#!/usr/bin/perl

# Converts a FASTA alignment of *sequences* to a concise file of the
# form alignX;seq name:seq where X is an incremental integer and seq is
# a comma seperated list of the sequence

use warnings;

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

my ( $seq, @seqs, @title );
while (<IN>) {
  if (s/^>//) {
    if ($seq) {
      $seq =~ s/\n|\s//g;
      $seq =~ s/(.)/$1,/g;
      push @seqs, $seq;
      $seq = "";
    }
    chomp;
    push @title, $_;
  } else {
    chomp;
    $seq .= $_;
  }
}
$seq =~ s/\n|\s//g;
$seq =~ s/(.)/$1,/g;
push @seqs, $seq;

if ( @title != @seqs ) { die("non matching number of titles and sequences!\n"); }

foreach ( 0 .. $#title ) {
  print "align" . ( $_ + 1 ) . ";$title[$_]:$seqs[$_]\n";
}