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:

  https://github.com/bioperl/bioperl-live/issues

set_attributes¶

 Title   : set_attributes
 Usage   :
 Function: Sets a whole array of parameters at once.
 Example :
 Returns : none
 Args    : Named parameters, in the form as they would otherwise be passed
           to new(). Currently recognized are:
                    -start          start position
                    -end            end position
                    -strand         strand
                    -phase          the phase of the feature (0..2)
                    -primary_tag    primary tag 
                    -primary        (synonym for -primary_tag)
                    -source_tag     source tag
                    -source         (synonym for -source_tag)
                    -frame          frame
                    -score          score value
                    -tag            a reference to a tag/value hash
                    -gff_string     GFF v.2 string to initialize from
                    -gff1_string    GFF v.1 string to initialize from
                    -seq_id         the display name of the sequence
                    -annotation     the AnnotationCollectionI object
                    -location       the LocationI object

direct_new¶

 Title   : direct_new
 Usage   : my $feat = Bio::SeqFeature::Generic->direct_new;
 Function: create a blessed hash - for performance improvement in 
           object creation
 Returns : Bio::SeqFeature::Generic object
 Args    : none

location¶

 Title   : location
 Usage   : my $location = $feat->location();
 Function: returns a location object suitable for identifying location 
           of feature on sequence or parent feature  
 Returns : Bio::LocationI object
 Args    : [optional] Bio::LocationI object to set the value to.

start¶

 Title   : start
 Usage   : my $start = $feat->start;
           $feat->start(20);
 Function: Get/set on the start coordinate of the feature
 Returns : integer
 Args    : none

end¶

 Title   : end
 Usage   : my $end = $feat->end;
           $feat->end($end);
 Function: get/set on the end coordinate of the feature
 Returns : integer
 Args    : none

length¶

 Title   : length
 Usage   : my $len = $feat->length;
 Function: Get the feature length computed as:
              $feat->end - $feat->start + 1
 Returns : integer
 Args    : none

strand¶

 Title   : strand
 Usage   : my $strand = $feat->strand();
           $feat->strand($strand);
 Function: get/set on strand information, being 1,-1 or 0
 Returns : -1,1 or 0
 Args    : none

score¶

 Title   : score
 Usage   : my $score = $feat->score();
           $feat->score($score);
 Function: get/set on score information
 Returns : float
 Args    : none if get, the new value if set

frame¶

 Title   : frame
 Usage   : my $frame = $feat->frame();
           $feat->frame($frame);
 Function: get/set on frame information
 Returns : 0,1,2, '.'
 Args    : none if get, the new value if set

primary_tag¶

 Title   : primary_tag
 Usage   : my $tag = $feat->primary_tag();
           $feat->primary_tag('exon');
 Function: get/set on the primary tag for a feature,
           eg 'exon'
 Returns : a string
 Args    : none

source_tag¶

 Title   : source_tag
 Usage   : my $tag = $feat->source_tag();
           $feat->source_tag('genscan');
 Function: Returns the source tag for a feature,
           eg, 'genscan'
 Returns : a string
 Args    : none

has_tag¶

 Title   : has_tag
 Usage   : my $value = $feat->has_tag('some_tag');
 Function: Tests whether a feature containings a tag
 Returns : TRUE if the SeqFeature has the tag,
           and FALSE otherwise.
 Args    : The name of a tag

add_tag_value¶

 Title   : add_tag_value
 Usage   : $feat->add_tag_value('note',"this is a note");
 Returns : TRUE on success
 Args    : tag (string) and one or more values (any scalar(s))

get_tag_values¶

 Title   : get_tag_values
 Usage   : my @values = $feat->get_tag_values('note');
 Function: Returns a list of all the values stored
           under a particular tag.
 Returns : A list of scalars
 Args    : The name of the tag

get_all_tags¶

 Title   : get_all_tags
 Usage   : my @tags = $feat->get_all_tags();
 Function: Get a list of all the tags in a feature
 Returns : An array of tag names
 Args    : none

# added a sort so that tags will be returned in a predictable order # I still think we should be able to specify a sort function # to the object at some point # -js

remove_tag¶

 Title   : remove_tag
 Usage   : $feat->remove_tag('some_tag');
 Function: removes a tag from this feature
 Returns : the array of values for this tag before removing it
 Args    : tag (string)

attach_seq¶

 Title   : attach_seq
 Usage   : $feat->attach_seq($seq);
 Function: Attaches a Bio::Seq object to this feature. This
           Bio::Seq object is for the *entire* sequence: ie
           from 1 to 10000
 Example :
 Returns : TRUE on success
 Args    : a Bio::PrimarySeqI compliant object

seq¶

 Title   : seq
 Usage   : my $tseq = $feat->seq();
 Function: returns the truncated sequence (if there) for this
 Example :
 Returns : sub seq (a Bio::PrimarySeqI compliant object) on attached sequence
           bounded by start & end, or undef if there is no sequence attached.
           If the strand is defined and set to -1, the returned sequence is
           the reverse-complement of the region
 Args    : none

entire_seq¶

 Title   : entire_seq
 Usage   : my $whole_seq = $feat->entire_seq();
 Function: gives the entire sequence that this seqfeature is attached to
 Example :
 Returns : a Bio::PrimarySeqI compliant object, or undef if there is no
           sequence attached
 Args    :

seq_id¶

 Title   : seq_id
 Usage   : $feat->seq_id($newval)
 Function: There are many cases when you make a feature that you
           do know the sequence name, but do not know its actual
           sequence. This is an attribute such that you can store
           the ID (e.g., display_id) of the sequence.
           This attribute should *not* be used in GFF dumping, as
           that should come from the collection in which the seq
           feature was found.
 Returns : value of seq_id
 Args    : newvalue (optional)

display_name¶

 Title   : display_name
 Usage   : my $featname = $feat->display_name;
 Function: Implements the display_name() method, which is a human-readable
           name for the feature. 
 Returns : value of display_name (a string)
 Args    : Optionally, on set the new value or undef

annotation¶

 Title   : annotation
 Usage   : $feat->annotation($annot_obj);
 Function: Get/set the annotation collection object for annotating this
           feature.
 Example : 
 Returns : A Bio::AnnotationCollectionI object
 Args    : newvalue (optional)

get_SeqFeatures¶

 Title   : get_SeqFeatures
 Usage   : my @feats = $feat->get_SeqFeatures();
 Function: Returns an array of sub Sequence Features
 Returns : An array
 Args    : none

add_SeqFeature¶

 Title   : add_SeqFeature
 Usage   : $feat->add_SeqFeature($subfeat);
           $feat->add_SeqFeature($subfeat,'EXPAND');
 Function: Adds a SeqFeature into the subSeqFeature array.
           With no 'EXPAND' qualifer, subfeat will be tested
           as to whether it lies inside the parent, and throw
           an exception if not.
           If EXPAND is used, the parent's start/end/strand will
           be adjusted so that it grows to accommodate the new
           subFeature
           !IMPORTANT! The coordinates of the subfeature should not be relative
           to the parent feature it is attached to, but relative to the sequence
           the parent feature is located on.
 Returns : nothing
 Args    : An object which has the SeqFeatureI interface

remove_SeqFeatures¶

 Title   : remove_SeqFeatures
 Usage   : $feat->remove_SeqFeatures;
 Function: Removes all SeqFeatures
           If you want to remove only a subset of features then remove that 
           subset from the returned array, and add back the rest.
 Example :
 Returns : The array of Bio::SeqFeatureI implementing features that was
           deleted.
 Args    : none

gff_format¶

 Title   : gff_format
 Usage   : # get:
           my $gffio = $feat->gff_format();
           # set (change the default version of GFF2):
           $feat->gff_format(Bio::Tools::GFF->new(-gff_version => 1));
 Function: Get/set the GFF format interpreter. This object is supposed to 
           format and parse GFF. See Bio::Tools::GFF for the interface.
           If this method is called as class method, the default for all
           newly created instances will be changed. Otherwise only this
           instance will be affected.
 Example : 
 Returns : a Bio::Tools::GFF compliant object
 Args    : On set, an instance of Bio::Tools::GFF or a derived object.

gff_string¶

 Title   : gff_string
 Usage   : my $str = $feat->gff_string;
           my $str = $feat->gff_string($gff_formatter);
 Function: Provides the feature information in GFF format.
           We override this here from Bio::SeqFeatureI in order to use the
           formatter returned by gff_format().
 Returns : A string
 Args    : Optionally, an object implementing gff_string().

slurp_gff_file¶

 Title   : slurp_file
 Usage   : my @features = Bio::SeqFeature::Generic::slurp_gff_file(\*FILE);
 Function: Sneaky function to load an entire file as in memory objects.
           Beware of big files.
           This method is deprecated. Use Bio::Tools::GFF instead, which can
           also handle large files.
 Example :
 Returns :
 Args    :

_from_gff_string¶

 Title   : _from_gff_string
 Usage   :
 Function: Set feature properties from GFF string. 
           This method uses the object returned by gff_format() for the
           actual interpretation of the string. Set a different GFF format
           interpreter first if you need a specific version, like GFF1. (The
           default is GFF2.)
 Example :
 Returns : 
 Args    : a GFF-formatted string

_expand_region¶

 Title   : _expand_region
 Usage   : $feat->_expand_region($feature);
 Function: Expand the total region covered by this feature to
           accommodate for the given feature.
           May be called whenever any kind of subfeature is added to this
           feature. add_SeqFeature() already does this.
 Returns : 
 Args    : A Bio::SeqFeatureI implementing object.

_parse¶

 Title   : _parse
 Usage   :
 Function: Parsing hints
 Example :
 Returns :
 Args    :

_tag_value¶

 Title   : _tag_value
 Usage   : 
 Function: For internal use only. Convenience method for those tags that
           may only have a single value.
 Returns : The first value under the given tag as a scalar (string)
 Args    : The tag as a string. Optionally, the value on set.