#!/bin/tcsh

# This is a simple script which will carry out all of the basic steps
# required to make a PSIPRED V2 prediction. Note that it assumes that the
# following programs are in the appropriate directories:
# blastpgp - PSIBLAST executable (from NCBI toolkit)
# makemat - IMPALA utility (from NCBI toolkit)
# psipred - PSIPRED V2 program
# psipass2 - PSIPRED V2 program

# The name of the BLAST data bank
#set dbname = nrfilt

# Where the NCBI programs have been installed
set ncbidir = /home/jpei/profile_hmm/profile_hmm/blastpgp/blast-2.2.14/bin

# Where the PSIPRED V2 programs have been installed
set execdir = /home/jpei/profile_hmm/profile_hmm/psipred/bin

# Where the PSIPRED V2 data files have been installed
set datadir = /home/jpei/profile_hmm/profile_hmm/psipred/data

set basename = $1:r
set rootname = $basename:t
set outname = $basename.chk

\cp -f $1 psitmp.fasta

echo "Running PSI-BLAST with sequence" $1 "..."

$ncbidir/blastpgp -v 5000 -b 0 -j 3 -h 0.001 -d $dbname -i psitmp.fasta -C psitmp.chk >& $rootname.blast

echo "Predicting secondary structure..."

echo psitmp.chk > psitmp.pn
echo psitmp.fasta > psitmp.sn
$ncbidir/makemat -P psitmp

echo Pass1 ...

$execdir/psipred psitmp.mtx $datadir/weights.dat $datadir/weights.dat2 $datadir/weights.dat3 $datadir/weights.dat4 > $rootname.ss

echo Pass2 ...

$execdir/psipass2 $datadir/weights_p2.dat 1 1.0 1.0 $rootname.ss2 $rootname.ss > $rootname.horiz

# Remove temporary files

echo Cleaning up ...
\rm -f psitmp.* error.log

echo "Final output files:" $rootname.ss2 $rootname.horiz
echo "Finished."