Bio::FeatureIO(3pm)					User Contributed Perl Documentation				       Bio::FeatureIO(3pm)

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

       NOTE:  This is a highly experimental I/O iterator subsystem for genomic sequence features. It is not complete, and is now undergoing a
       significant refactoring in a separate branch of BioPerl to address specific issues regarding the current implementation. Use at your own
       risk.

       Bio::FeatureIO is a handler module for the formats in the FeatureIO set (eg, Bio::FeatureIO::GFF).

       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:

	 https://redmine.open-bio.org/projects/bioperl/

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"

perl v5.14.2							    2012-03-02						       Bio::FeatureIO(3pm)