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.
[email protected] - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list: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 [email protected]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"