#!/usr/bin/perl -w
use strict;

my $dir = shift @ARGV || ".";

opendir(DIR, $dir) || die $!;
my @files;
for my $file ( readdir(DIR) ) {
 if( $file =~ /\.pep$/) {
  warn("$file\n");
  push @files, $file;
 }
}
for my $file ( @files ) {
 for my $file2 ( @files ) {
  if( -f "$file-vs-$file2.BLASTP" ) {
   warn("skipping $file-vs-$file2.BLASTP it already exists\n"); 
 }
 # make the formatdb
 `wu-formatdb -i $file2 -p T >& format.out`;
 `blastp -i $file -d $file2 -o $file-vs-$file2.BLASTP -cpus 2 E=1e-10 -postsw -links -topcomboN 1`;
 }
}