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Summary

Bio::Variation::IO - Handler for sequence variation IO Formats

Package variables

Included modules

Inherit

Bio::SeqIO

Synopsis

    use Bio::Variation::IO;

    $in  = Bio::Variation::IO->new(-file => "inputfilename" , '-format' => 'flat');
    $out = Bio::Variation::IO->new(-file => ">outputfilename" , '-format' => 'xml');
    # note: we quote -format to keep older perl's from complaining.

    while ( my $seq = $in->next() ) {
	$out->write($seq);
    }

or

    use Bio::Variation::IO;

    #input file format can be read from the file extension (dat|xml)
    $in  = Bio::Variation::IO->newFh(-file => "inputfilename");
    $out = Bio::Variation::IO->newFh('-format' => 'xml');

    # World's shortest flat<->xml format converter:
    print $out $_ while <$in>;

Description

Bio::Variation::IO is a handler module for the formats in the Variation IO set (eg,
Bio::Variation::IO::flat). It is the officially sanctioned way of getting at
the format objects, which most people should use.
The structure, conventions and most of the code is inherited from
Bio::SeqIO module. The main difference is that instead of using
methods next_seq and write_seq, you drop '_seq' from the method names.
The idea is that you request a stream object for a particular format.
All the stream objects have a notion of an internal file that is read
from or written to. A particular SeqIO object instance is configured
for either input or output. A specific example of a stream object is
the Bio::Variation::IO::flat object.
Each stream object has functions

   $stream->next();

and

   $stream->write($seqDiff);

also

   $stream->type() # returns 'INPUT' or 'OUTPUT'

As an added bonus, you can recover a filehandle that is tied to the
SeqIO object, allowing you to use the standard <> and print operations
to read and write sequence objects:

    use Bio::Variation::IO;

    $stream = Bio::Variation::IO->newFh(-format => 'flat'); # read from standard input

    while ( $seq = <$stream> ) {
	# do something with $seq
    }

and

    print $stream $seq; # when stream is in output mode

This makes the simplest ever reformatter

    #!/usr/local/bin/perl

    $format1 = shift;
    $format2 = shift || die "Usage: reformat format1 format2 < input > output";

    use Bio::Variation::IO;

    $in  = Bio::Variation::IO->newFh(-format => $format1 );
    $out = Bio::Variation::IO->newFh(-format => $format2 );
    #note: you might want to quote -format to keep older perl's from complaining.

    print $out $_ while <$in>;

Methods

Methods description

 Title   : _guess_format
 Usage   : $obj->_guess_format($filename)
 Function:
 Example :
 Returns : guessed format of filename (lower case)
 Args    :

 Title   : new
 Usage   : $stream = Bio::Variation::IO->new(-file => $filename, -format => 'Format')
 Function: Returns a new seqstream
 Returns : A Bio::Variation::IO::Handler initialised with the appropriate format
 Args    : -file => $filename
           -format => format
           -fh => filehandle to attach to

 Title   : next
 Usage   : $seqDiff = $stream->next
 Function: reads the next $seqDiff object from the stream
 Returns : a Bio::Variation::SeqDiff object
 Args    :

 Title   : write
 Usage   : $stream->write($seq)
 Function: writes the $seq object into the stream
 Returns : 1 for success and 0 for error
 Args    : Bio::Variation::SeqDiff object

Methods code

sub _guess_format {

   my $class = shift;
   return unless $_ = shift;
   return 'flat'     if /\.dat$/i;
   return 'xml'     if /\.xml$/i;
}


1;

}

sub _load_format_module {

  my ($class, $format) = @_;
  my $module = "Bio::Variation::IO::" . $format;
  my $ok;  
  eval {
      $ok = $class->_load_module($module);
  };
  if ( $@ ) {
    print STDERR <<END;
$class: $format cannot be found
Exception $@
For more information about the IO system please see the IO docs.
This includes ways of checking for formats at compile time, not run time
END
  ;
  }
  return $ok;

}

sub new {

   my ($class, %param) = @_;
   my ($format);

   @param{ map { lc $_ } keys %param } = values %param;  # lowercase keys
   $format = $param{'-format'}
             || $class->_guess_format( $param{-file} || $ARGV[0] )
             || 'flat';
   $format = "\L$format"; # normalize capitalization to lower case

   return undef unless $class->_load_format_module($format);
   return "Bio::Variation::IO::$format"->new(%param);

}

sub next {

   my ($self, $seq) = @_;
   $self->throw("Sorry, you cannot read from a generic Bio::Variation::IO object.");

}

sub next_seq {

   my ($self, $seq) = @_;
   $self->throw("These are not sequence objects. Use method 'next' instead of 'next_seq'.");
   $self->next($seq);

}

sub write {

    my ($self, $seq) = @_;
    $self->throw("Sorry, you cannot write to a generic Bio::Variation::IO object.");

}

sub write_seq {

   my ($self, $seq) = @_;
   $self->warn("These are not sequence objects. Use method 'write' instead of 'write_seq'.");
   $self->write($seq);

}

General documentation

   $seqIO = Bio::Variation::IO->new(-file => 'filename',   -format=>$format);
   $seqIO = Bio::Variation::IO->new(-fh   => \*FILEHANDLE, -format=>$format);
   $seqIO = Bio::Variation::IO->new(-format => $format);

The new() class method constructs a new Bio::Variation::IO object. The
returned object can be used to retrieve or print BioSeq objects. new()
accepts the following parameters:
    A file path to be opened for reading or writing. The usual Perl
conventions apply:

   'file'       # open file for reading
   '>file'      # open file for writing
   '>>file'     # open file for appending
   '+<file'     # open file read/write
   'command |'  # open a pipe from the command
   '| command'  # open a pipe to the command

    You may provide new() with a previously-opened filehandle. For
example, to read from STDIN:

   $seqIO = Bio::Variation::IO->new(-fh => \*STDIN);

    Note that you must pass filehandles as references to globs.
    If neither a filehandle nor a filename is specified, then the module
will read from the @ARGV array or STDIN, using the familiar <>
semantics.
    Specify the format of the file. Supported formats include:

   flat        pseudo EMBL format
   xml         seqvar xml format

    If no format is specified and a filename is given, then the module
will attempt to deduce it from the filename. If this is unsuccessful,
Fasta format is assumed.
    The format name is case insensitive. 'FLAT', 'Flat' and 'flat' are
all supported.

   $fh = Bio::Variation::IO->newFh(-fh   => \*FILEHANDLE, -format=>$format);
   $fh = Bio::Variation::IO->newFh(-format => $format);
   # etc.

   #e.g.
   $out = Bio::Variation::IO->newFh( '-FORMAT' => 'flat');
   print $out $seqDiff;

This constructor behaves like new(), but returns a tied filehandle
rather than a Bio::Variation::IO object. You can read sequences from this
object using the familiar <> operator, and write to it using print().
The usual array and $_ semantics work. For example, you can read all
sequence objects into an array like this:

  @mutations = <$fh>;

Other operations, such as read(), sysread(), write(), close(), and printf()
are not supported.

See below for more detailed summaries. The main methods are:

Fetch the next sequence from the stream.

Write the specified sequence(s) to the stream.

These provide the tie interface. See perltie for more details.

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to the
Bioperl mailing lists Your participation is much appreciated.

  bioperl-l@bioperl.org                         - General discussion
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report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via
email or the web:

  bioperl-bugs@bio.perl.org
  http://bugzilla.bioperl.org/

Email: heikki@ebi.ac.uk
Address:

     EMBL Outstation, European Bioinformatics Institute
     Wellcome Trust Genome Campus, Hinxton
     Cambs. CB10 1SD, United Kingdom

The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _