#------------------- mrtrans (10/ 1/09) ---------------------------------
item:mrtrans - protein/DNA alignment
# Modified for compatability with both GDE and biolegato. bioLegato
# can't read pseudo-Genbank files created by readseq, so output now
# goes to a GDE flat file, which both can read.
# sed edits out ":CDS" or "_CDS" that is added by FEATURES
# tr gets rid of extra > and ASCII 128 added by mrtrans
# sed lops off the  comma and extra junk readseq adds to the name line
# including the " from >name..." that needs to be removed.
# mrtrans has been modified to allow sequence names longer than
# 9 char. Install mrtrans from mrtrans.tar.
# Finally, we have to translate the protein sequence to 
# uppercase, which is required by mrtrans.
itemmethod:(readseq -a -f=Pearson -C -pipe $PROTFILE |sed "s/[:_]CDS/_/" | sed "s/,.*//" >in1.prot; readseq -a -f=Pearson -pipe $DNAFILE |sed "s/[:_]CDS/_/" |sed "s/,.*//" | cut -f1 -d" " > in1.dna; mrtrans.csh in1.prot in1.dna; mrtrans in1.prot in1.dna.reordered | sed "s/> from >/>/" |tr -d '€' | readseq -pipe -a -f8 | sed "s/>>/#/"|sed 's/ from.*//' > in1.flat; (gde in1.flat; $RM_CMD in1.flat)& $RM_CMD in1.prot in1.dna in1.dna.reordered)&

itemhelp:doc/fasta/mrtrans.txt
itemopen:gde_help_viewer.csh

arg:PROTFILE
argtype:text
#@argtype:file_chooser
arglabel:MULTIPLY-ALIGNED PROTEIN FILE
argtext:

 
arg:DNAFILE
argtype:text
#@argtype:file_chooser
arglabel:UNALIGNED DNA FILE
argtext:


# even though we don't use the in1 file, we still
# need to declare it to generate the unique name in1
in:in1
informat:genbank
insave: