Skip site navigation (1)Skip section navigation (2)

FreeBSD Manual Pages

  
 
  

home | help
Bio::FeatureIO(3)     User Contributed Perl Documentation    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:

       next_feature
	  Fetch	the next feature from the stream.

       write_feature
	  Write	the specified feature(s) to the	stream.

       feature_factory
	  This gets/sets the specific Bio::Factory::FeatureFactoryI

       The following methods delegate to the inter

       feature_class
	  Set the specific Bio::SeqFeatureI class to return

       type_features
	  Boolean flag,	ensures	the returned features are typed

       unflatten_features
	  Ensure the returned features are unflattened

   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"

perl v5.32.0			  2014-09-05		     Bio::FeatureIO(3)

NAME | SYNOPSIS | DESCRIPTION | SUPPORTED FORMATS | CONSTRUCTORS | OBJECT METHODS | FEEDBACK | AUTHOR - Allen Day | APPENDIX

Want to link to this manual page? Use this URL:
<https://www.freebsd.org/cgi/man.cgi?query=Bio::FeatureIO&sektion=3&manpath=FreeBSD+12.2-RELEASE+and+Ports>

home | help