Bio::Tools::GFF.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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()
 
 

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 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.
   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 the web:
   http://bugzilla.open-bio.org/
 
 

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 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)