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.\" ========================================================================
.\"
.IX Title "Ace::Sequence::Feature 3pm"
.TH Ace::Sequence::Feature 3pm "2001-09-17" "perl v5.14.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
.if n .ad l
.nh
.SH "NAME"
Ace::Sequence::Feature \- Examine Sequence Feature Tables
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 2
\&    # 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   => \*(AqCHROMOSOME_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(\*(AqSimilarity\*(Aq);
\&
\&    # 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\*(Aqs start and end positions
\&    print $target\->start,\*(Aq\-\*(Aq,$target\->end, "\en";
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
\&\fIAce::Sequence::Feature\fR is a subclass of Ace::Sequence::Feature
specialized for returning information about particular features in a
\&\s-1GFF\s0 format feature table.
.SH "OBJECT CREATION"
.IX Header "OBJECT CREATION"
You will not ordinarily create an \fIAce::Sequence::Feature\fR object
directly.  Instead, objects will be created in response to a \fIfeature()\fR
call to an \fIAce::Sequence\fR object.  If you wish to create an
\&\fIAce::Sequence::Feature\fR object directly, please consult the source
code for the \fI\fInew()\fI\fR method.
.SH "OBJECT METHODS"
.IX Header "OBJECT METHODS"
Most methods are inherited from \fIAce::Sequence\fR.  The following
methods are also supported:
.IP "\fIseqname()\fR" 4
.IX Item "seqname()"
.Vb 1
\&  $object = $feature\->seqname;
.Ve
.Sp
Return the ACeDB Sequence object that this feature is attached to.
The return value is an \fIAce::Object\fR of the Sequence class.  This
corresponds to the first field of the \s-1GFF\s0 format and does not
necessarily correspond to the \fIAce::Sequence\fR object from which the
feature was obtained (use \fIsource_seq()\fR for that).
.IP "\fIsource()\fR" 4
.IX Item "source()"
.PD 0
.IP "\fImethod()\fR" 4
.IX Item "method()"
.IP "\fIsubtype()\fR" 4
.IX Item "subtype()"
.PD
.Vb 1
\&  $source = $feature\->source;
.Ve
.Sp
These three methods are all synonyms for the same thing.  They return
the second field of the \s-1GFF\s0 format, called \*(L"source\*(R" in the
documentation.  This is usually the method or algorithm used to
predict the feature, such as \*(L"GeneFinder\*(R" or \*(L"tRNA\*(R" scan.  To avoid
ambiguity and enhance readability, the \fImethod()\fR and \fIsubtype()\fR synonyms
are also recognized.
.IP "\fIfeature()\fR" 4
.IX Item "feature()"
.PD 0
.IP "\fItype()\fR" 4
.IX Item "type()"
.PD
.Vb 1
\&  $type = $feature\->type;
.Ve
.Sp
These two methods are also synonyms.  They return the type of the
feature, such as \*(L"exon\*(R", \*(L"similarity\*(R" or \*(L"Predicted_gene\*(R".  In the \s-1GFF\s0
documentation this is called the \*(L"feature\*(R" field.  For readability,
you can also use \fItype()\fR to fetch the field.
.IP "\fIabs_start()\fR" 4
.IX Item "abs_start()"
.Vb 1
\&  $start = $feature\->abs_start;
.Ve
.Sp
This method returns the absolute start of the feature within the
sequence segment indicated by \fIseqname()\fR.  As in the \fIAce::Sequence\fR
method, use \fIstart()\fR to obtain the start of the feature relative to its
source.
.IP "\fIabs_start()\fR" 4
.IX Item "abs_start()"
.Vb 1
\&  $start = $feature\->abs_start;
.Ve
.Sp
This method returns the start of the feature relative to the sequence
segment indicated by \fIseqname()\fR.  As in the \fIAce::Sequence\fR method,
you will more usually use the inherited \fIstart()\fR method to obtain the
start of the feature relative to its source sequence (the
\&\fIAce::Sequence\fR from which it was originally derived).
.IP "\fIabs_end()\fR" 4
.IX Item "abs_end()"
.Vb 1
\&  $start = $feature\->abs_end;
.Ve
.Sp
This method returns the end of the feature relative to the sequence
segment indicated by \fIseqname()\fR.  As in the \fIAce::Sequence\fR method,
you will more usually use the inherited \fIend()\fR method to obtain the end
of the feature relative to the \fIAce::Sequence\fR from which it was
derived.
.IP "\fIscore()\fR" 4
.IX Item "score()"
.Vb 1
\&  $score = $feature\->score;
.Ve
.Sp
For features that are associated with a numeric score, such as
similarities, this returns that value.  For other features, this
method returns undef.
.IP "\fIstrand()\fR" 4
.IX Item "strand()"
.Vb 1
\&  $strand = $feature\->strand;
.Ve
.Sp
Returns the strandedness of this feature, either \*(L"+1\*(R" or \*(L"\-1\*(R".  For
features that are not stranded, returns 0.
.IP "\fIreversed()\fR" 4
.IX Item "reversed()"
.Vb 1
\&  $reversed = $feature\->reversed;
.Ve
.Sp
Returns true if the feature is reversed relative to its source
sequence.
.IP "\fIframe()\fR" 4
.IX Item "frame()"
.Vb 1
\&  $frame = $feature\->frame;
.Ve
.Sp
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.
.IP "\fIgroup()\fR" 4
.IX Item "group()"
.PD 0
.IP "\fIinfo()\fR" 4
.IX Item "info()"
.IP "\fItarget()\fR" 4
.IX Item "target()"
.PD
.Vb 1
\&  $info = $feature\->info;
.Ve
.Sp
These methods (synonyms for one another) return an Ace::Object
containing other information about the feature derived from the 8th
field of the \s-1GFF\s0 format, the so-called \*(L"group\*(R" field.  The type of the
Ace::Object is dependent on the nature of the feature.  The
possibilities are shown in the table below:
.Sp
.Vb 2
\&  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.
.Ve
.IP "\fIasString()\fR" 4
.IX Item "asString()"
.Vb 1
\&  $label = $feature\->asString;
.Ve
.Sp
Returns a human-readable identifier describing the nature of the
feature.  The format is:
.Sp
.Vb 1
\& $type:$name/$start\-$end
.Ve
.Sp
for example:
.Sp
.Vb 1
\& exon:ZK154.3/1\-67
.Ve
.Sp
This method is also called automatically when the object is treated in
a string context.
.SH "SEE ALSO"
.IX Header "SEE ALSO"
Ace, Ace::Object, Ace::Sequence,Ace::Sequence::Homol,
Ace::Sequence::FeatureList, \s-1GFF\s0
.SH "AUTHOR"
.IX Header "AUTHOR"
Lincoln Stein <lstein@cshl.org> with extensive help from Jean
Thierry-Mieg <mieg@kaa.crbm.cnrs\-mop.fr>
.PP
Copyright (c) 1999, Lincoln D. Stein
.PP
This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.  See \s-1DISCLAIMER\s0.txt for
disclaimers of warranty.