#------------------- DNA - FASTA  ( 1/23/06) --------------------------
# Note: This menu requires that the shell script 'GBfilter' be
# in your bin directory.
item:DNA (FASTA) from GI
itemmethod: ($METHOD; $WHERE) &
itemhelp:$doc/dGDE/README.Leash

arg:METHOD
arglabel:Retrieval method
argtype:choice_menu
argchoice:SHoundGetFastafList (default,fast):python $BIRCH/script/flat2list.py in1 in1.list; leash -mn SHoundGetFastaList -mpf in1.list -of in1.tmp; rm in1 in1.list
argchoice:SHoundGetFasta (slow,reliable):python $BIRCH/script/SHGetSeq.py in1 -f fasta in1.tmp
argvalue:0

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:($GDE_TEXTEDIT in1.tmp;rm in1.*) &
argchoice:Output file:mv in1.tmp $OUTFILE; echo ' SEQHOUND - GET completed'
argvalue:0

arg:OUTFILE
arglabel:Output file name
argtype:text

in:in1
informat:flat
insave: