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Ace::Sequence::Feature.3pm

NAME

Ace::Sequence::Feature - Examine Sequence Feature Tables

SYNOPSIS

     # open database connection and get an Ace::Object sequence
     use Ace::Sequence;
 
     # get a megabase from the middle of chromosome I
     $seq = Ace::Sequence->new(-name   => 'CHROMOSOME_I,
                               -db     => $db,
                               -offset => 3_000_000,
                               -length => 1_000_000);
 
     # get all the homologies (a list of Ace::Sequence::Feature objs)
     @homol = $seq->features('Similarity');
 
     # Get information about the first one
     $feature = $homol[0];
     $type    = $feature->type;
     $subtype = $feature->subtype;
     $start   = $feature->start;
     $end     = $feature->end;
     $score   = $feature->score;
 
     # Follow the target
     $target  = $feature->info;
 
     # print the target's start and end positions
     print $target->start,'-',$target->end, "\n";
 
 

DESCRIPTION

Ace::Sequence::Feature is a subclass of Ace::Sequence::Feature specialized for returning information about particular features in a GFF format feature table.

OBJECT CREATION

You will not ordinarily create an Ace::Sequence::Feature object directly. Instead, objects will be created in response to a feature() call to an Ace::Sequence object. If you wish to create an Ace::Sequence::Feature object directly, please consult the source code for the new() method.

OBJECT METHODS

Most methods are inherited from Ace::Sequence. The following methods are also supported:

seqname()

   $object = $feature->seqname;
 
 

Return the ACeDB Sequence object that this feature is attached to. The return value is an Ace::Object of the Sequence class. This corresponds to the first field of the GFF format and does not necessarily correspond to the Ace::Sequence object from which the feature was obtained (use source_seq() for that).

source()

method()

subtype()

   $source = $feature->source;
 
 

These three methods are all synonyms for the same thing. They return the second field of the GFF format, called ``source'' in the documentation. This is usually the method or algorithm used to predict the feature, such as ``GeneFinder'' or ``tRNA'' scan. To avoid ambiguity and enhance readability, the method() and subtype() synonyms are also recognized.

feature()

type()

   $type = $feature->type;
 
 

These two methods are also synonyms. They return the type of the feature, such as ``exon'', ``similarity'' or ``Predicted_gene''. In the GFF documentation this is called the ``feature'' field. For readability, you can also use type() to fetch the field.

abs_start()

   $start = $feature->abs_start;
 
 

This method returns the absolute start of the feature within the sequence segment indicated by seqname(). As in the Ace::Sequence method, use start() to obtain the start of the feature relative to its source.

abs_start()

   $start = $feature->abs_start;
 
 

This method returns the start of the feature relative to the sequence segment indicated by seqname(). As in the Ace::Sequence method, you will more usually use the inherited start() method to obtain the start of the feature relative to its source sequence (the Ace::Sequence from which it was originally derived).

abs_end()

   $start = $feature->abs_end;
 
 

This method returns the end of the feature relative to the sequence segment indicated by seqname(). As in the Ace::Sequence method, you will more usually use the inherited end() method to obtain the end of the feature relative to the Ace::Sequence from which it was derived.

score()

   $score = $feature->score;
 
 

For features that are associated with a numeric score, such as similarities, this returns that value. For other features, this method returns undef.

strand()

   $strand = $feature->strand;
 
 

Returns the strandedness of this feature, either ``+1'' or ``-1''. For features that are not stranded, returns 0.

reversed()

   $reversed = $feature->reversed;
 
 

Returns true if the feature is reversed relative to its source sequence.

frame()

   $frame = $feature->frame;
 
 

For features that have a frame, such as a predicted coding sequence, returns the frame, either 0, 1 or 2. For other features, returns undef.

group()

info()

target()

   $info = $feature->info;
 
 

These methods (synonyms for one another) return an Ace::Object containing other information about the feature derived from the 8th field of the GFF format, the so-called ``group'' field. The type of the Ace::Object is dependent on the nature of the feature. The possibilities are shown in the table below:

   Feature Type           Value of Group Field
   ------------            --------------------
   
   note                   A Text object containing the note.
   
   similarity             An Ace::Sequence::Homology object containing
                          the target and its start/stop positions.
 
   intron                 An Ace::Object containing the gene from 
   exon                   which the feature is derived.
   misc_feature
 
   other                  A Text object containing the group data.
 
 

asString()

   $label = $feature->asString;
 
 

Returns a human-readable identifier describing the nature of the feature. The format is:

  $type:$name/$start-$end
 
 

for example:

  exon:ZK154.3/1-67
 
 

This method is also called automatically when the object is treated in a string context.

SEE ALSO

Ace, Ace::Object, Ace::Sequence,Ace::Sequence::Homol, Ace::Sequence::FeatureList, GFF

AUTHOR

Lincoln Stein <lstein@cshl.org> with extensive help from Jean Thierry-Mieg <mieg@kaa.crbm.cnrs-mop.fr>

Copyright (c) 1999, Lincoln D. Stein

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See DISCLAIMER.txt for disclaimers of warranty.