get_annotation.sh

#!/bin/bash

set -e

for f in `cat 00_FILES`
do
    d=`date`
    echo "[$d] working on $f ..."
    svr_assign_to_dna_using_figfams < $f > svr_assign_to_dna_using_figfams.txt
    papi-gen-annotation-database -f $f -o ANNOTATION.db
    papi-populate-genes-table ANNOTATION.db -i svr_assign_to_dna_using_figfams.txt -p myrast_cmdline_dont_use
    papi-export-genes-table ANNOTATION.db -o $f-RAST.txt
    rm ANNOTATION.db
    rm svr_assign_to_dna_using_figfams.txt
done