Convert contigs of an ACE file into a FASTA file.

ace2fas.pl

#!/usr/bin/perl
#
# Convert contigs of an ACE file into a FASTA file.
# Usage: ace2fas.pl < my.ace > my.fas
#
use strict;
use warnings;

while(<>){
  next until /^CO\s+(\S+).+?$/;  # read ACE file till next contig starts
  my $contig = $1;
  my $seq;
  while(<>){
    last if /^\s*$/;             # stop reading at end of sequence
    chomp;
    $seq .= $_;                  # append sequence
  }
  $seq =~ tr/*//d;
  print ">$contig\n$seq\n";
}