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Ace::Sequence::Multi(3User Contributed Perl DocumentatiAce::Sequence::Multi(3)

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.  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 v5.24.1			  2001-04-07	       Ace::Sequence::Multi(3)

NAME | SYNOPSIS | DESCRIPTION | OBJECT CREATION | OBJECT METHODS | SEE ALSO | AUTHOR

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