Provided by: libace-perl_1.92-11build2_amd64 
NAME
Ace::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. 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.
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::Sequence new()
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 re-enabled
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.