EM算法的改进

				#!@WHICHPERL@				#				# $Id: fasta-make-index.txt 1339 2006-09-21 19:46:28Z tbailey $				# $Log$				# 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:					$pgm  [-f] [-sp] [-l] [-aa] [-gc] [-gi]											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|" replace							it with 									Make an index for a FASTA file for use by fasta-fetch.									Creates 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 $usage;				    exit(1);				  }				  shift;				}								open FILE, "				if (!$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";				$byte = 0;				while () {				  if (/^>/) {				    #if (++$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]); }				}