$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 = $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.
$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.
$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.
$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).
$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 = $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 = $feature->strand;
Returns the strandedness of this feature, either +1 or -1. For features that are not stranded, returns 0.
$reversed = $feature->reversed;
$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.
$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:
$label = $feature->asString;
Returns a human-readable identifier describing the nature of the feature. The format is:
This method is also called automatically when the object is treated in a string context.
Lincoln Stein <firstname.lastname@example.org> with extensive help from Jean Thierry-Mieg <email@example.com>
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.
|perl v5.20.3||ACE::SEQUENCE::FEATURE (3)||2001-09-17|