#!/usr/bin/perl

# Converts concise file into fasta format
# also puts in the consensus.

use strict;
use warnings;

my ( @seqs, %seq, @pred, %pred );

my @var = (
  "Lupas_21",  "Lupas_14", "Lupas_28", "JNETPSSM",  "MULTCOIL", "MULTCOIL_TRIMER", "MULTCOIL_DIMER", "JNETFREQ",
  "JNETALIGN", "JNETHMM",  "JNETSOL5", "JNETSOL25", "JNETSOL0", "jnetpred",        "jpred",          "JNETCONF"
);

if   ( $ARGV[0] ) { open( IN, "<$ARGV[0]" ) or die($!); }
else              { open( IN, "<-" )        or die($!); }

while (<IN>) {
  if (/^\n/) { next; }
  my ( $id, $seq ) = split( ":", $_ );
  if ( !$id || !$seq ) { next; }    # Check we have proper values
  $seq =~ s/,//g;
  chomp($seq);
  if ( $id =~ /;/ ) {               # Then it's an alignment
    @_ = split( ";", $id );
    push @seqs, $_[1];
    $seq{ $_[1] } = $seq;
  }
  foreach (@var) {
    if ( $_ eq $id ) {
      push @pred, $_;
      $pred{$_} = $seq;
    }
  }
}
close(IN);

foreach (@seqs) {
  $seq{$_} =~ s/(.{72})/$1\n/g;
  print ">$_\n$seq{$_}\n";
}

foreach (@pred) {
  $pred{$_} =~ s/[TCYWXZSI\?_]/-/g;
  $pred{$_} =~ s/B/E/g;
  $pred{$_} =~ s/G/H/g;

  if (/SOL/) { $pred{$_} =~ s/E/B/g; }
  $pred{$_} =~ s/(.{72})/$1\n/g;
  print ">$_\n$pred{$_}\n";
}