/ 
Boulder-1.30
River stage zero No dependents
/ Boulder::Stream

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;

  • delim

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

  • record_start

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

  • record_end

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

  • 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