#------------------- Convert to GI ( 4/10/06) --------------------------

item:Convert Name/Acc to GI

# For ACCESSION numbers in the form AB005432.1, the version number is deleted,
# because SeqHound can't handle it.
# This is a problem with SeqHound 2.5, and appears to be fixed in
# the most recent SeqHound.
itemmethod: python $BIRCH/script/flat2list.py in1 in1.tmp; cut -f1 -d"." <in1.tmp >in1.nam;  leash -mn $SHMETHOD -mpf in1.nam -of in1.gi; python $BIRCH/script/list2flat.py in1.gi in1.flat;rm in1.nam in1.tmp in1.gi; $GDEOUTPUT
itemhelp:doc/dGDE/SeqHound_API_Functions.html#SHoundFindAccList
itemopen:browser.csh

in:in1
informat:flat

arg:SHMETHOD
arglabel:Convert
argtype:chooser
argchoice:Name to GI:SHoundFindNameList
argchoice:Accession to GI:SHoundFindAccList
argvalue:0

arg:GDEOUTPUT
arglabel:Output to new GDE window?
argtype:chooser
# Problem with Linux-Intel version of GDE (doesn't affect Solaris):
# If we declare an 'out' file, then it must always exist,
# even if we don't use it. Otherwise, gde will look for the file
# after it is done, and crash.
argchoice:Yes:(echo '' > out1.gi; dgde in1.flat; $RM_CMD -f in1.*)&
argchoice:No:mv in1.flat out1.gi
argvalue:0

out:out1.gi
outformat:gde