#!/usr/bin/perl -w

# Fri Nov 25 16:58:43 PST 2005 Kevin Karplus

# extract-guide < foo.a2m > guide.a2m
#
# reads the first sequence from the input a2m file and copies it to output.

=pod

=head1 NAME

extract-guide -- extracts the first sequence from an a2m file

=head1 SYNOPSIS

extract-guide < foo.a2m > guide.a2m
 
 Options:
 	-help	brief help 
	-man	detailed help


=head1 OPTIONS

=over 4

=item B<-help>

Print a brief help message and exits.

=item B<-man>

Prints the manual page and exits.

=back

=head1 DESCRIPTION

extract-guide is a very simple script that simply copies the first
sequence out of an a2m or fasta formatted input on STDIN.

=cut


use strict;

use FileHandle;
STDERR->autoflush(1);
use English;
use Getopt::Long;
use Pod::Usage;

# function prototypes

#main
{    
    GetOptions(
	      "help|?"	=>	sub {pod2usage("verbose"=>1);}
	    , "man"		=> 	sub {pod2usage("verbose"=>2);}
	    )
	    or pod2usage("verbose"=>0);
    
    my $id_line_seen=0;
    while(<STDIN>)
    {   if (/^>/)
    	{  exit (0) if ($id_line_seen);	# copied first sequence
	   $id_line_seen=1;
	}
	tr/\r//d;
	print $_ if ($id_line_seen);
    }
    
    print "\n";		# make sure there is a new-line at the end
    exit ($id_line_seen? 0: -1);
}