#!/usr/local/bin/perl5 -w

( ($fasta_dir  = shift @ARGV) && 
  ($n          = shift @ARGV) && 
  ($output_dir = shift @ARGV) &&
  ($name       = shift @ARGV)) ||
    die "usage: run_hmmer fasta_dir n_fasta_file output_dir name (of fasta_files -- name.14.fasta)\n";

(-d "Temp") || 
    die "\"Temp\" directory does not exist, create it, and try again.\n";

open(FASTA, "<$fasta_dir/$name.$n.fasta") ||
    die "could not open file: \"$fasta_dir/$name.$n.fasta\"";
$/ = "\n>";

while (defined($rec = <FASTA>))
{
    $rec =~ s/^>//;
    $rec =~ s/>$//;

    open(TMP, ">Temp/$name.$n.fasta") ||
        die "could not open file: Temp/$name.$n.fasta\n";
    print TMP ">$rec";
    close(TMP);

    `npri -w hmmpfam Pfam Temp/$name.$n.fasta >> $output_dir/$name.$n.pfam_output`;
}

close(FASTA);
