doOfs

#!/bin/bash

# Launch OFS on a genome to predict the presence of operons
# Citation: http://bioinformatics.oxfordjournals.org/content/21/7/880.long

if [ "$#" -lt 1 ]; then
    echo 'doOFS ORGANISM'
    exit 65
fi

ORG=$1

mkdir $ORG
cd $ORG

cp ../near/all.faa .
cp ../near/all.ptt .
cp ../$ORG.faa .
cp ../$ORG.ptt .
cp ../src/* .

cat all.faa $ORG.faa > all-genomes.faa
cat all.ptt $ORG.ptt > all-genomes.ptt

formatdb -i all-genomes.faa
formatdb -i $ORG.faa

perl get_blast_hits.pl "$ORG" all-genomes.faa > all.blast
perl get_orthologs.pl all.blast $ORG.faa all-genomes.faa > all.orthologs
perl calc_bp_distance.pl all.orthologs all-genomes.ptt > all.bp_dist
perl bp_stats.pl all.bp_dist 0.7 > informants.species
perl filter_informants.pl informants.species  all-genomes.faa all-genomes.ptt informants
formatdb -i informants.faa
perl cluster_finder.pl $ORG.faa informants.faa $ORG.ptt informants.ptt 
perl operon_finder.pl $ORG.ptt query_clusters.dat
./op2tab $ORG"_operon_preds.dat" gi_2_loc.tab 0.5 > $ORG.tab

mv $ORG.tab ../
cd ..
rm -rf $ORG