Provided by: libbio-featureio-perl_1.6.905-2_all 
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"