#!/bin/bash

DATADIR="$CONDA_PREFIX/share/psipred_4.01/data"

echo $DATADIR

i_a3m="$1"

o_ss="$2"

ID=$(basename $i_a3m .a3m).tmp

$PIPEDIR/csblast-2.2.3/bin/csbuild -i $i_a3m -I a3m -D $PIPEDIR/csblast-2.2.3/data/K4000.crf -o $ID.chk -O chk

head -n 2 $i_a3m > $ID.fasta

echo $ID.chk > $ID.pn

echo $ID.fasta > $ID.sn

makemat -P $ID

psipred $ID.mtx $DATADIR/weights.dat $DATADIR/weights.dat2 $DATADIR/weights.dat3 > $ID.ss

psipass2 $DATADIR/weights_p2.dat 1 1.0 1.0 $i_a3m.csb.hhblits.ss2 $ID.ss > $ID.horiz

(

echo ">ss_pred"

grep "^Pred" $ID.horiz | awk '{print $2}'

echo ">ss_conf"

grep "^Conf" $ID.horiz | awk '{print $2}'

) | awk '{if(substr($1,1,1)==">") {print "\n"$1} else {printf "%s", $1}} END {print ""}' | sed "1d" > $o_ss

rm ${i_a3m}.csb.hhblits.ss2

rm $ID.*