SYNOPSIS
use Bio::Tools::GFF;
# specify input via -fh or -file
my $gffio = Bio::Tools::GFF->new(-fh => \*STDIN, -gff_version => 2);
my $feature;
# loop over the input stream
while($feature = $gffio->next_feature()) {
# do something with feature
}
$gffio->close();
# you can also obtain a GFF parser as a SeqAnalasisParserI in
# HT analysis pipelines (see Bio::SeqAnalysisParserI and
# Bio::Factory::SeqAnalysisParserFactory)
my $factory = Bio::Factory::SeqAnalysisParserFactory->new();
my $parser = $factory->get_parser(-input => \*STDIN, -method => "gff");
while($feature = $parser->next_feature()) {
# do something with feature
}
DESCRIPTION
This class provides a simple GFF parser and writer. In the sense of a SeqAnalysisParser, it parses an input file or stream into SeqFeatureI objects, but is not in any way specific to a particular analysis program and the output that program produces.That is, if you can get your analysis program spit out GFF, here is your result parser.
GFF3 AND SEQUENCE DATA
GFF3 supports sequence data; seehttp://www.sequenceontology.org/gff3.shtml
There are a number of ways to deal with this -
If you call
$gffio->ignore_sequence(1)
prior to parsing the sequence data is ignored; this is useful if you just want the features. It avoids the memory overhead in building and caching sequences
Alternatively, you can call either
$gffio->get_seqs()
Or
$gffio->seq_id_by_h()
At the end of parsing to get either a list or hashref of Bio::Seq objects (see the documentation for each of these methods)
Note that these objects will not have the features attached - you have to do this yourself, OR call
$gffio->features_attached_to_seqs(1)
PRIOR to parsing; this will ensure that the Seqs have the features attached; ie you will then be able to call
$seq->get_SeqFeatures();
And use Bio::SeqIO methods
Note that auto-attaching the features to seqs will incur a higher memory overhead as the features must be cached until the sequence data is found
TODO
Make a Bio::SeqIO class specifically for GFF3 with sequence dataFEEDBACK
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 the web:
https://github.com/bioperl/bioperl-live/issues
AUTHOR - Matthew Pocock
Email mrp-at-sanger.ac.ukCONTRIBUTORS
Jason Stajich, jason-at-biperl-dot-org Chris Mungall, cjm-at-fruitfly-dot-org Steffen Grossmann [SG], grossman at molgen.mpg.de Malcolm Cook, mec-at-stowers-institute.orgAPPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _new
Title : new
Usage : my $parser = Bio::Tools::GFF->new(-gff_version => 2,
-file => "filename.gff");
or
my $writer = Bio::Tools::GFF->new(-gff_version => 3,
-file => ">filename.gff3");
Function: Creates a new instance. Recognized named parameters are -file, -fh,
and -gff_version.
Returns : a new object
Args : named parameters
-gff_version => [1,2,3]
_parse_header
Title : _parse_header
Usage : $gffio->_parse_header()
Function: used to turn parse GFF header lines. currently
produces Bio::LocatableSeq objects from ##sequence-region
lines
Returns : 1 on success
Args : none
next_segment
Title : next_segment
Usage : my $seq = $gffio->next_segment;
Function: Returns a Bio::LocatableSeq object corresponding to a
GFF "##sequence-region" header line.
Example :
Returns : A Bio::LocatableSeq object, or undef if
there are no more sequences.
Args : none
next_feature
Title : next_feature
Usage : $seqfeature = $gffio->next_feature();
Function: Returns the next feature available in the input file or stream, or
undef if there are no more features.
Example :
Returns : A Bio::SeqFeatureI implementing object, or undef if there are no
more features.
Args : none
from_gff_string
Title : from_gff_string
Usage : $gff->from_gff_string($feature, $gff_string);
Function: Sets properties of a SeqFeatureI object from a GFF-formatted
string. Interpretation of the string depends on the version
that has been specified at initialization.
This method is used by next_feature(). It actually dispatches to
one of the version-specific (private) methods.
Example :
Returns : void
Args : A Bio::SeqFeatureI implementing object to be initialized
The GFF-formatted string to initialize it from
_from_gff1_string
Title : _from_gff1_string
Usage :
Function:
Example :
Returns : void
Args : A Bio::SeqFeatureI implementing object to be initialized
The GFF-formatted string to initialize it from
_from_gff2_string
Title : _from_gff2_string
Usage :
Function:
Example :
Returns : void
Args : A Bio::SeqFeatureI implementing object to be initialized
The GFF2-formatted string to initialize it from
write_feature
Title : write_feature
Usage : $gffio->write_feature($feature);
Function: Writes the specified SeqFeatureI object in GFF format to the stream
associated with this instance.
Returns : none
Args : An array of Bio::SeqFeatureI implementing objects to be serialized
gff_string
Title : gff_string
Usage : $gffstr = $gffio->gff_string($feature);
Function: Obtain the GFF-formatted representation of a SeqFeatureI object.
The formatting depends on the version specified at initialization.
This method is used by write_feature(). It actually dispatches to
one of the version-specific (private) methods.
Example :
Returns : A GFF-formatted string representation of the SeqFeature
Args : A Bio::SeqFeatureI implementing object to be GFF-stringified
_gff1_string
Title : _gff1_string Usage : $gffstr = $gffio->_gff1_string Function: Example : Returns : A GFF1-formatted string representation of the SeqFeature Args : A Bio::SeqFeatureI implementing object to be GFF-stringified
_gff2_string
Title : _gff2_string Usage : $gffstr = $gffio->_gff2_string Function: Example : Returns : A GFF2-formatted string representation of the SeqFeature Args : A Bio::SeqFeatureI implementing object to be GFF2-stringified
_gff25_string
Title : _gff25_string Usage : $gffstr = $gffio->_gff2_string Function: To get a format of GFF that is peculiar to Gbrowse/Bio::DB::GFF Example : Returns : A GFF2.5-formatted string representation of the SeqFeature Args : A Bio::SeqFeatureI implementing object to be GFF2.5-stringified
_gff3_string
Title : _gff3_string Usage : $gffstr = $gffio->_gff3_string Function: Example : Returns : A GFF3-formatted string representation of the SeqFeature Args : A Bio::SeqFeatureI implementing object to be GFF3-stringified
gff_version
Title : _gff_version Usage : $gffversion = $gffio->gff_version Function: Example : Returns : The GFF version this parser will accept and emit. Args : none
newFh
Title : newFh
Usage : $fh = Bio::Tools::GFF->newFh(-file=>$filename,-format=>'Format')
Function: does a new() followed by an fh()
Example : $fh = Bio::Tools::GFF->newFh(-file=>$filename,-format=>'Format')
$feature = <$fh>; # read a feature object
print $fh $feature; # write a feature object
Returns : filehandle tied to the Bio::Tools::GFF class
Args :
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::Tools::GFF class
Args : none
get_seqs
Title : get_seqs Usage : Function: Returns all Bio::Seq objects populated by GFF3 file Example : Returns : Args :
features_attached_to_seqs
Title : features_attached_to_seqs Usage : $obj->features_attached_to_seqs(1); Function: For use with GFF3 containg sequence only Setting this B<before> parsing ensures that all Bio::Seq object created will have the appropriate features added to them defaults to false (off) Note that this mode will incur higher memory usage because features will have to be cached until the relevant feature comes along Example : Returns : value of features_attached_to_seqs (a boolean) Args : on set, new value (a boolean, optional)
ignore_sequence
Title : ignore_sequence Usage : $obj->ignore_sequence(1); Function: For use with GFF3 containg sequence only Setting this B<before> parsing means that all sequence data will be ignored Example : Returns : value of ignore_sequence (a boolean) Args : on set, new value (a boolean, optional)