Search database against itself

[Xillanne]

Hello,

I've build my own database with msa file infered with mafft. I want to compare all of the profile against each other, now I've made a loop against each entry of my db to get their hhm profile and search it against my db.
Do I have another way to do it ? For example, to search directly a db against a db ?

Thanks for your answer !

There is my code.

ffindex_build -s -f ${current_path}/msa_files.txt ${current_path}/msa.ffdata ${current_path}/msa.ffindex

# Create A3M format
echo "Converting to A3M format..."
# Rebuild ffindex for A3M
OMP_NUM_THREADS=1 mpirun -np $num_threads \
  ffindex_apply_mpi ${current_path}/msa.ff{data,index}  \
   -i ${current_path}/msa_a3m.ffindex -d ${current_path}/msa_a3m.ffdata \
    -- hhconsensus -M 50 -maxres 65535 -i stdin -oa3m stdout -v 0 > "${current_path}/hhconsensus_mpi_errors.log"

# Create HHMs
# Create ffindex for HHM
echo "Creating HHM profiles..."
OMP_NUM_THREADS=1 mpirun -np $num_threads \
  ffindex_apply_mpi ${current_path}/msa_a3m.ff{data,index} \
  -i ${current_path}/msa_hhm.ffindex -d ${current_path}/msa_hhm.ffdata \
  -- hhmake -i stdin -o stdout -v 0 -id 100 > "${current_path}/hhmake_mpi_errors.log"

cd ${current_path}

sort msa_hhm.ffindex > msa_hhm.ffindex.simpleSort
sort msa_a3m.ffindex > msa_a3m.ffindex.simpleSort
mv msa_a3m.ffindex msa_a3m.ffindex.orig
mv msa_hhm.ffindex msa_hhm.ffindex.orig
ln -s msa_a3m.ffindex.simpleSort msa_a3m.ffindex
ln -s msa_hhm.ffindex.simpleSort msa_hhm.ffindex


# Create index for hhdatabase
cstranslate -f -i msa -o msa_cs219 -A /data/desmarais/Applications/hh-suite/data/cs219.lib -D /data/desmarais/Applications/hh-suite/data/context_data.lib -x 0.3 -c 4 -I a3m -b

# Putting everything together
sort -k3 -n msa_cs219.ffindex | cut -f1 > sorting.dat

ffindex_order sorting.dat msa_hhm.ff{data,index} msa_hhm_ordered.ff{data,index}
mv msa_hhm_ordered.ffindex msa_hhm.ffindex
mv msa_hhm_ordered.ffdata msa_hhm.ffdata

ffindex_order sorting.dat msa_a3m.ff{data,index} msa_a3m_ordered.ff{data,index}
mv msa_a3m_ordered.ffindex msa_a3m.ffindex
mv msa_a3m_ordered.ffdata msa_a3m.ffdata

cd "$output_dir" || exit
count=0

echo "Performing profile-profile comparison..."
for i in *.msa; do
  (
    name=$(sed -n '1p' "$i" | tr -d ">")
    file_prefix=$(basename "$i" .msa)

    # Create hhm
    ffindex_get ${current_path}/msa_hhm.ffdata ${current_path}/msa_hhm.ffindex $i > "${file_prefix}.hhm"

    # Run hhsearch
    hhsearch -i "${file_prefix}.hhm" -d ${current_path}/msa -o "${current_path}/${output_hhr_dir}/${file_prefix}_result.hhr"
  ) &

  ((count++))
  if (( count % max_jobs == 0 )); then
    wait  # Wait for the current batch
  fi
done