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#! /bin/sh
# usage ./rast2sqn.sh template filename locus_tag_prefix product_id_prefix
PATH=$PATH:.
export PATH
x=`dirname "$2"`/`basename "$2" ".gb"`
gbf2tbl.pl "$x".gb
mv "$x".tbl "$x".tmp
tblfix.pl -product_to_codon_recognized < "$x".tmp | \
tblfix.pl -revcomp_codon_recognized | \
tblfix.pl -split_compound_product | \
tblfix.pl -product_to_tc_number | \
tblfix.pl -product_to_ec_number | \
tblfix.pl -clean_rrna_product | \
tblfix.pl -create_locus_tag $3 | \
tblfix.pl -create_protein_id $4 > "$x".tbl
rm "$x".tmp
tbl2asn -t $1 -i "$x".fsa -U -a s6 -j "[gcode=11]" -R -T -c f -V v -Z "$x".dsc
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