Bio::FeatureIO(3)

NAME
Bio::FeatureIO - Handler for FeatureIO

SYNOPSIS
  use Bio::FeatureIO;

  #read from a file
  $in  = Bio::FeatureIO->new(-file => "my.gff" , -format => 'GFF');

  #read from a filehandle
  $in  = Bio::FeatureIO->new(-fh => \*GFF , -format => 'GFF');

  #read features already attached to a sequence
  my $feat = Bio::FeatureIO->new(-seq => $seq , -format => 'features');

  #read new features for existing sequence
  my $seq = Bio::FeatureIO->new(-seq => $seq , -format => 'Das');

  #write out features
  $out = Bio::FeatureIO->new(-file    => ">outputfilename" ,
                             -format  => 'GFF' ,
                             -version => 3);

  while ( my $feature = $in->next_feature() ) {
    $out->write_feature($feature);
  }

DESCRIPTION
An I/O iterator subsystem for genomic sequence features.

Bio::FeatureIO is a handler module for the formats in the FeatureIO set (eg, Bio::FeatureIO::GFF). It is the officially sanctioned way of getting at the format objects, which most people should use.

The Bio::FeatureIO system can be thought of like biological file handles. They are attached to filehandles with smart formatting rules (eg, GFF format, or BED format) and can either read or write feature objects (Bio::SeqFeature objects, or more correctly, Bio::FeatureHolderI implementing objects, of which Bio::SeqFeature is one such object). If you want to know what to do with a Bio::SeqFeatureI object, read Bio::SeqFeatureI.

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 FeatureIO object instance is configured for either input or output. A specific example of a stream object is the Bio::FeatureIO::gff object.

Each stream object has functions:

  $stream->next_feature();
  $stream->write_feature($feature);

SUPPORTED FORMATS
 name                         module
 -----------------------------------
 BED                          bed.pm
 GFF                          gff.pm
 GTF                          gtf.pm
 InterPro (IPRScan 4.0)  interpro.pm
 PTT (NCBI protein table)     ptt.pm

CONSTRUCTORS

  Bio::FeatureIO->new()
   $featureIO = Bio::FeatureIO->new(-file => 'filename',   -format=>$format);
   $featureIO = Bio::FeatureIO->new(-fh   => \*FILEHANDLE, -format=>$format);
   $featureIO = Bio::FeatureIO->new(-seq  => $seq,         -format=>$format);

The new() class method constructs a new Bio::FeatureIO object. The returned object can be used to retrieve or print Seq 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:

       $featio = Bio::FeatureIO->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.

    A string filehandle is handy if you want to modify the output in the memory, before printing it out. The following program reads in EMBL formatted entries from a file and prints them out in fasta format with some HTML tags:

      use Bio::FeatureIO;
      use IO::String;
      my $in  = Bio::FeatureIO->new('-file' => "my.gff" ,
                                '-format' => 'EMBL');
      while ( my $f = $in->next_feature() ) {
          # the output handle is reset for every file
          my $stringio = IO::String->new($string);
          my $out = Bio::FeatureIO->new('-fh' => $stringio,
                                    '-format' => 'gtf');
          # output goes into $string
          $out->write_feature($f);
          # modify $string
          $string =~ s|(>)(\w+)|$1<font color="Red">$2</font>|g;
          # print into STDOUT
          print $string;
      }

-format
    Specify the format of the file. See above for list of supported formats

-flush
    By default, all files (or filehandles) opened for writing sequences will be flushed after each write_seq() (making the file immediately usable). If you don't need this facility and would like to marginally improve the efficiency of writing multiple sequences to the same file (or filehandle), pass the -flush option '0' or any other value that evaluates as defined but false:

      my $f1 = Bio::FeatureIO->new -file   => "<a.f1",
                                  -format => "f1";
      my $f2 = Bio::FeatureIO->new -file   => ">a.f2",
                                  -format => "f2",
                                  -flush  => 0; # go as fast as we can!

      while($feature = $f1->next_feature) { $f2->write_feature($feature) }

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

This constructor behaves like new(), but returns a tied filehandle rather than a Bio::FeatureIO 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:

  @features = <$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:

  $feature = $featureIO->next_feature()
Fetch the next feature from the stream.

  $featureIO->write_feature($feature [,$another_feature,...])
Write the specified feature(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 one of 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:

  http://bugzilla.open-bio.org/

AUTHOR - Allen Day
Email allenday@ucla.edu

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::FeatureIO->new(-file => $filename, -format => 'Format')
 Function: Returns a new feature stream
 Returns : A Bio::FeatureIO stream initialised with the appropriate format
 Args    : Named parameters:
             -file => $filename
             -fh => filehandle to attach to
             -format => format

  newFh
 Title   : newFh
 Usage   : $fh = Bio::FeatureIO->newFh(-file=>$filename,-format=>'Format')
 Function: does a new() followed by an fh()
 Example : $fh = Bio::FeatureIO->newFh(-file=>$filename,-format=>'Format')
           $feature = <$fh>;   # read a feature object
           print $fh $feature; # write a feature object
 Returns : filehandle tied to the Bio::FeatureIO::Fh class
 Args    :

See Bio::FeatureIO::Fh

  fh
 Title   : fh
 Usage   : $obj->fh
 Function:
 Example : $fh = $obj->fh;      # make a tied filehandle
           $feature = <$fh>;   # read a feature object
           print $fh $feature; # write a feature object
 Returns : filehandle tied to Bio::FeatureIO class
 Args    : none

  next_feature
 Title   : next_feature
 Usage   : $feature = stream->next_feature
 Function: Reads the next feature object from the stream and returns it.

           Certain driver modules may encounter entries in the stream
           that are either misformatted or that use syntax not yet
           understood by the driver. If such an incident is
           recoverable, e.g., by dismissing a feature of a feature
           table or some other non-mandatory part of an entry, the
           driver will issue a warning. In the case of a
           non-recoverable situation an exception will be thrown.  Do
           not assume that you can resume parsing the same stream
           after catching the exception. Note that you can always turn
           recoverable errors into exceptions by calling
           $stream->verbose(2).

 Returns : a Bio::SeqFeatureI feature object
 Args    : none

See Bio::Root::RootI, Bio::SeqFeatureI

  write_feature
 Title   : write_feature
 Usage   : $stream->write_feature($feature)
 Function: writes the $feature object into the stream
 Returns : 1 for success and 0 for error
 Args    : Bio::SeqFeature object

  _load_format_module
 Title   : _load_format_module
 Usage   : *INTERNAL FeatureIO stuff*
 Function: Loads up (like use) a module at run time on demand
 Example :
 Returns :
 Args    :

  seq
 Title   : seq
 Usage   : $obj->seq() OR $obj->seq($newSeq)
 Example :
 Returns : Bio::SeqI object
 Args    : newSeq (optional)

  _filehandle
 Title   : _filehandle
 Usage   : $obj->_filehandle($newval)
 Function: This method is deprecated. Call _fh() instead.
 Example :
 Returns : value of _filehandle
 Args    : newvalue (optional)

  _guess_format
 Title   : _guess_format
 Usage   : $obj->_guess_format($filename)
 Function: guess format based on file suffix
 Example :
 Returns : guessed format of filename (lower case)
 Args    :
 Notes   : See "SUPPORTED FORMATS"