Ace::Sequence::Multi(3User Contributed Perl DocumentatiAce::Sequence::Multi(3)NAMEAce::Sequence::Multi - Combine Feature Tables from Multiple Databases
SYNOPSIS
use Ace::Sequence::Multi;
# open reference database
$ref = Ace->connect(-host=>'stein.cshl.org',-port=>200009);
# open some secondary databases
$db1 = Ace->connect(-host=>'stein.cshl.org',-port=>200010);
$db2 = Ace->connect(-path=>'/usr/local/acedb/mydata');
# Make an Ace::Sequence::Multi object
$seq = Ace::Sequence::Multi->new(-name => 'CHROMOSOME_I,
-db => $ref,
-offset => 3_000_000,
-length => 1_000_000);
# add the secondary databases
$seq->add_secondary($db1,$db2);
# get all the homologies (a list of Ace::Sequence::Feature objs)
@homol = $seq->features('Similarity');
# Get information about the first one -- goes to the correct db
$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";
DESCRIPTIONAce::Sequence::Multi transparently combines information stored about a
sequence in a reference database with features tables from any number
of annotation databases. The resulting object can be used just like an
Ace::Sequence object, except that the features remember their database
of origin and go back to that database for information.
This class will only work properly if the reference database and all
annotation databases share the same cosmid map.
OBJECT CREATION
You will use the new() method to create new Ace::Sequence::Multi
objects. The arguments are identical to the those in the Ace::Sequence
parent class, with the addition of an option -secondary argument, which
points to one or more secondary databases from which to fetch
annotation information.
-source
The sequence source. This must be an Ace::Object of the "Sequence"
class, or be a sequence-like object containing the SMap tag (see
below).
-offset
An offset from the beginning of the source sequence. The retrieved
Ace::Sequence will begin at this position. The offset can be any
positive or negative integer. Offets are 0-based.
-length
The length of the sequence to return. Either a positive or
negative integer can be specified. If a negative length is given,
the returned sequence will be complemented relative to the source
sequence.
-refseq
The sequence to use to establish the coordinate system for the
returned sequence. Normally the source sequence is used to
establish the coordinate system, but this can be used to override
that choice. You can provide either an Ace::Object or just a
sequence name for this argument. The source and reference
sequences must share a common ancestor, but do not have to be
directly related. An attempt to use a disjunct reference sequence,
such as one on a different chromosome, will fail.
-name
As an alternative to using an Ace::Object with the -source
argument, you may specify a source sequence using -name and -db.
The Ace::Sequence module will use the provided database accessor to
fetch a Sequence object with the specified name. new() will return
undef is no Sequence by this name is known.
-db This argument is required if the source sequence is specified by
name rather than by object reference. It must be a previously
opened handle to the reference database.
-secondary
This argument points to one or more previously-opened annotation
databases. You may use a scalar if there is only one annotation
database. Otherwise, use an array reference. You may add and
delete annotation databases after the object is created by using
the add_secondary() and delete_secondary() methods.
If new() is successful, it will create an Ace::Sequence::Multi object
and return it. Otherwise it will return undef and return a descriptive
message in Ace->error(). Certain programming errors, such as a failure
to provide required arguments, cause a fatal error.
OBJECT METHODS
Most methods are inherited from Ace::Sequence. The following
additional methods are supported:
secondary()
@databases = $seq->secondary;
Return a list of the secondary databases currently in use, or an
empty list if none.
add_secondary()
$seq->add_secondary($db1,$db2,...)
Add one or more secondary databases to the list of annotation
databases. Duplicate databases will be silently ignored.
delete_secondary()
$seq->delete_secondary($db1,$db2,...)
Delete one or more secondary databases from the list of annotation
databases. Databases not already in use will be silently ignored.
SEE ALSO
Ace, Ace::Object, Ace::Sequence,Ace::Sequence::Homol,
Ace::Sequence::FeatureList, Ace::Sequence::Feature, GFF
AUTHOR
Lincoln Stein <lstein@w3.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.
perl v5.14.1 2001-04-07 Ace::Sequence::Multi(3)
