#------------------------- NUMSEQ ( 2/ 8/05) --------------------------
item:NUMSEQ - number a sequence

# INSTALLATION NOTE: The $GDE_HELP_DIR must contain a directory called 
# fsapdat that contains the genetic code files eg. ugc.dat These files contain
# the genetic codes as described in the FSAP documentation. 
# If you already have FSAP installed elsewhere, simply create a 
# symbolic link in the $GDE_HELP_DIR. For example:
# ln -s $DAT/fsap fsapdat
# will create a symbolic link to $DAT/fsap using the name fsapdat

# The directory fsapdoc must also be available in the $GDE_HELP_DIR,
# containing the file numseq.asc from the FSAP package. Again, this
# directory can be implemented as a symbolic link.
itemmethod: (numseq.csh in1 in1.out $GCFILE $START $FINISH $NUCCASE $SNUM $GROUP $GPL $WHICH $STRANDS $KIND $NUMBERS $NUCS $PEPTIDES $FRAMES $FORM; $RM_CMD in1; ($GDE_TEXTEDIT in1.out; $RM_CMD in1*) & )&
itemhelp:doc/fsap/numseq.txt
itemopen:gde_help_viewer.csh


arg:START
argtype:slider
arglabel:START
argmin:1
argmax:500000
argvalue:1

arg:FINISH
argtype:slider
arglabel:FINISH
argmin:1
argmax:500000
argvalue:500000

arg:NUCCASE
argtype:chooser
argchoice:UPPERCASE:U
argchoice:lowercase:l
argvalue:0

arg:SNUM
argtype:slider
arglabel:Number of starting nucleotide
argmin:-500000
argmax:500000
argvalue:0

arg:GROUP
argtype:slider
arglabel:write in GROUPs of
argmin:1
argmax:100
argvalue:10

arg:GPL
argtype:slider
arglabel:number of GROUPs printed per line
argmin:1
argmax:20
argvalue:7

arg:WHICH
arglabel:Which strand?
argtype:chooser
argchoice:original:i
argchoice:opposite:o
argvalue:0

arg:STRANDS
argtype:chooser
argchoice:One strand:1
argchoice:Both strands:2
argvalue:0

arg:KIND
argtype:chooser
arglabel:Print as
argchoice:DNA:D
argchoice:RNA:R
argvalue:0

arg:NUMBERS
arglabel:Numbering
argtype:chooser
argchoice:YES:Y
argchoice:NO:N
argvalue:0

arg:NUCS
arglabel:Print nucleotides
argtype:chooser
argchoice:YES:Y
argchoice:NO:N
argvalue:0

arg:PEPTIDES
argtype:chooser
arglabel:TRANSLATION
argchoice:YES:Y
argchoice:NO:N
argvalue:1

arg:FRAMES
argtype:chooser
arglabel:Reading frames
argchoice:One:1
argchoice:Three:3
argvalue:0

arg:FORM
argtype:chooser
arglabel:aa code
argchoice:Three letter:L
argchoice:One letter:S
argvalue:1

arg:GCFILE
argtype:choice_menu
arglabel:Genetic Code
argchoice:Standard:$DAT/fsap/gc/1.standard.gc
argchoice:Vertebrate Mitochondrial:$DAT/fsap/gc/2.vert_mito.gc
argchoice:Yeast Mitochondrial:$DAT/fsap/gc/3.yeast_mito.gc
argchoice:Mold, Protozoan, and Coelenterate Mitochondrial:$DAT/fsap/gc/4.MPC.mito.gc
argchoice:Invertebrate Mitochondrial:$DAT/fsap/gc/5.inv_mito.gc
argchoice:Ciliate, Dasycladacean and Hexamita:$DAT/fsap/gc/6.CDH.gc
argchoice:Echinoderm and Flatworm:$DAT/fsap/gc/9.EF_mito.gc
argchoice:Euplotid:$DAT/fsap/gc/10.Euplotid.gc
argchoice:Bacterial and Plant Plastid:$DAT/fsap/gc/11.Bact_Plastid.gc
argchoice:Alternative Yeast Nuclear:$DAT/fsap/gc/12.alt_yeast.gc
argchoice:Ascidian Mitochondrial:$DAT/fsap/gc/13.Ascidian_mito.gc
argchoice:Alternative Flatworm Mitochondrial:$DAT/fsap/gc/14.alt_flatworm_mito.gc
argchoice:Blepharisma:$DAT/fsap/gc/15.Blepharisma.gc
argchoice:Chlorophycean Mitochondrial:$DAT/fsap/gc/16.Chlorophycean_mito.gc
argchoice:Trematode Mitochondrial:$DAT/fsap/gc/21.Trematode_mito.gc
argchoice:Scenedesmus obliquus mitochondrial:$DAT/fsap/gc/22.Scenedesmus_mito.gc
argchoice:Thraustochytrium Mitochondrial:$DAT/fsap/gc/23.Thraustochytrium_mito.gc
argvalue:0

in:in1
informat:genbank
insave: