#!@WHICHPERL@
#
# $Id: fasta-make-index.pl.in 5026 2010-10-20 07:00:35Z james_johnson $
# $Log$
# Revision 1.2  2005/10/05 06:18:35  nadya
# use full path for "rm". Asssume everybody has /bin/rm.
#
# Revision 1.1.1.1  2005/07/28 23:53:45  nadya
# Importing from meme-3.0.14, and adding configure/make
#
#

$pgm = $0;			# name of program
$pgm =~ s#.*/##;                # remove part up to last slash
@args = @ARGV;			# arguments to program
$status = 0;			# exit status 
$SIG{'INT'} = 'cleanup';	# interrupt handler

$usage = <<USAGE;		# usage message
  USAGE:
	$pgm <file> [-f] [-sp] [-l] [-aa] [-gc] [-gi]

	<file>		name of FASTA file

	[-f]		overwrite existing index file if one exists
	[-sp]		make a swissprot index by stripping all but
			last part of sequence names
	[-l]		index by sequence name and lowercased name
	[-aa]		include first amino acid index found in parens
	[-gc]		genechip format: first field in pipes
	[-gi]		if identifier starts with "gi|<number>" replace
			it with <number>

	Make an index for a FASTA file for use by fasta-fetch.

	Creates file <file>.index.
USAGE

$nargs = 1;
if ($#ARGV+1 < $nargs) {		# wrong number of arguments
  print $usage;
  exit(1);
}

# get input arguments
$file = shift;
while ($#ARGV >= 0) {
  if ($ARGV[0] eq "-sp") {
    $sprot = 1;
  } elsif ($ARGV[0] eq "-l") {
    $lower = 1;
  } elsif ($ARGV[0] eq "-aa") {
    $aa = 1;
  } elsif ($ARGV[0] eq "-gc") {
    $gc = 1;
  } elsif ($ARGV[0] eq "-gi") {
    $gi = 1;
  } elsif ($ARGV[0] eq "-f") {
    $force = 1;
  } else {
    print $usage;
    exit(1);
  }
  shift;
}

open FILE, "<$file" || die "Couldn't open $file";
if (!$force && -e "$file.index") {
  print STDERR "Can't create fetch index file for file $file.\n";
  print STDERR "File $file.index already exists.\n";
  print STDERR "Move or rename file $file.index and try again.\n";
  exit 1;
}

open INDEX, ">$file.index" || die "Couldn't open $file.index";
$byte = 0;
while (<FILE>) {
  if (/^>/) {
    #if (++$i % 1000 == 0) {print stderr "seq: $i\r";}
    @words = split;
    $id = $words[0] eq ">" ? $words[1] : $words[0];
    $id =~ s/>//;			# remove ">"
    if ($sprot) {
      $id =~ s/.*\|//;			# remove up to last "|"
    } elsif ($gc) {
      # first to last field between "|"
      @words = split(/\|/, $id);	# split on pipes
      $id = $words[0];
    } elsif ($gi) {
      if ($id =~ /^gi\|(\d+)/) { $id = $1; }
    }
    @ids = ($id);
    if ($aa) {				# add amino acid id
      foreach $id (@words[1..$#words]) {
        if ($id =~ /^\(([A-Z][0-9]+)\)$/) {
          push @ids, "$1";
          last;
        } 
      }
    }
    foreach $id (@ids) {
      printf INDEX ">%s %d\n", $id, $byte;
      if ($lower) {
	$l = $id;
	$l =~ tr/A-Z/a-z/;
	printf INDEX ">%s %d\n", $l, $byte;
      }
    }
  }
  $byte += length;
}
    
# cleanup files
# note: "if ($status == 130) {cleanup(1);}" must follow $status = system(...)
#&cleanup($status);
 
sub cleanup {
  system "/bin/rm $pgm.$$.*.tmp";
  if ($_[0] eq "INT") { exit(1); } else { exit($_[0]); }
}
