Ace::Sequence::Homol(3pm) User Contributed Perl Documentation Ace::Sequence::Homol(3pm)NAME
Ace::Sequence::Homol - Temporary Sequence Homology Class
SYNOPSIS
# Get all similarity features from an Ace::Sequence
@homol = $seq->features('Similarity');
# sort by score
@sorted = sort { $a->score <=> $b->score } @homol;
# the last one has the highest score
$best = $sorted[$#sorted];
# fetch its associated Ace::Sequence::Homol
$homol = $best->target;
# print out the sequence name, DNA, start and end
print $homol->name,' ',$homol->start,'-',$homol->end,"
";
print $homol->asDNA;
DESCRIPTION
Ace::Sequence::Homol is a subclass of Ace::Object (not Ace::Sequence) which is specialized for returning information about a DNA or protein
homology. This is a temporary placeholder for a more sophisticated homology class which will include support for alignments.
OBJECT CREATION
You will not ordinarily create an Ace::Sequence::Homol object directly. Instead, objects will be created in response to an info() or
group() method call on a similarity feature in an Ace::Sequence::Feature object. If you wish to create an Ace::Sequence::Homol object
directly, please consult the source code for the new() method.
OBJECT METHODS
Most methods are inherited from Ace::Object. The following methods are also supported:
start()
$start = $homol->start;
Returns the start of the area that is similar to the Ace::Sequence::Feature from which his homology was derived. Coordinates are
relative to the target homology.
end()
$end = $homol->end;
Returns the end of the area that is similar to the Ace::Sequence::Feature from which his homology was derived. Coordinates are
relative to the target homology.
asString()
$label = $homol->asString;
Returns a human-readable identifier describing the nature of the feature. The format is:
$name/$start-$end
for example:
HUMGEN13/1-67
This method is also called automatically when the object is treated in a string context.
SEE ALSO
Ace, Ace::Object, Ace::Sequence,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 v5.14.2 2001-09-17 Ace::Sequence::Homol(3pm)
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Ace::Sequence::Multi(3pm) User Contributed Perl Documentation Ace::Sequence::Multi(3pm)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, "
";
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 v5.14.2 2001-04-07 Ace::Sequence::Multi(3pm)