NAME

       Bio::Variation::IO - 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.

         bioperl-l@bioperl.org                  - General discussion
         http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

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

       bioperl-l@bioperl.org

       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

   next
        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    :