# exonerate-refine.sh : exonerate with region refinement 
# a shell script for gg_job processing

$bin_dir/exonerate \
  --model protein2genome \
  --refine region  --refineboundary 5000 \
  --minintron 20 --maxintron 25000 \
  --showtargetgff --showvulgar 0 --showalignment 0 \
  --ryo '#qi %qi length=%ql alnlen=%qal\\n#ti %ti length=%tl alnlen=%tal\\n' \
  --query  $part_dir/$proteins \
  --target $part_dir/$genome \
  > $part_dir/$output_file_name.gff

# fixme: the ryo \\n were not converted to newlines
# perl -pi -e's,\\n,\n,g;' output.gff

#... sample use at ncsa.teragrid.org ...
# $aug/scripts/gg_job.pl  \
# --jobtype script --script $aug/scripts/exonerate-refine.sh \
# --QTYPE PBS --CLASS dque --CLOCKTIME "8:55:00" --ACCOUNT "TG-xxx" \
# --do_parts_batch 10 --bin_dir $exn/bin/  \
# --genome acyr-genome.fa --proteins nasv_gnomon.aa \
# --output acyr-exonr-nasv5aa --partitions partitions.list
# 
#... and collate results ... 
# cat SCAFFOLD*/acyr-exonr-nasv5a?.gff combo_*/acyr-exonr-nasv5a?.gff | \
# perl -pe's,\\n,\n,g;' |\
# $aug/scripts/process_exonerate_gff3.perl -sou exonr_nasv5 | \
# perl -pe's/lcl.hmm/nasonia_g/;' \
# > acyr-exonr-nasv5a.gff3