NAME

Ace::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";

DESCRIPTION

Ace::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. Offsets 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.

AUTHOR

Lincoln Stein <lstein@w3.org> with extensive help from Jean Thierry-Mieg <mieg@kaa.crbm.cnrs-mop.fr>

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.

2021-02-20