#!/bin/csh -f
unlimit
limit core 0

# from swir20:
# wormpep to end, using accnum as the ID
# this means trembl/inv.dat has to be part of the main data so
# wormpep can be compared to it

 ~pubseq/nuswir/nuswir -b swir21 \
                -fSW ~pubseq/swiss38/swir21/new_seq.dat -K -P \
                -fSW ~pubseq/swiss38/swir21/upd_seq.dat -K -P \
                -fSW ~pubseq/swiss38/swir21/upd_ann.dat -K -P \
                -fSW ~pubseq/swiss38/seq.dat -K -P \
                -fTR ~pubseq/trembl13/arc.dat -S \
                -fTR ~pubseq/trembl13/fun.dat -S \
                -fTR ~pubseq/trembl13/hum.dat -S \
                -fTR ~pubseq/trembl13/mam.dat -S \
                -fTR ~pubseq/trembl13/mhc.dat -S \
                -fTR ~pubseq/trembl13/org.dat -S \
                -fTR ~pubseq/trembl13/phg.dat -S \
                -fTR ~pubseq/trembl13/pln.dat -S \
                -fTR ~pubseq/trembl13/pro.dat -S \
                -fTR ~pubseq/trembl13/rod.dat -S \
                -fTR ~pubseq/trembl13/unc.dat -S \
                -fTR ~pubseq/trembl13/vrl.dat -S \
                -fTR ~pubseq/trembl13/vrt.dat -S \
                -fTR ~pubseq/trembl13/inv.dat \
                -fWP ~pubseq/wormpep20/wormpep -w -I \
	-p12 -t1000 -N350 >&! swir21.out

# combine the main database with the stored TREMBL survivors

 cat swir21.fasta swir21.store >! swir21

# later, need to compare all these to tremblnew
# because the above only compares each trembl division to SW and
# we actually want to compare tremblnew to everything.
