templateAlignment.sh

#!/bin/bash
# Set environment
if [ "$HOSTNAME" = "olt" ]
  then
    source /ebio/abt1_share/toolkit_support1/code/bioprogs/env/environment.sh

elif [ "$HOSTNAME" = "rye" ]
  then
    source /cluster/toolkit/production/bioprogs/env/environment_rye.sh
  fi

HHSUITE=${DATABASES}/hh-suite/
PFAMREGEX="(pfam[0-9]+)|(^PF[0-9]+ ?(.[0-9]+))"
FILESTRING=$(cat  params/dbs|tr "\n" " ")

echo $accession
DBS=($FILESTRING)

echo $FILESTRING

if [ ! -e "results/$accession.fas" ]
then
    for i in "${DBS[@]}"
    do
    :
    echo $i $accession
    if [[ "$accession" =~ $PFAMREGEX ]]
    then
        ffindex_get ${HHSUITE}${i}_a3m.ffdata ${HHSUITE}${i}_a3m.ffindex "$accession.a3m" >> results/$accession.a3m
    else
        ffindex_get ${HHSUITE}${i}_a3m.ffdata ${HHSUITE}${i}_a3m.ffindex $accession >> results/$accession.a3m
    fi
    done


    # Align two sequences or MSAs
    if [[ $FILESTRING == "" ]]
    then
        ffindex_get results/db_a3m.ffdata results/db_a3m.ffindex "db.a3m" >> results/$accession.a3m
        ffindex_get results/db_a3m.ffdata results/db_a3m.ffindex $accession >> results/$accession.a3m
    fi

    hhfilter -i results/$accession.a3m -o results/$accession.reduced.a3m -diff 100
    reformat.pl a3m a3m results/$accession.reduced.a3m results/${accession}_tmp.a3m -noss

    mv results/${accession}_tmp.a3m results/$accession.a3m

    sed -i "1 i\#A3M#" results/$accession.a3m

fi