man Bio::Variation::IO (3): Handler for sequence variation IO Formats

SYNOPSIS

use Bio::Variation::IO;
$in = Bio::Variation::IO->new(-file => "inputfilename" ,
-format => 'flat');
$out = Bio::Variation::IO->new(-file => ">outputfilename" ,
-format => 'xml');
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;
    use Bio::Variation::IO;
    $in  = Bio::Variation::IO->newFh(-format => $format1 );
    $out = Bio::Variation::IO->newFh(-format => $format2 );
    print $out $_ while <$in>;

CONSTRUCTORS

Bio::Variation::IO->new()

   $seqIO = Bio::Variation::IO->new(-file => 'filename',   -format=>$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:

-file

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

-fh

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.

-format

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.

Bio::Variation::IO->newFh()

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

OBJECT METHODS

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

$sequence = $seqIO->next()

Fetch the next sequence from the stream.

$seqIO->write($sequence [,$another_sequence,...])

Write the specified sequence(s) to the stream.

TIEHANDLE(), READLINE(), PRINT()

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

FEEDBACK

Mailing Lists

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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:

  https://github.com/bioperl/bioperl-live/issues

AUTHOR - Heikki Lehvaslaiho

Email: heikki-at-bioperl-dot-org

APPENDIX

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

new

 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

format

 Title   : format
 Usage   : $format = $stream->format()
 Function: Get the variation format
 Returns : variation format
 Args    : none

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

write

 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

_guess_format

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