#!/usr/local/bin/perl -w
# AUTHOR: Timothy L. Bailey
# CREATE DATE: 24 Nov 2006
#use strict;
use File::Basename;

$PGM = $0;			# name of program
$PGM =~ s#.*/##;                # remove part up to last slash
#@args = @ARGV;			# arguments to program
$| = 1;				# flush after all prints
$SIG{'INT'} = \&cleanup;	# interrupt handler
# Note: so that interrupts work, always use for system calls:
# 	if ($status = system("$command")) {&cleanup($status)}

# requires
push(@INC, split(":", $ENV{'PATH'}));	# look in entire path

# defaults
$get_all = 0;

my $usage = <<USAGE;		# usage message
  USAGE:
	$PGM [options]

	[-id <modif_id>]+	id of motif to extract from MEME .txt file
	[-all]			get all motifs in the MEME .txt file
	[-noll]			MEME file is missing log-odds matrices

	Extract a motifs from a MEME-formated motif database
	or from a MEME output file (.txt format).

	Reads standard input.
	Writes standard output.

        Copyright
        (2006) The University of Queensland
        All Rights Reserved.
        Author: Timothy L. Bailey
USAGE

$nargs = 1;			# number of required args
if ($#ARGV+1 < $nargs) { &print_usage("$usage", 1); }

# get input arguments
%id_list = ();
$n_needed = 0;
while ($#ARGV >= 0) {
  $_ = shift;
  if ($_ eq "-h") {				# help
    &print_usage("$usage", 0);
  } elsif ($_ eq "-all") {
    $get_all = 1;
  } elsif ($_ eq "-noll") {
    $no_ll = 1;
  } elsif ($_ eq "-id") {
    $_ = shift;
    $id_list{$_} = 1; 
    $n_needed++;
  } else {
    &print_usage("$usage", 1);
  }
}

$header = "";
$n_left = $n_needed;				# number of ids not found yet
while (<STDIN>) {
  next if (/^#/ || /^\s*$/);                    # skip comment, blank lines

  # save header lines
  $header .= "$_\n" if (/^MEME version/ || /^ALPHABET/ || /^strands/);
  if (/^Background/) {
      $header .= $_;
      # keep lines lines starting with a letter then digit
      while (<STDIN>) {
          if (/^\s*[a-zA-Z]\s*\d/) {
              $header .= $_;
          } else {
              last;
          }
      }
  }

  next if (/^#/ || /^\s*$/);                    # skip comment, blank lines
  my @words = split;
  if ($words[0] eq "MOTIF" && ($get_all || $id_list{$words[1]})) {	# found a target motif
    print "$header\n" if ($n_needed == $n_left--);	# print header first time
    print "\n$_\n";					# print motif line
    my $n_reps = 0;
    while (<STDIN>) {					# find matrix representations
      print if (/^BL /);				# print block line
      if (/^log-odds/ || /^letter-probability/) {	# motif matrix
        print;
        @words = split;
        my $w = $words[5];				# motif width
        for (my $i=0; $i<$w; $i++) {			# print the motif matrix
          $_ = <STDIN>;
          print;
        }
        last if ($no_ll || $n_reps++ >= 1);		# done after letter-probability printed
      }
    }
    exit(1) if (!$get_all && $n_left<=0);			# all done
  }

};

# cleanup files
#&cleanup($status);
 
################################################################################
#                       Subroutines                                            #
################################################################################
 
################################################################################
#
#       print_usage
#
#	Print the usage message and exit.
#
################################################################################
sub print_usage {
  my($usage, $status) = @_;
 
  if (-c STDOUT) {			# standard output is a terminal
    open(C, "| more");
    print C $usage;
    close C;
  } else {				# standard output not a terminal
    print STDERR $usage;
  }

  exit $status;
}
 
################################################################################
#       cleanup
#
#       cleanup stuff
#
################################################################################
sub cleanup {
  my($status, $msg) = @_;
  if ($status && "$msg") {print STDERR "$msg: $status\n";}
  exit($status);
}