1Ace::Sequence::Feature(U3s)er Contributed Perl DocumentatAicoen::Sequence::Feature(3)
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NAME

6       Ace::Sequence::Feature - Examine Sequence Feature Tables
7

SYNOPSIS

9           # open database connection and get an Ace::Object sequence
10           use Ace::Sequence;
11
12           # 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
18           # get all the homologies (a list of Ace::Sequence::Feature objs)
19           @homol = $seq->features('Similarity');
20
21           # 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
29           # Follow the target
30           $target  = $feature->info;
31
32           # print the target's start and end positions
33           print $target->start,'-',$target->end, "\n";
34

DESCRIPTION

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

OBJECT CREATION

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

OBJECT METHODS

48       Most methods are inherited from Ace::Sequence.  The following methods
49       are also supported:
50
51       seqname()
52             $object = $feature->seqname;
53
54           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
60       source()
61       method()
62       subtype()
63             $source = $feature->source;
64
65           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
72       feature()
73       type()
74             $type = $feature->type;
75
76           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
81       abs_start()
82             $start = $feature->abs_start;
83
84           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
89       abs_start()
90             $start = $feature->abs_start;
91
92           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
98       abs_end()
99             $start = $feature->abs_end;
100
101           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
107       score()
108             $score = $feature->score;
109
110           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
114       strand()
115             $strand = $feature->strand;
116
117           Returns the strandedness of this feature, either "+1" or "-1".  For
118           features that are not stranded, returns 0.
119
120       reversed()
121             $reversed = $feature->reversed;
122
123           Returns true if the feature is reversed relative to its source
124           sequence.
125
126       frame()
127             $frame = $feature->frame;
128
129           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
133       group()
134       info()
135       target()
136             $info = $feature->info;
137
138           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
144             Feature Type           Value of Group Field
145             ------------            --------------------
146
147             note                   A Text object containing the note.
148
149             similarity             An Ace::Sequence::Homology object containing
150                                    the target and its start/stop positions.
151
152             intron                 An Ace::Object containing the gene from
153             exon                   which the feature is derived.
154             misc_feature
155
156             other                  A Text object containing the group data.
157
158       asString()
159             $label = $feature->asString;
160
161           Returns a human-readable identifier describing the nature of the
162           feature.  The format is:
163
164            $type:$name/$start-$end
165
166           for example:
167
168            exon:ZK154.3/1-67
169
170           This method is also called automatically when the object is treated
171           in a string context.
172

SEE ALSO

174       Ace, Ace::Object, Ace::Sequence,Ace::Sequence::Homol,
175       Ace::Sequence::FeatureList, GFF
176

AUTHOR

178       Lincoln Stein <lstein@cshl.org> with extensive help from Jean Thierry-
179       Mieg <mieg@kaa.crbm.cnrs-mop.fr>
180
181       Copyright (c) 1999, Lincoln D. Stein
182
183       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.
186
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189perl v5.38.0                      2023-07-20         Ace::Sequence::Feature(3)
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