Ace::Sequence(3) User Contributed Perl Documentation Ace::Sequence(3)NAMEAce::Sequence - Examine ACeDB Sequence Objects
SYNOPSIS
# open database connection and get an Ace::Object sequence
use Ace::Sequence;
$db = Ace->connect(-host => 'stein.cshl.org',-port => 200005);
$obj = $db->fetch(Predicted_gene => 'ZK154.3');
# Wrap it in an Ace::Sequence object
$seq = Ace::Sequence->new($obj);
# Find all the exons
@exons = $seq->features('exon');
# Find all the exons predicted by various versions of "genefinder"
@exons = $seq->features('exon:genefinder.*');
# Iterate through the exons, printing their start, end and DNA
for my $exon (@exons) {
print join "\t",$exon->start,$exon->end,$exon->dna,"\n";
}
# Find the region 1000 kb upstream of the first exon
$sub = Ace::Sequence->new(-seq=>$exons[0],
-offset=>-1000,-length=>1000);
# Find all features in that area
@features = $sub->features;
# Print its DNA
print $sub->dna;
# Create a new Sequence object from the first 500 kb of chromosome 1
$seq = Ace::Sequence->new(-name=>'CHROMOSOME_I',-db=>$db,
-offset=>0,-length=>500_000);
# Get the GFF dump as a text string
$gff = $seq->gff;
# Limit dump to Predicted_genes
$gff_genes = $seq->gff(-features=>'Predicted_gene');
# Return a GFF object (using optional GFF.pm module from Sanger)
$gff_obj = $seq->GFF;
DESCRIPTION
Ace::Sequence, and its allied classes Ace::Sequence::Feature and
Ace::Sequence::FeatureList, provide a convenient interface to the ACeDB
Sequence classes and the GFF sequence feature file format.
Using this class, you can define a region of the genome by using a
landmark (sequenced clone, link, superlink, predicted gene), an offset
from that landmark, and a distance. Offsets and distances can be
positive or negative. This will return an Ace::Sequence object. Once
a region is defined, you may retrieve its DNA sequence, or query the
database for any features that may be contained within this region.
Features can be returned as objects (using the Ace::Sequence::Feature
class), as GFF text-only dumps, or in the form of the GFF class defined
by the Sanger Centre's GFF.pm module.
This class builds on top of Ace and Ace::Object. Please see their
manual pages before consulting this one.
Creating New Ace::Sequence Objects, the new() Method
$seq = Ace::Sequence->new($object);
$seq = Ace::Sequence->new(-source => $object,
-offset => $offset,
-length => $length,
-refseq => $reference_sequence);
$seq = Ace::Sequence->new(-name => $name,
-db => $db,
-offset => $offset,
-length => $length,
-refseq => $reference_sequence);
In order to create an Ace::Sequence you will need an active Ace
database accessor. Sequence regions are defined using a "source"
sequence, an offset, and a length. Optionally, you may also provide a
"reference sequence" to establish the coordinate system for all
inquiries. Sequences may be generated from existing Ace::Object
sequence objects, from other Ace::Sequence and Ace::Sequence::Feature
objects, or from a sequence name and a database handle.
The class method named new() is the interface to these facilities. In
its simplest, one-argument form, you provide new() with a previously-
created Ace::Object that points to Sequence or sequence-like object
(the meaning of "sequence-like" is explained in more detail below.)
The new() method will return an Ace::Sequence object extending from the
beginning of the object through to its natural end.
In the named-parameter form of new(), the following arguments are
recognized:
-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.
If new() is successful, it will create an Ace::Sequence 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.
Reference Sequences and the Coordinate System
When retrieving information from an Ace::Sequence, the coordinate
system is based on the sequence segment selected at object creation
time. That is, the "+1" strand is the natural direction of the
Ace::Sequence object, and base pair 1 is its first base pair. This
behavior can be overridden by providing a reference sequence to the
new() method, in which case the orientation and position of the
reference sequence establishes the coordinate system for the object.
In addition to the reference sequence, there are two other sequences
used by Ace::Sequence for internal bookeeping. The "source" sequence
corresponds to the smallest ACeDB sequence object that completely
encloses the selected sequence segment. The "parent" sequence is the
smallest ACeDB sequence object that contains the "source". The parent
is used to derive the length and orientation of source sequences that
are not directly associated with DNA objects.
In many cases, the source sequence will be identical to the sequence
initially passed to the new() method. However, there are exceptions to
this rule. One common exception occurs when the offset and/or length
cross the boundaries of the passed-in sequence. In this case, the
ACeDB database is searched for the smallest sequence that contains both
endpoints of the Ace::Sequence object.
The other common exception occurs in Ace 4.8, where there is support
for "sequence-like" objects that contain the "SMap" ("Sequence Map")
tag. The "SMap" tag provides genomic location information for
arbitrary object -- not just those descended from the Sequence class.
This allows ACeDB to perform genome map operations on objects that are
not directly related to sequences, such as genetic loci that have been
interpolated onto the physical map. When an "SMap"-containing object
is passed to the Ace::Sequencenew() method, the module will again
choose the smallest ACeDB Sequence object that contains both end-points
of the desired region.
If an Ace::Sequence object is used to create a new Ace::Sequence
object, then the original object's source is inherited.
Object Methods
Once an Ace::Sequence object is created, you can query it using the
following methods:
asString()
$name = $seq->asString;
Returns a human-readable identifier for the sequence in the form
Source/start-end, where "Source" is the name of the source sequence,
and "start" and "end" are the endpoints of the sequence relative to the
source (using 1-based indexing). This method is called automatically
when the Ace::Sequence is used in a string context.
source_seq()
$source = $seq->source_seq;
Return the source of the Ace::Sequence.
parent_seq()
$parent = $seq->parent_seq;
Return the immediate ancestor of the sequence. The parent of the top-
most sequence (such as the CHROMOSOME link) is itself. This method is
used internally to ascertain the length of source sequences which are
not associated with a DNA object.
NOTE: this procedure is a trifle funky and cannot reliably be used to
traverse upwards to the top-most sequence. The reason for this is that
it will return an Ace::Sequence in some cases, and an Ace::Object in
others. Use get_parent() to traverse upwards through a uniform series
of Ace::Sequence objects upwards.
refseq([$seq])
$refseq = $seq->refseq;
Returns the reference sequence, if one is defined.
$seq->refseq($new_ref);
Set the reference sequence. The reference sequence must share the same
ancestor with $seq.
start()
$start = $seq->start;
Start of this sequence, relative to the source sequence, using 1-based
indexing.
end()
$end = $seq->end;
End of this sequence, relative to the source sequence, using 1-based
indexing.
offset()
$offset = $seq->offset;
Offset of the beginning of this sequence relative to the source
sequence, using 0-based indexing. The offset may be negative if the
beginning of the sequence is to the left of the beginning of the source
sequence.
length()
$length = $seq->length;
The length of this sequence, in base pairs. The length may be negative
if the sequence's orientation is reversed relative to the source
sequence. Use abslength() to obtain the absolute value of the sequence
length.
abslength()
$length = $seq->abslength;
Return the absolute value of the length of the sequence.
strand()
$strand = $seq->strand;
Returns +1 for a sequence oriented in the natural direction of the
genomic reference sequence, or -1 otherwise.
reversed()
Returns true if the segment is reversed relative to the canonical
genomic direction. This is the same as $seq->strand < 0.
dna()
$dna = $seq->dna;
Return the DNA corresponding to this sequence. If the sequence length
is negative, the reverse complement of the appropriate segment will be
returned.
ACeDB allows Sequences to exist without an associated DNA object (which
typically happens during intermediate stages of a sequencing project.
In such a case, the returned sequence will contain the correct number
of "-" characters.
name()
$name = $seq->name;
Return the name of the source sequence as a string.
get_parent()
$parent = $seq->parent;
Return the immediate ancestor of this Ace::Sequence (i.e., the sequence
that contains this one). The return value is a new Ace::Sequence or
undef, if no parent sequence exists.
get_children()
@children = $seq->get_children();
Returns all subsequences that exist as independent objects in the ACeDB
database. What exactly is returned is dependent on the data model. In
older ACeDB databases, the only subsequences are those under the
catchall Subsequence tag. In newer ACeDB databases, the objects
returned correspond to objects to the right of the S_Child subtag using
a tag[2] syntax, and may include Predicted_genes, Sequences, Links, or
other objects. The return value is a list of Ace::Sequence objects.
features()
@features = $seq->features;
@features = $seq->features('exon','intron','Predicted_gene');
@features = $seq->features('exon:GeneFinder','Predicted_gene:hand.*');
features() returns an array of Sequence::Feature objects. If called
without arguments, features() returns all features that cross the
sequence region. You may also provide a filter list to select a set of
features by type and subtype. The format of the filter list is:
type:subtype
Where type is the class of the feature (the "feature" field of the GFF
format), and subtype is a description of how the feature was derived
(the "source" field of the GFF format). Either of these fields can be
absent, and either can be a regular expression. More advanced
filtering is not supported, but is provided by the Sanger Centre's GFF
module.
The order of the features in the returned list is not specified. To
obtain features sorted by position, use this idiom:
@features = sort { $a->start <=> $b->start } $seq->features;
feature_list()
my $list = $seq->feature_list();
This method returns a summary list of the features that cross the
sequence in the form of a Ace::Feature::List object. From the
Ace::Feature::List object you can obtain the list of feature names and
the number of each type. The feature list is obtained from the ACeDB
server with a single short transaction, and therefore has much less
overhead than features().
See Ace::Feature::List for more details.
transcripts()
This returns a list of Ace::Sequence::Transcript objects, which are
specializations of Ace::Sequence::Feature. See
Ace::Sequence::Transcript for details.
clones()
This returns a list of Ace::Sequence::Feature objects containing
reconstructed clones. This is a nasty hack, because ACEDB currently
records clone ends, but not the clones themselves, meaning that we will
not always know both ends of the clone. In this case the missing end
has a synthetic position of -99,999,999 or +99,999,999. Sorry.
gff()
$gff = $seq->gff();
$gff = $seq->gff(-abs => 1,
-features => ['exon','intron:GeneFinder']);
This method returns a GFF file as a scalar. The following arguments
are optional:
-abs
Ordinarily the feature entries in the GFF file will be returned in
coordinates relative to the start of the Ace::Sequence object.
Position 1 will be the start of the sequence object, and the "+"
strand will be the sequence object's natural orientation. However
if a true value is provided to -abs, the coordinate system used
will be relative to the start of the source sequence, i.e. the
native ACeDB Sequence object (usually a cosmid sequence or a link).
If a reference sequence was provided when the Ace::Sequence was
created, it will be used by default to set the coordinate system.
Relative coordinates can be reenabled by providing a false value to
-abs.
Ordinarily the coordinate system manipulations automatically "do
what you want" and you will not need to adjust them. See also the
abs() method described below.
-features
The -features argument filters the features according to a list of
types and subtypes. The format is identical to the one described
for the features() method. A single filter may be provided as a
scalar string. Multiple filters may be passed as an array
reference.
See also the GFF() method described next.
GFF()
$gff_object = $seq->gff;
$gff_object = $seq->gff(-abs => 1,
-features => ['exon','intron:GeneFinder']);
The GFF() method takes the same arguments as gff() described above, but
it returns a GFF::GeneFeatureSet object from the GFF.pm module. If the
GFF module is not installed, this method will generate a fatal error.
absolute()
$abs = $seq->absolute;
$abs = $seq->absolute(1);
This method controls whether the coordinates of features are returned
in absolute or relative coordinates. "Absolute" coordinates are
relative to the underlying source or reference sequence. "Relative"
coordinates are relative to the Ace::Sequence object. By default,
coordinates are relative unless new() was provided with a reference
sequence. This default can be examined and changed using absolute().
automerge()
$merge = $seq->automerge;
$seq->automerge(0);
This method controls whether groups of features will automatically be
merged together by the features() call. If true (the default), then
the left and right end of clones will be merged into "clone" features,
introns, exons and CDS entries will be merged into
Ace::Sequence::Transcript objects, and similarity entries will be
merged into Ace::Sequence::GappedAlignment objects.
db()
$db = $seq->db;
Returns the Ace database accessor associated with this sequence.
SEE ALSO
Ace, Ace::Object, Ace::Sequence::Feature, Ace::Sequence::FeatureList,
GFF
AUTHOR
Lincoln Stein <lstein@cshl.org> with extensive help from Jean Thierry-
Mieg <mieg@kaa.crbm.cnrs-mop.fr>
Many thanks to David Block <dblock@gene.pbi.nrc.ca> for finding and
fixing the nasty off-by-one errors.
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 2004-12-01 Ace::Sequence(3)
