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#!/bin/csh
foreach embossinst (`embossversion -full -auto| grep '^InstallDirectory'`)
# echo "$embossinst"
end
setenv EMBOSS_TIMETODAY "2013-07-15 12:00:00"
set top = ~/devemboss/test
set itop = $embossinst/share/EMBOSS/test
echo "$top"
cd $top
cd swiss
echo "Indexing swiss"
dbiflat -fields "acnum,seqvn,des,keyword,taxon" \
-dbname SWISSPROT -auto
diff entrynam.idx $itop/swiss/
cd ../swnew
echo "Indexing swnew"
dbiflat -fields "acnum,seqvn,des,keyword,taxon" \
-dbname SWISSNEW -auto
diff entrynam.idx $itop/swnew/
cd ../embl
echo "Indexing embl"
dbiflat -fields "acnum,seqvn,des,keyword,taxon" \
-dbname EMBL -idformat embl -auto
diff entrynam.idx $itop/embl/
cd ../genbank
echo "Indexing genbank"
dbiflat -fields "acnum,seqvn,des,keyword,taxon" \
-dbname GENBANK -idformat gb -filenames '*.seq' -auto
diff entrynam.idx $itop/genbank/
#cd ../gb
#echo "Indexing gb"
#dbigcg -fields "acnum,seqvn,des,keyword,taxon" \
# -dbname GENBANK -idformat genbank -auto
#diff entrynam.idx $top/gb/
cd ../pir
echo "Indexing pir"
dbigcg -fields "acnum,seqvn,des,keyword,taxon" \
-dbname PIR -idformat pir -auto
diff entrynam.idx $itop/pir/
cd ../testdb
echo "Indexing testdb"
dbifasta -fields "acnum,des" \
-dbname TESTDB -idformat idacc -filenames 'testdb.fasta' -auto
diff entrynam.idx $itop/testdb/
#cd ../wormpep
#echo "Indexing wormpep"
#dbifasta -fields "acnum,des" \
# -dbname WORMPEP -filenames 'wormpep' -auto
#diff entrynam.idx $top/wormpep/
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