Boulder::Stream(3pm)					User Contributed Perl Documentation				      Boulder::Stream(3pm)

NAME

       Boulder::Stream - Read and write tag/value data from an input stream

SYNOPSIS

	  #!/bin/perl
	  # Read a series of People records from STDIN.
	  # Add an "Eligible" tag to all those whose
	  # Age >= 35 and Friends list includes "Fred"
	  use Boulder::Stream;

	  # filestream way:
	  my $stream = Boulder::Stream->newFh;
	  while ( my $record = <$stream> ) {
	     next unless $record->Age >= 35;
	     my @friends = $record->Friends;
	     next unless grep {$_ eq 'Fred'} @friends;

	     $record->insert(Eligible => 'yes');
	     print $stream $record;
	   }

	   # object oriented way:
	  my $stream = Boulder::Stream->new;
	  while (my $record = $stream->get ) {
	     next unless $record->Age >= 35;
	     my @friends = $record->Friends;
	     next unless grep {$_ eq 'Fred'} @friends;

	     $record->insert(Eligible => 'yes');
	     print $stream $record;
	   }

DESCRIPTION

       Boulder::Stream provides stream-oriented access to Boulder IO hierarchical tag/value data.  It can be used in a magic tied filehandle mode,
       as shown in the synopsis, or in object-oriented mode.  Using tied filehandles, Stone objects are read from input using the standard <>
       operator.  Stone objects printed to the tied filehandle appear on the output stream in Boulder format.

       By default, data is read from the magic ARGV filehandle (STDIN or a list of files provided on the command line) and written to STDOUT.
       This can be changed to the filehandles of your choice.

   Pass through behavior
       When using the object-oriented form of Boulder::Stream, tags which aren't specifically requested by the get() method are passed through to
       output unchanged.  This allows pipes of programs to be constructed easily. Most programs will want to put the tags back into the boulder
       stream once they're finished, potentially adding their own.  Of course some programs will want to behave differently.  For example, a
       database query program will generate but not read a boulderio stream, while a report generator will read but not write the stream.

       This convention allows the following type of pipe to be set up:

	 query_database | find_vector | find_dups | 
	   | blast_sequence | pick_primer | mail_report

       If all the programs in the pipe follow the conventions, then it will be possible to interpose other programs, such as a repetitive element
       finder, in the middle of the pipe without disturbing other components.

SKELETON BOULDER PROGRAM

       Here is a skeleton example.

	  #!/bin/perl
	  use Boulder::Stream;

	  my $stream = Boulder::Stream->newFh;

	  while ( my $record = <$stream> ) {
	     next unless $record->Age >= 35;
	     my @friends = $record->Friends;
	     next unless grep {$_ eq 'Fred'} @friends;

	     $record->insert(Eligible => 'yes');
	     print $stream $record;
	   }

       The code starts by creating a Boulder::Stream object to handle the I/O.	It reads from the stream one record at a time, returning a Stone
       object.	We recover the Age and Friends tags, and continue looping unless the Age is greater or equal to 35, and the list of Friends
       contains "Fred".  If these criteria match, then we insert a new tag named Eligible and print the record to the stream.  The output may look
       like this:

	 Name=Janice
	 Age=36
	 Eligible=yes
	 Friends=Susan
	 Friends=Fred
	 Friends=Ralph
	 =
	 Name=Ralph
	 Age=42
	 Eligible=yes
	 Friends=Janice
	 Friends=Fred
	 =
	 Name=Susan
	 Age=35
	 Eligible=yes
	 Friends=Susan
	 Friends=Fred
	 =

       Note that in this case only records that meet the criteria are echoed to standard output.  The object-oriented version of the program looks
       like this:

	  #!/bin/perl
	  use Boulder::Stream;

	  my $stream = Boulder::Stream->new;

	  while ( my $record = $stream->get('Age','Friends') ) {
	     next unless $record->Age >= 35;
	     my @friends = $record->Friends;
	     next unless grep {$_ eq 'Fred'} @friends;

	     $record->insert(Eligible => 'yes');
	     $stream->put($record);
	   }

       The get() method is used to fetch Stones containing one or more of the indicated tags.  The put() method is used to send the result to
       standard output.  The pass-through behavior might produce a set of records like this one:

	 Name=Janice
	 Age=36
	 Eligible=yes
	 Friends=Susan
	 Friends=Fred
	 Friends=Ralph
	 =
	 Name=Phillip
	 Age=30
	 =
	 Name=Ralph
	 Age=42
	 Eligible=yes
	 Friends=Janice
	 Friends=Fred
	 =
	 Name=Barbara
	 Friends=Agatha
	 Friends=Janice
	 =
	 Name=Susan
	 Age=35
	 Eligible=yes
	 Friends=Susan
	 Friends=Fred
	 =

       Notice that there are now two records ("Phillip" and "Barbara") that do not contain the Eligible tag.

Boulder::Stream METHODS
   $stream = Boulder::Stream->new(*IN,*OUT)
   $stream = Boulder::Stream->new(-in=>*IN,-out=>*OUT)
       The new() method creates a new Boulder::Stream object.  You can provide input and output filehandles. If you leave one or both undefined
       new() will default to standard input or standard output.  You are free to use files, pipes, sockets, and other types of file handles.  You
       may provide the filehandle arguments as bare words, globs, or glob refs. You are also free to use the named argument style shown in the
       second heading.

   $fh = Boulder::Stream->newFh(-in=>*IN, -out=>*OUT)
       Returns a filehandle object tied to a Boulder::Stream object.  Reads on the filehandle perform a get().	Writes invoke a put().

       To retrieve the underlying Boulder::Stream object, call Perl's built-in tied() function:

	 $stream = tied $fh;

   $stone = $stream->get(@taglist)
   @stones = $stream->get(@taglist)
       Every time get() is called, it will return a new Stone object.  The Stone will be created from the input stream, using just the tags
       provided in the argument list.  Pass no tags to receive whatever tags are present in the input stream.

       If none of the tags that you specify are in the current boulder record, you will receive an empty Stone.  At the end of the input stream,
       you will receive undef.

       If called in an array context, get() returns a list of all stones from the input stream that contain one or more of the specified tags.

   $stone = $stream->read_record(@taglist)
       Identical to get(>, but the name is longer.

   $stream->put($stone)
       Write a Stone to the output filehandle.

   $stream->write_record($stone)
       Identical to put(), but the name is longer.

   Useful State Variables in a Boulder::Stream
       Every Boulder::Stream has several state variables that you can adjust.  Fix them in this fashion:

	       $a = new Boulder::Stream;
	       $a->{delim}=':';
	       $a->{record_start}='[';
	       $a->{record_end}=']';
	       $a->{passthru}=undef;

       o   delim

	   This is the delimiter character between tags and values, "=" by default.

       o   record_start

	   This is the start of nested record character, "{" by default.

       o   record_end

	   This is the end of nested record character, "}" by default.

       o   passthru

	   This determines whether unrecognized tags should be passed through from the input stream to the output stream.  This is 'true' by
	   default.  Set it to undef to override this behavior.

BUGS

       Because the delim, record_start and record_end characters in the Boulder::Stream object are used in optimized (once-compiled) pattern
       matching, you cannot change these values once get() has once been called.  To change the defaults, you must create the Boulder::Stream, set
       the characters, and only then begin reading from the input stream.  For the same reason, different Boulder::Stream objects cannot use
       different delimiters.

AUTHOR

       Lincoln D. Stein <lstein@cshl.org>, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.  This module can be used and distributed on the
       same terms as Perl itself.

SEE ALSO

       Boulder, Boulder::Blast, Boulder::Genbank, Boulder::Medline, Boulder::Unigene, Boulder::Omim, Boulder::SwissProt

perl v5.10.1							    2001-06-11						      Boulder::Stream(3pm)