:subrevCDS.fasta:/database/DNA/subtyperef/subrevCDS.fasta
|
||
argchoice:subrevexon1.fasta:/database/DNA/subtyperef/subrevexon1.fasta
|
||
argchoice:subrevexon2.fasta:/database/DNA/subtyperef/subrevexon2.fasta
|
||
argchoice:subrevintron.fasta:/database/DNA/subtyperef/subrevintron.fasta
|
||
argchoice:subTAR.fasta:/database/DNA/subtyperef/subTAR.fasta
|
||
argchoice:subtatCDS.fasta:/database/DNA/subtyperef/subtatCDS.fasta
|
||
argchoice:subtatexon1.fasta:/database/DNA/subtyperef/subtatexon1.fasta
|
||
argchoice:subtatexon2.fasta:/database/DNA/subtyperef/subtatexon2.fasta
|
||
argchoice:subtatintron.fasta:/database/DNA/subtyperef/subtatintron.fasta
|
||
argchoice:subvif.fasta:/database/DNA/subtyperef/subvif.fasta
|
||
argchoice:subvpr.fasta:/database/DNA/subtyperef/subvpr.fasta
|
||
argchoice:subvpu.fasta:/database/DNA/subtyperef/subvpu.fasta
|
||
argchoice:subnef.fasta:/database/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:textedit in1.rpt&
|
||
|
||
in:in1
|
||
informat:flat
|
||
insave:
|
||
|
||
|
||
#Menu for Protein
|
||
|
||
item:blastp
|
||
itemmethod:(sed "s/[#%]/>/" <in1 > in1.f; cp /var/www/cgi-bin/db/PAM30; /usr/local/biotools/blast/blastall -p blastp -d $BLASTDB -i in1.f -W $WORDLEN -M $Matrix > in1.tmp; /usr/openwin/bin/textedit in1.tmp; rm in1* PAM30)&
|
||
|
||
|
||
in:in1
|
||
informat:flat
|
||
insave:
|
||
|
||
arg:BLASTDB
|
||
argtype:choice_list
|
||
arglabel:Which Database
|
||
argchoice:HIV Proteins Tulio:/var/www/cgi-bin/db/HIV-PROTEINS-tulio.fasta
|
||
argchoice:HIV Proteins:/var/www/cgi-bin/db/hiv17-08-01.PROT.fasta
|
||
argchoice:HIV-1 Structures at PDB:/var/www/cgi-bin/db/Prot.3d.fasta
|
||
argchoice:local:$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 /var/www/cgi-bin/db/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: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:VESPA PROTEASE
|
||
itemmethod:cat in1 > infile ;/usr/local/biotools/GDE/bin/fasta2VESPA.pl > outfile; sed "s/[%]/ /" <outfile > outfile.f ;/home/tulio/biotools/VESPA/VESPA -b $SUBTYPE -q outfile.f > outVESPA; textedit outVESPA;
|
||
|
||
arg:SUBTYPE
|
||
argtype:chooser
|
||
arglabel:Subtype
|
||
argchoice:B:/database/AA/subB.prot.aa.vespa
|
||
argchoice:C:/database/AA/subC.prot.aa.vespa
|
||
argchoice:D:/database/AA/subD.prot.aa.vespa
|
||
in:in1
|
||
informat:flat
|
||
out:out1
|
||
outformat:text
|
||
|
||
item:VESPA Reverse Transcriptase
|
||
itemmethod: cat in1 > infile ;/usr/local/biotools/GDE/bin/fasta2VESPA.pl > outfile; sed "s/[%]/ /" <outfile > outfile.f ;/home/tulio/biotools/VESPA/VESPA -b $SUBTYPE -q outfile.f > outVESPA; textedit outVESPA;
|
||
|
||
arg:SUBTYPE
|
||
argtype:chooser
|
||
arglabel:Subtype
|
||
argchoice:B:/database/AA/subB.rt.aa.vespa
|
||
argchoice:C:/database/AA/subC.rt.aa.vespa
|
||
argchoice:D:/database/AA/subD.rt.aa.vespa
|
||
in:in1
|
||
informat:flat
|
||
out:out1
|
||
outformat:text
|
||
|
||
item:FASTA (Protein)
|
||
itemmethod:(sed "s/[#%]/>/"<in1 >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 >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:Coalescence
|
||
itemmethod: (readseq -a -f11 in1 | sed "s/ YF//1" > infile2;cat tt infile2> infile; /usr/bin/X11/xterm -e /usr/local/biotools/lamarc/coalesce/coalesce;)&
|
||
itemhelp:lsadt.help
|
||
|
||
in:in1
|
||
informat:genbank
|
||
insave:
|
||
inmask:
|
||
|
||
item:tree-puzzle
|
||
itemmethod: (readseq -a -f12 in1 > infile; /usr/bin/X11/xterm -e; (echo b; echo y) | puzzle; textedit outfile; gv outlm.eps)&
|
||
itemhelp:lsadt.help
|
||
|
||
in:in1
|
||
informat:genbank
|
||
insave:
|
||
inmask:
|
||
item:DeSoete Tree fit
|
||
itemmethod: (readseq -a -f8 in1>in1.flat;count -t $CORR in1.flat> in1.tmp ; lsadt<in1.tmp -seed $SEED -init $INIT -empty -99.9 > 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 /usr/bin/X11/xterm -e $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:PAUP
|
||
itemmethod:(readseq -a -f17 in1 > work.nxs; /usr/bin/X11/xterm -e paup work.nxs;/bin/rm -f gde*)&
|
||
|
||
in:in1
|
||
informat:genbank
|
||
inmask:
|
||
insave:
|
||
|
||
item:MrBaynes
|
||
itemmethod:(readseq -a -f17 in1 | sed "s/interleave /interleave=yes /" > work.nxs;cat work.nxs /home/tulio/biotools/mbaynes/mbcommant.txt > workmb.nxs; /usr/bin/X11/xterm -e; (echo execute workmb.nxs) | mb workmb.nxs;treetool workmb.nxs.out.t; /bin/rm in1)&
|
||
|
||
in:in1
|
||
informat:genbank
|
||
inmask:
|
||
insave:
|
||
|
||
item:codeml
|
||
itemmethod:(readseq -a -f11 in1 | sed "s/ YF//1" > test.phy; /usr/bin/X11/xterm -e codeml $METHOD)&
|
||
|
||
|
||
arg:METHOD
|
||
arglabel:Which method ?
|
||
argtype:chooser
|
||
argchoice:0:/home/tulio/biotools/paml/method0.ctl
|
||
argchoice:1:/home/tulio/biotools/paml/method1.ctl
|
||
argchoice:2:/home/tulio/biotools/paml/method2.ctl
|
||
argchoice:3:/home/tulio/biotools/paml/method3.ctl
|
||
argchoice:4:/home/tulio/biotools/paml/method4.ctl
|
||
argchoice:5:/home/tulio/biotools/paml/method5.ctl
|
||
argchoice:6:/home/tulio/biotools/paml/method6.ctl
|
||
|
||
|
||
in:in1
|
||
informat:genbank
|
||
inmask:
|
||
insave:
|
||
|
||
|
||
item:Phylip Distance methods
|
||
itemmethod:(readseq -a -f12 in1 | sed "s/ YF//1" > infile ;$PROG mv -f outfile infile; /usr/bin/X11/xterm -e dnadist;mv -f outfile infile; /usr/bin/X11/xterm -e neighbor; cp outtree intree; $PROGRAM textedit outfile;treetool outtree;/bin/rm -f in1 infile outfile)&
|
||
|
||
arg:PROGRAM
|
||
arglabel:Which method?
|
||
argtype:chooser
|
||
argchoice:DNADIST+NEIGHBOR:
|
||
argchoice:Fitch: /usr/bin/X11/xterm -e fitch;
|
||
argchoice:Kitsch: /usr/bin/X11/xterm -e kitsch;
|
||
argchoice:Neighbor: /usr/bin/X11/xterm -e neighbor;
|
||
argchoice:Bootstrap+consense: /usr/bin/X11/xterm -e consense;
|
||
|
||
arg:PROG
|
||
arglabel:Which method?
|
||
argtype:chooser
|
||
argchoice:Bootstrap: /usr/bin/X11/xterm -e seqboot;
|
||
argchoice:No Bootstrap:
|
||
|
||
arg:PREEDIT
|
||
argtype:chooser
|
||
arglabel:Edit input before running?
|
||
argchoice:No:
|
||
argchoice:Yes:textedit infile;
|
||
|
||
in:in1
|
||
informat:genbank
|
||
inmask:
|
||
insave:
|
||
|
||
menu:On-Line Res.
|
||
item:Search Los Alamos DB Search
|
||
itemmethod:(netscape http://hiv-web.lanl.gov/cgi-bin/hivDB3/public/wdb/ssampublic)
|
||
arg:term
|
||
argtype:text
|
||
arglabel:Search sequence accession
|
||
argtext:
|
||
item:Search Entrez
|
||
itemmethod:(netscape http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=search&db=Entrez&term=$search)&
|
||
|
||
arg:search
|
||
argtype:text
|
||
arglabel:Search Entrez
|
||
argtext:
|
||
|
||
item:Search PubMed
|
||
itemmethod:(netscape http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=search&db=PubMed&term=$term)&
|
||
|
||
arg:term
|
||
argtype:text
|
||
arglabel:Search PubMed for Literature:
|
||
argtext:
|
||
|
||
item:Online Resources at Retroviruses in NCBI
|
||
itemmethod:(netscape http://www.ncbi.nlm.nih.gov/retroviruses/)&
|
||
|
||
item:SNAP Analysis online (dn/ds)
|
||
itemmethod:(netscape http://hiv-web.lanl.gov/SNAP/WEBSNAP/SNAP.html)&
|
||
|
||
item:RIP Analysis online (Recombination)
|
||
itemmethod:(netscape http://hiv-web.lanl.gov/RIP/RIP.html)&
|
||
|
||
item:Search Stanford for Resistance mutations
|
||
itemmethod:(readseq in1 -a -f8 > infile.fasta; netscape http://hiv-4.stanford.edu/cgi-bin/hivseqweb.pl?uploaded_file=infile.fasta)&
|
||
in:in1
|
||
informat:genbank
|
||
inmask:
|
||
insave:
|
||
|
||
menu:Tree Viewer
|
||
item:TreeTool
|
||
itemmethod:(treetool &);
|
||
item:TreeView
|
||
itemmethod:(tv &);
|
||
item:Xsplit-tree
|
||
itemmethod:(/usr/local/biotools/splitstree3.1/xsplits &);
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
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; rm in1 in1.tmp) &
|
||
|
||
arg:REGISTER
|
||
argtype:chooser
|
||
arglabel:Have you previously registered for Grail services?
|
||
argchoice:YES
|
||
argchoice:NO:echo "YOU MUST REGISTER"
|
||
|
||
arg:TOTALSEQS
|
||
argtype:text
|
||
arglabel:Number of Sequences Being Sent to Grail?
|
||
|
||
arg:ID
|
||
argtype:text
|
||
arglabel:User ID (MUST HAVE PREVIOUSLY REGISTERED)
|
||
|
||
in:in1
|
||
informat:flat
|
||
insave:
|
||
|
||
item:Grail Registration
|
||
itemmethod:(echo Register > 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
|
||
|
||
|
||
menu:Xylem
|
||
#------------ Open XYLEM Dataset (GenBank) ( 9/ 6/94) ---------------
|
||
item:Open_XYLEM (GenBank)
|
||
itemlabel:Open XYLEM Dataset (GenBank)
|
||
itemmethod:getloc $DBNAME.ind $DBNAME.ano $DBNAME.wrp $DBNAME.ind out1
|
||
|
||
arg:DBNAME
|
||
arglabel:XYLEM-format GenBank Dataset
|
||
argtype:text
|
||
|
||
out:out1
|
||
outformat:genbank
|
||
|
||
#-------------- Open XYLEM Database (PIR) ( 9/ 6/94) --------------
|
||
item:Open_XYLEM (PIR)
|
||
itemlabel:Open XYLEM Dataset (GenBank)
|
||
itemmethod:getloc -p $DBNAME.ind $DBNAME.ano $DBNAME.wrp $DBNAME.ind out1.pir; readseq -a -f2 out1.pir > out1
|
||
|
||
arg:DBNAME
|
||
arglabel:XYLEM-format PIR Dataset
|
||
argtype:text
|
||
#argtype:file_chooser
|
||
|
||
out:out1
|
||
outformat:genbank
|
||
|
||
|
||
################################# PROTEIN ################################
|
||
#--------------- PROT2NUC - Reverse Translation ( 8/10/94) -----------------
|
||
item:PROT2NUC - reverse translation
|
||
itemmethod: sed "s/[#%]/>/" <in1 | prot2nuc -l$LINLEN -g$GROUP > in1.out; (textedit in1.out; rm in1*)&
|
||
itemhelp: xylem/prot2nuc.doc
|
||
|
||
arg:LINLEN
|
||
arglabel:CODONS PER LINE
|
||
argtype:slider
|
||
argmin:5
|
||
argmax:100
|
||
argvalue:25
|
||
|
||
arg:GROUP
|
||
arglabel:NUMBERING INTERVAL (amino acids/codons)
|
||
argtype:slider
|
||
argmin:5
|
||
argmax:100
|
||
argvalue:5
|
||
|
||
in:in1
|
||
informat:flat
|
||
|
||
########################### DATABASE MENU ###############################
|
||
#------------------- FINDKEY (3/13/97)-----------------------
|
||
item:FINDKEY - Keyword Search
|
||
itemmethod: $KEYWORDS; (findkey $DATABASE in1.kw in1.nam in1.fnd; rm in1.kw; (textedit in1.fnd; rm in1.fnd)& (textedit in1.nam -Ws 150 628; rm in1.nam)& )&
|
||
itemhelp:xylem/findkey.asc
|
||
|
||
arg:KEYWORDS
|
||
arglabel:KEYWORDS
|
||
argtype:chooser
|
||
argchoice:Single keyword:echo $KEY > in1.kw
|
||
argchoice:Create list of keywords:cat $GDE_HELP_DIR/xylem/GDE/keyfile.template > in1.tmp; textedit in1.tmp; egrep -v -e \; in1.tmp >in1.kw;rm in1.tmp*
|
||
argvalue:0
|
||
|
||
arg:KEY
|
||
arglabel:Single keyword
|
||
argtype:text
|
||
|
||
arg:DATABASE
|
||
arglabel:DATABASE
|
||
argtype:choice_menu
|
||
argchoice:HIV GB:-G /database/DNA/hiv1entries
|
||
argchoice:PIR:-p
|
||
argchoice:PIR Dataset:-P $DBFILE
|
||
argchoice:GB bacterial:-b
|
||
argchoice:GB mamalian:-m
|
||
argchoice:GB phage:-g
|
||
argchoice:GB primate:-r
|
||
argchoice:GB rodent:-d
|
||
argchoice:GB unannotated:-u
|
||
argchoice:GB vertebrate:-t
|
||
argchoice:GB invertebrate:-i
|
||
argchoice:GB plant:-l
|
||
argchoice:GB rna:-n
|
||
argchoice:GB synthetic:-s
|
||
argchoice:GB viral:-a
|
||
argchoice:GB patented:-x
|
||
argchoice:GB Seq. Tagged Sites:-z
|
||
argchoice:GB expressed seq. tag:-e
|
||
argchoice:GB Genome Survey Seq.:-S
|
||
argchoice:GB High Throughput Genomic:-h
|
||
argchoice:GenBank Dataset:-G $DBFILE
|
||
argchoice:VecBase:-v
|
||
argvalue:0
|
||
|
||
arg:DBFILE
|
||
arglabel:Dataset name
|
||
argtype:text
|
||
|
||
in:in1
|
||
informat:flat
|
||
|
||
#------------------- FETCH ( 2/ 7/94) --------------------------
|
||
# Note: This menu requires that the shell script 'GBfilter' be
|
||
# in your bin directory.
|
||
item:FETCH
|
||
itemmethod: $NAMES; (fetch $WHATTOGET $DATABASE in1.nam in1.tmp; rm in1.nam; $WHERE) &
|
||
itemhelp:xylem/fetch.doc
|
||
|
||
arg:NAMES
|
||
arglabel:NAMES/ACCESSION #'S
|
||
argtype:chooser
|
||
argchoice:Single name/acc:echo $NAMEFILE > in1.nam
|
||
argchoice:Create list of names/acc#'s:cat $GDE_HELP_DIR/xylem/GDE/namefile.template > in1.tmpname; textedit in1.tmpname; egrep -v -e \; in1.tmpname >in1.nam;rm in1.tmpname*
|
||
argchoice:File of Names/Acc.#'s:cat $NAMEFILE >in1.nam
|
||
argvalue:0
|
||
|
||
arg:NAMEFILE
|
||
arglabel:Single name, accession # or file of names/acc. #'s
|
||
argtype:text
|
||
|
||
arg:WHATTOGET
|
||
arglabel:WHAT TO GET
|
||
argtype:chooser
|
||
argchoice:annotation:-a
|
||
argchoice:sequence:-s
|
||
argchoice:both:-b
|
||
argvalue:2
|
||
|
||
arg:DATABASE
|
||
arglabel:DATABASE
|
||
argtype:chooser
|
||
argchoice:GenBank:-g
|
||
argchoice:GenBank Dataset:-G $DBFILE
|
||
argchoice:HIV Dataset:-G /database/DNA/hiventries
|
||
argchoice:PIR:-p
|
||
argchoice:PIR Dataset:-P $DBFILE
|
||
argchoice:VecBase:-v
|
||
argvalue:0
|
||
|
||
arg:DBFILE
|
||
arglabel:Dataset
|
||
argtype:text
|
||
|
||
arg:WHERE
|
||
arglabel:WHERE TO SEND OUTPUT
|
||
argtype:chooser
|
||
# If GenBank file, read directly, otherwise, convert to GenBank.
|
||
argchoice:GDE:(GBfilter in1.tmp in1.gen; gde in1.gen; rm in1.*)&
|
||
argchoice:Textedit window:(textedit in1.tmp;rm in1.tmp) &
|
||
argchoice:Output file:mv in1.tmp $OUTFILE; echo ' Fetch completed'
|
||
argchoice:GenBank Dataset:splitdb -g in1.tmp $OUTFILE.ano $OUTFILE.wrp $OUTFILE.ind; rm in1.*; echo ' Fetch completed'
|
||
argchoice:PIR Dataset:splitdb -p in1.tmp $OUTFILE.ano $OUTFILE.wrp $OUTFILE.ind; rm in1.*; echo ' Fetch completed'
|
||
argvalue:0
|
||
|
||
arg:OUTFILE
|
||
arglabel:Output file or Dataset name
|
||
argtype:text
|
||
|
||
in:in1
|
||
informat:genbank
|
||
|
||
out:OUTPUT
|
||
outformat:genbank
|
||
|
||
#---------------- FEATURES - by feature key ( 3/14/94) -------------------
|
||
item:FEATURES - Extract by feature keys
|
||
# sed corrects errors in GDE-generated genbank output
|
||
itemmethod: sed -e "s/^LOCUS */LOCUS /" -e "s/^ ACCESSION/ACCESSION /" -e "/^$/d" in1 > in1.gen; $FEALIST; ($FCOMMAND -F in1.feafile $DATABASE; rm in1.feafile in1.efile in1.gen; $WHERE) &
|
||
itemhelp:xylem/features.doc
|
||
|
||
arg:FEALIST
|
||
arglabel:FEATURES TO EXTRACT
|
||
argtype:chooser
|
||
argchoice:Single feature:echo $FEAKEY > in1.feafile
|
||
argchoice:Create list of features:cat $GDE_HELP_DIR/xylem/GDE/feafile.template > in1.tmpfeafile; textedit in1.tmpfeafile; egrep -v -e \; in1.tmpfeafile >in1.feafile; rm in1.tmpfeafile
|
||
argvalue:0
|
||
|
||
arg:FEAKEY
|
||
arglabel:Single feature key
|
||
argtype:choice_list
|
||
argchoice:allele:allele
|
||
argchoice:attenuator:attenuator
|
||
argchoice:binding:binding
|
||
argchoice:CAAT_signal:CAAT_signal
|
||
argchoice:CDS:CDS
|
||
argchoice:chromosome:chromosome
|
||
argchoice:conflict:conflict
|
||
argchoice:contig:contig
|
||
argchoice:C_region:C_region
|
||
argchoice:D_loop:D_loop
|
||
argchoice:D_region:D_region
|
||
argchoice:D_segment:D_segment
|
||
argchoice:enhancer:enhancer
|
||
argchoice:exon:exon
|
||
argchoice:GC_signal:GC_signal
|
||
argchoice:iDNA:iDNA
|
||
argchoice:intron:intron
|
||
argchoice:J_region:J_region
|
||
argchoice:J_segment:J_segment
|
||
argchoice:LTR:LTR
|
||
argchoice:mat_peptide:mat_peptide
|
||
argchoice:misc_binding:misc_binding
|
||
argchoice:misc_difference:misc_difference
|
||
argchoice:misc_feature:misc_feature
|
||
argchoice:misc_recomb:misc_recomb
|
||
argchoice:misc_RNA:misc_RNA
|
||
argchoice:misc_signal:misc_signal
|
||
argchoice:misc_structure:misc_structure
|
||
argchoice:modified_base:modified_base
|
||
argchoice:mRNA:mRNA
|
||
argchoice:mutation:mutation
|
||
argchoice:N_region:N_region
|
||
argchoice:old_sequence:old_sequence
|
||
argchoice:polyA_signal:polyA_signal
|
||
argchoice:polyA_site:polyA_site
|
||
argchoice:precursor_RNA:precursor_RNA
|
||
argchoice:primer_bind:primer_bind
|
||
argchoice:prim_transcript:prim_transcript
|
||
argchoice:promoter:promoter
|
||
argchoice:protein_bind:protein_bind
|
||
argchoice:RBS:RBS
|
||
argchoice:repeat_region:repeat_region
|
||
argchoice:repeat_unit:repeat_unit
|
||
argchoice:rep_origin:rep_origin
|
||
argchoice:rRNA:rRNA
|
||
argchoice:satellite:satellite
|
||
argchoice:scRNA:scRNA
|
||
argchoice:sig_peptide:sig_peptide
|
||
argchoice:snRNA:snRNA
|
||
argchoice:source:source
|
||
argchoice:S_region:S_region
|
||
argchoice:stem_loop:stem_loop
|
||
argchoice:STS:STS
|
||
argchoice:TATA_signal:TATA_signal
|
||
argchoice:terminator:terminator
|
||
argchoice:transit_peptide:transit_peptide
|
||
argchoice:tRNA:tRNA
|
||
argchoice:unsure:unsure
|
||
argchoice:variation:variation
|
||
argchoice:virion:virion
|
||
argchoice:V_region:V_region
|
||
argchoice:V_segment:V_segment
|
||
argchoice:3'clip:3\'clip
|
||
argchoice:3'UTR:3\'UTR
|
||
argchoice:5'UTR:5\'UTR
|
||
argchoice:5'clip:5\'clip
|
||
argchoice:-10_signal:-10_signal
|
||
argchoice:-35 signal:-35 signal
|
||
argvalue:5
|
||
|
||
arg:FCOMMAND
|
||
arglabel:NAMES/ACCESSION #'S OF ENTRIES
|
||
argtype:choice_menu
|
||
argchoice:Single name:echo $EFILE > in1.efile; features -N in1.efile
|
||
argchoice:Create list of names:cat $GDE_HELP_DIR/xylem/GDE/names.template > in1.tmpefile; textedit in1.tmpefile; egrep -v -e \; in1.tmpefile >in1.efile; rm in1.tmpefile; features -N in1.efile
|
||
argchoice:File of names:cat $EFILE >in1.efile; features -N in1.efile
|
||
argchoice:Single Acc#:echo $EFILE > in1.efile; features -A in1.efile
|
||
argchoice:Create list of Acc#s:cat $GDE_HELP_DIR/xylem/GDE/acc.template > in1.tmpefile; textedit in1.tmpefile; egrep -v -e \; in1.tmpefile >in1.efile; rm in1.tmpefile; features -A in1.efile
|
||
argchoice:File of Acc#s:cat $EFILE >in1.efile; features -A in1.efile
|
||
argvalue:0
|
||
|
||
arg:EFILE
|
||
arglabel:Name, Accession # or filename
|
||
argtype:text
|
||
|
||
arg:DATABASE
|
||
arglabel:DATABASE
|
||
argtype:chooser
|
||
argchoice:GenBank:-g
|
||
argchoice:GenBank Dataset:-u $DBFILE
|
||
argchoice:Selected sequences:-U in1.gen
|
||
argvalue:0
|
||
|
||
arg:DBFILE
|
||
arglabel:Dataset name
|
||
argtype:text
|
||
|
||
arg:WHERE
|
||
arglabel:WHERE TO SEND OUTPUT
|
||
argtype:chooser
|
||
argchoice:GDE:readseq -a -f2 in1.out >in1.result; (gde in1.result;rm in1.*)&
|
||
argchoice:Textedit windows:(textedit in1.msg -Ws 450 350;rm in1.msg)& (textedit in1.exp -Ws 350 350; rm in1.exp) & (textedit in1.out -Ws 400 350;rm in1.out)&
|
||
argchoice:Output file:mv in1.msg $OUTNAME.msg; mv in1.out $OUTNAME.out; mv in1.exp $OUTNAME.exp; echo 'Features completed'
|
||
argvalue:0
|
||
|
||
arg:OUTNAME
|
||
arglabel:Output file name
|
||
argtype:text
|
||
|
||
in:in1
|
||
informat:genbank
|
||
|
||
out:RESULT
|
||
outformat:genbank
|
||
|
||
#-------------------- FEATURES - by expression ( 3/14/94)---------------------
|
||
item:FEATURES - Extract using expressions
|
||
itemmethod: $CHOOSEEXP; sed -e "s/^LOCUS */LOCUS /" -e "s/^ ACCESSION/ACCESSION /" -e "/^$/d" in1 > in1.gen; (features -E in1.efile $DATABASE; rm in1.gen in1.efile; $WHERE)&
|
||
itemhelp:xylem/features.doc
|
||
|
||
arg:CHOOSEEXP
|
||
arglabel:EXPRESSION(S)
|
||
argtype:chooser
|
||
argchoice:Single expression:echo '$EXPRESSION'|cut -f1 -d":" > in1.accfile; echo \>`cat in1.accfile` >in1.efile; echo '@$EXPRESSION' >> in1.efile; rm in1.accfile
|
||
argchoice:Expression file:cat $EFILE >in1.efile
|
||
argchoice:Create list of expressions:cat $GDE_HELP_DIR/xylem/GDE/expfile.template > in1.tmpexpfile; textedit in1.tmpexpfile; egrep -v -e \; in1.tmpexpfile >in1.efile; rm in1.tmpexpfile
|
||
argvalue:0
|
||
|
||
arg:EXPRESSION
|
||
arglabel:Feature expression
|
||
argtype:text
|
||
|
||
arg:EFILE
|
||
arglabel:Expression file
|
||
argtype:text
|
||
|
||
arg:DATABASE
|
||
arglabel:DATABASE
|
||
argtype:chooser
|
||
argchoice:GenBank:-g
|
||
argchoice:GenBank Dataset:-u $DBFILE
|
||
argchoice:Selected sequences:-u in1.gen
|
||
argvalue:0
|
||
|
||
arg:DBFILE
|
||
arglabel:Dataset name
|
||
argtype:text
|
||
|
||
arg:WHERE
|
||
arglabel:WHERE TO SENT OUTPUT
|
||
argtype:chooser
|
||
argchoice:GDE:readseq -a -f2 in1.out >in1.result; (gde in1.result;rm in1.*)&
|
||
argchoice:Textedit windows:(textedit in1.msg -Ws 450 350;rm in1.msg)& (textedit in1.out -Ws 400 350;rm in1.out)&
|
||
argchoice:Output file:mv in1.msg $OUTNAME.msg; mv in1.out $OUTNAME.out;echo 'Features completed'
|
||
argvalue:0
|
||
|
||
arg:OUTNAME
|
||
arglabel:Output file name
|
||
argtype:text
|
||
|
||
in:in1
|
||
informat:genbank
|
||
|
||
out:RESULT
|
||
outformat:genbank
|
||
|
||
######################## ALIGNMENT MENU ###############################
|
||
#--------------- REFORM - print multiple alignment (2/ 2/95) -----------------
|
||
item:REFORM - print mult. align.
|
||
#Note: do not use flat or gde .
|
||
itemmethod:(cat in1 |readseq -pipe -a -f8 | reform $TYPE -fp $GAPS $CAPS $DOTS -l$LINESIZE -s$START > in1.out; textedit in1.out;rm in1*) &
|
||
itemhelp: xylem/reform.doc
|
||
|
||
arg:TYPE
|
||
argtype:chooser
|
||
arglabel:Type:
|
||
argchoice:Protein:
|
||
argchoice:Nucleic acid:-n
|
||
argvalue:0
|
||
|
||
arg:GAPS
|
||
argtype:chooser
|
||
arglabel:Print gaps as
|
||
argchoice:Dashes:-g
|
||
argchoice:Spaces:
|
||
argvalue:0
|
||
|
||
arg:CAPS
|
||
argtype:chooser
|
||
arglabel:Capitalize conserved sites in consensus seq.
|
||
argchoice:Yes:-c
|
||
argchoice:No:
|
||
argvalue:0
|
||
|
||
arg:DOTS
|
||
argtype:chooser
|
||
arglabel:Print conserved sites in alignment as dots
|
||
argchoice:Yes:-p
|
||
argchoice:No:
|
||
argvalue:0
|
||
|
||
arg:LINESIZE
|
||
arglabel:# residues per line
|
||
argtype:slider
|
||
argmin:40
|
||
argmax:150
|
||
argvalue:70
|
||
|
||
arg:START
|
||
arglabel:Begin numbering at
|
||
argtype:slider
|
||
argmin:-500000
|
||
argmax:500000
|
||
argvalue:1
|
||
|
||
in:in1
|
||
#informat:flat
|
||
informat:genbank
|
||
insave:
|
||
|
||
|
||
############################## SIMILARITY MENU ############################
|
||
#--------------- SHUFFLE - randomize sequences (11/10/93) -----------------
|
||
item:SHUFFLE - randomize sequences
|
||
itemmethod: sed "s/[#%]/>/" <in1 >in1.tmp; shuffle -s$SEED -w$WINDOW -o$OVERLAP <in1.tmp |tail +3> in1.shuf; readseq -a -f2 in1.shuf >out1; rm in1*
|
||
itemhelp: xylem/shuffle.doc
|
||
|
||
arg:SEED
|
||
arglabel:RANDOM SEED
|
||
argtype:slider
|
||
argmin:1
|
||
argmax:32767
|
||
argvalue:7777
|
||
|
||
arg:WINDOW
|
||
arglabel:WINDOW
|
||
argtype:slider
|
||
argmin:5
|
||
argmax:500000
|
||
argvalue:10
|
||
|
||
arg:OVERLAP
|
||
arglabel:OVERLAP BETWEEN ADJACENT WINDOWS
|
||
argtype:slider
|
||
argmin:0
|
||
argmax:100
|
||
argvalue:0
|
||
|
||
in:in1
|
||
informat:flat
|
||
|
||
out:out1
|
||
outformat:genbank
|
||
|
||
|