#!/usr/bin/perl

#
# Removes insertions (represented by "-" or ".") from FASTA files
#

use strict;
use warnings;

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

my $seq;

while (<FILE>) {
	if (! /^>/) {
		s/-|\.|\n//g;
		$seq .= $_;
		}
	else {		# If there's a sequence print it
		if ($seq) { $seq =~ s/(.{72})/$1\n/g; print "$seq\n"; }
		print $_;	# Then the title
		$seq = "";
		}
	}
if ($seq) { $seq =~ s/(.{72})/$1\n/g; print "$seq\n"; }