1Ace::Sequence::Feature(U3s)er Contributed Perl DocumentatAicoen::Sequence::Feature(3)
2
6 Ace::Sequence::Feature - Examine Sequence Feature Tables
7
9 # open database connection and get an Ace::Object sequence
10 use Ace::Sequence;
11 # get a megabase from the middle of chromosome I
13 $seq = Ace::Sequence->new(-name => 'CHROMOSOME_I,
14 -db => $db,
15 -offset => 3_000_000,
16 -length => 1_000_000);
17 # get all the homologies (a list of Ace::Sequence::Feature objs)
19 @homol = $seq->features('Similarity');
20 # Get information about the first one
22 $feature = $homol[0];
23 $type = $feature->type;
24 $subtype = $feature->subtype;
25 $start = $feature->start;
26 $end = $feature->end;
27 $score = $feature->score;
28 # Follow the target
30 $target = $feature->info;
31 # print the target's start and end positions
33 print $target->start,'-',$target->end, "\n";
34
36 Ace::Sequence::Feature is a subclass of Ace::Sequence::Feature
37 specialized for returning information about particular features in a
38 GFF format feature table.
39
41 You will not ordinarily create an Ace::Sequence::Feature object
42 directly. Instead, objects will be created in response to a feature()
43 call to an Ace::Sequence object. If you wish to create an
44 Ace::Sequence::Feature object directly, please consult the source code
45 for the new() method.
46
48 Most methods are inherited from Ace::Sequence. The following methods
49 are also supported:
50 seqname()
52 $object = $feature->seqname;
53 Return the ACeDB Sequence object that this feature is attached to.
55 The return value is an Ace::Object of the Sequence class. This
56 corresponds to the first field of the GFF format and does not
57 necessarily correspond to the Ace::Sequence object from which the
58 feature was obtained (use source_seq() for that).
59 source()
61 method()
62 subtype()
63 $source = $feature->source;
64 These three methods are all synonyms for the same thing. They
66 return the second field of the GFF format, called "source" in the
67 documentation. This is usually the method or algorithm used to
68 predict the feature, such as "GeneFinder" or "tRNA" scan. To avoid
69 ambiguity and enhance readability, the method() and subtype()
70 synonyms are also recognized.
71 feature()
73 type()
74 $type = $feature->type;
75 These two methods are also synonyms. They return the type of the
77 feature, such as "exon", "similarity" or "Predicted_gene". In the
78 GFF documentation this is called the "feature" field. For
79 readability, you can also use type() to fetch the field.
80 abs_start()
82 $start = $feature->abs_start;
83 This method returns the absolute start of the feature within the
85 sequence segment indicated by seqname(). As in the Ace::Sequence
86 method, use start() to obtain the start of the feature relative to
87 its source.
88 abs_start()
90 $start = $feature->abs_start;
91 This method returns the start of the feature relative to the
93 sequence segment indicated by seqname(). As in the Ace::Sequence
94 method, you will more usually use the inherited start() method to
95 obtain the start of the feature relative to its source sequence
96 (the Ace::Sequence from which it was originally derived).
97 abs_end()
99 $start = $feature->abs_end;
100 This method returns the end of the feature relative to the sequence
102 segment indicated by seqname(). As in the Ace::Sequence method,
103 you will more usually use the inherited end() method to obtain the
104 end of the feature relative to the Ace::Sequence from which it was
105 derived.
106 score()
108 $score = $feature->score;
109 For features that are associated with a numeric score, such as
111 similarities, this returns that value. For other features, this
112 method returns undef.
113 strand()
115 $strand = $feature->strand;
116 Returns the strandedness of this feature, either "+1" or "-1". For
118 features that are not stranded, returns 0.
119 reversed()
121 $reversed = $feature->reversed;
122 Returns true if the feature is reversed relative to its source
124 sequence.
125 frame()
127 $frame = $feature->frame;
128 For features that have a frame, such as a predicted coding
130 sequence, returns the frame, either 0, 1 or 2. For other features,
131 returns undef.
132 group()
134 info()
135 target()
136 $info = $feature->info;
137 These methods (synonyms for one another) return an Ace::Object
139 containing other information about the feature derived from the 8th
140 field of the GFF format, the so-called "group" field. The type of
141 the Ace::Object is dependent on the nature of the feature. The
142 possibilities are shown in the table below:
143 Feature Type Value of Group Field
145 ------------ --------------------
146 note A Text object containing the note.
148 similarity An Ace::Sequence::Homology object containing
150 the target and its start/stop positions.
151 intron An Ace::Object containing the gene from
153 exon which the feature is derived.
154 misc_feature
155 other A Text object containing the group data.
157 asString()
159 $label = $feature->asString;
160 Returns a human-readable identifier describing the nature of the
162 feature. The format is:
163 $type:$name/$start-$end
165 for example:
167 exon:ZK154.3/1-67
169 This method is also called automatically when the object is treated
171 in a string context.
172
174 Ace, Ace::Object, Ace::Sequence,Ace::Sequence::Homol,
175 Ace::Sequence::FeatureList, GFF
176
178 Lincoln Stein <lstein@cshl.org> with extensive help from Jean Thierry-
179 Mieg <mieg@kaa.crbm.cnrs-mop.fr>
180 Copyright (c) 1999, Lincoln D. Stein
182 This library is free software; you can redistribute it and/or modify it
184 under the same terms as Perl itself. See DISCLAIMER.txt for
185 disclaimers of warranty.
186perl v5.12.0 2001-09-17 Ace::Sequence::Feature(3)