Bio::Tools::GFF(3pm)

NAME

Bio::Tools::GFF - A Bio::SeqAnalysisParserI compliant GFF format parser

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; see

http://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()

  $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 data

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:

[email protected]

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.uk

CONTRIBUTORS

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.org

APPENDIX

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 containing 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 containing 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)