view release on metacpan or  search on metacpan

Ace/Sequence.pm  view on Meta::CPAN

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:

=over 4

=item -source

The sequence source.  This must be an I<Ace::Object> of the "Sequence" 
class, or be a sequence-like object containing the SMap tag (see
below).

=item -offset

An offset from the beginning of the source sequence.  The retrieved
I<Ace::Sequence> will begin at this position.  The offset can be any
positive or negative integer.  Offets are B<0-based>.

=item -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.

=item -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 I<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.

=item -name

As an alternative to using an I<Ace::Object> with the B<-source>
argument, you may specify a source sequence using B<-name> and B<-db>.
The I<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.

=item -db

This argument is required if the source sequence is specified by name
rather than by object reference.

=back

If new() is successful, it will create an I<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.

=head2 Reference Sequences and the Coordinate System

When retrieving information from an I<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
I<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 I<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 I<Ace::Sequence> object.

The other common exception occurs in Ace 4.8, where there is support
for "sequence-like" objects that contain the C<SMap> ("Sequence Map")
tag.  The C<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 C<SMap>-containing object
is passed to the I<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 I<Ace::Sequence> object is used to create a new I<Ace::Sequence>
object, then the original object's source is inherited.

=head1 Object Methods

Once an I<Ace::Sequence> object is created, you can query it using the
following methods:

=head2 asString()

  $name = $seq->asString;

Returns a human-readable identifier for the sequence in the form
I<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 I<Ace::Sequence> is used in a string
context.

=head2 source_seq()

  $source = $seq->source_seq;

Return the source of the I<Ace::Sequence>.

=head2 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 I<Ace::Sequence> in some cases, and an
I<Ace::Object> in others.  Use get_parent() to traverse upwards

Ace/Sequence.pm  view on Meta::CPAN

=head2 strand()

  $strand = $seq->strand;

Returns +1 for a sequence oriented in the natural direction of the
genomic reference sequence, or -1 otherwise.

=head2 reversed()

Returns true if the segment is reversed relative to the canonical
genomic direction.  This is the same as $seq->strand < 0.

=head2 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.

=head2 name()

  $name = $seq->name;

Return the name of the source sequence as a string.

=head2 get_parent()

  $parent = $seq->parent;

Return the immediate ancestor of this I<Ace::Sequence> (i.e., the
sequence that contains this one).  The return value is a new
I<Ace::Sequence> or undef, if no parent sequence exists.

=head2 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
I<Ace::Sequence> objects.

=head2 features()

  @features = $seq->features;
  @features = $seq->features('exon','intron','Predicted_gene');
  @features = $seq->features('exon:GeneFinder','Predicted_gene:hand.*');

features() returns an array of I<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 I<type> is the class of the feature (the "feature" field of the
GFF format), and I<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;

=head2 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 L<Ace::Feature::List> object.  From the
L<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 L<Ace::Feature::List> for more details.

=head2 transcripts()

This returns a list of Ace::Sequence::Transcript objects, which are
specializations of Ace::Sequence::Feature.  See L<Ace::Sequence::Transcript>
for details.

=head2 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.

=head2 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:

=over 4

=item -abs

Ordinarily the feature entries in the GFF file will be returned in
coordinates relative to the start of the I<Ace::Sequence> object.
Position 1 will be the start of the sequence object, and the "+"