/ 
Bio-DB-Das-Chado-0.3
River stage zero No dependents
/ Bio::DB::Das::Chado::Segment

NAME

Bio::DB::Das::Chado::Segment - DAS-style access to a chado database

SYNOPSIS

# Get a Bio::Das::SegmentI object from a Bio::DB::Das::Chado database...

$segment = $das->segment(-name => 'Landmark',
                         -start=> $start,
                         -stop => $stop);

@features = $segment->overlapping_features(-type=>['type1','type2']);
# each feature is a Bio::SeqFeatureI-compliant object

@features = $segment->contained_features(-type=>['type1','type2']);

@features = $segment->contained_in(-type=>['type1','type2']);

$stream = $segment->get_feature_stream(-type=>['type1','type2','type3'];
while (my $feature = $stream->next_seq) {
   # do something with feature
}

$count = $segment->features_callback(-type=>['type1','type2','type3'],
                                     -callback => sub { ... { }
                                     );

DESCRIPTION

Bio::DB::Das::Chado::Segment is a simplified alternative interface to sequence annotation databases used by the distributed annotation system. In this scheme, the genome is represented as a series of landmarks. Each Bio::DB::Das::Chado::Segment object ("segment") corresponds to a genomic region defined by a landmark and a start and end position relative to that landmark. A segment is created using the Bio::DasI segment() method.

Features can be filtered by the following attributes:

1) their location relative to the segment (whether overlapping,
        contained within, or completely containing)

2) their type

3) other attributes using tag/value semantics

Access to the feature list uses three distinct APIs:

1) fetching entire list of features at a time

2) fetching an iterator across features

3) a callback

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.

bioperl-l@bio.perl.org

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web:

bioperl-bugs@bio.perl.org
http://bio.perl.org/bioperl-bugs/

AUTHOR - Scott Cain

Email cain@cshl.org

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

name

Title   : name
Usage   : $segname = $seg->name();
Function: Returns the name of the segment
Returns : see above
Args    : none
Status  : public

feature_id()

Title   : feature_id
Usage   : $obj->feature_id($newval)
Function: holds feature.feature_id
Returns : value of feature_id (a scalar)
Args    : on set, new value (a scalar or undef, optional)

strand()

Title   : strand
Usage   : $obj->strand()
Function: Returns the strand of the feature.  Unlike the other
          methods, the strand cannot be changed once the object is
          created (due to coordinate considerations).
          corresponds to featureloc.strand
Returns : -1, 0, or 1
Args    : on set, new value (a scalar or undef, optional)

attributes

Title   : attributes 
Usage   : @attributes = $obj->attributes;
Function: get the "attributes" of this segment
Returns : An array of strings
Args    : None

This is a object-specific wrapper on the more generic attributes method in Bio::DB::Das::Chado.

_search_by_name

Title   : _search_by_name 
Usage   : _search_by_name($name);
Function: Searches for segments based on a name
Returns : Either a scalar (a feature_id) or an arrary ref (containing feature_ids)
Args    : A string (name)
Status  : private (used by new)

class

Needed for backward compatability; always returns 'Sequence'.

type

Title   : type
Usage   : $obj->type($newval)
Function: used to be alias of class() for backward compatibility,
          now behaves the same as Bio::DB::Das::Chado::Segment::Feature->type
Returns : A Bio::DB::GFF::Typename object
Args    : on set, new value: Bio::DB::GFF::Typename object

seq_id

Title   : seq_id
Usage   : $ref = $s->seq_id
Function: return the ID of the landmark, aliased to name() for backward compatibility
Returns : a string
Args    : none
Status  : Public

start

Title   : start
Usage   : $s->start
Function: start of segment
Returns : integer
Args    : none
Status  : Public

low

Title   : low
Usage   : $s->low
Function: start of segment
Returns : integer
Args    : none
Status  : Public

Alias of start for backward compatibility

end

Title   : end
Usage   : $s->end
Function: end of segment
Returns : integer
Args    : none
Status  : Public

high

Title   : high
Usage   : $s->high
Function: end of segment
Returns : integer
Args    : none
Status  : Public

Alias of end for backward compatiblity

stop

Title   : stop
Usage   : $s->stop
Function: end of segment
Returns : integer
Args    : none
Status  : Public

Alias of end for backward compatiblity

length

Title   : length
Usage   : $s->length
Function: length of segment
Returns : integer
Args    : none
Status  : Public

Returns the length of the segment. Always a positive number.

features

Title   : features
Usage   : @features = $s->features(@args)
Function: get features that overlap this segment
Returns : a list of Bio::SeqFeatureI objects
Args    : see below
Status  : Public

This method will find all features that intersect the segment in a variety of ways and return a list of Bio::SeqFeatureI objects. The feature locations will use coordinates relative to the reference sequence in effect at the time that features() was called.

The returned list can be limited to certain types, attributes or range intersection modes. Types of range intersection are one of:

"overlaps"      the default
"contains"      return features completely contained within the segment
"contained_in"  return features that completely contain the segment

Two types of argument lists are accepted. In the positional argument form, the arguments are treated as a list of feature types. In the named parameter form, the arguments are a series of -name=>value pairs.

  Argument    Description
  --------   ------------

  -types      An array reference to type names in the format
	      "method:source"

  -attributes A hashref containing a set of attributes to match

  -rangetype  One of "overlaps", "contains", or "contained_in".

  -iterator   Return an iterator across the features.

  -callback   A callback to invoke on each feature

The -attributes argument is a hashref containing one or more attributes to match against:

-attributes => { Gene => 'abc-1',
                 Note => 'confirmed' }

Attribute matching is simple string matching, and multiple attributes are ANDed together. More complex filtering can be performed using the -callback option (see below).

If -iterator is true, then the method returns an object reference that implements the next_seq() method. Each call to next_seq() returns a new Bio::SeqFeatureI object.

If -callback is passed a code reference, the code reference will be invoked on each feature returned. The code will be passed two arguments consisting of the current feature and the segment object itself, and must return a true value. If the code returns a false value, feature retrieval will be aborted.

-callback and -iterator are mutually exclusive options. If -iterator is defined, then -callback is ignored.

_features2level

See: features

Its a crude copy past from feature + additionnal code to handle prefetching of 2 levels features. The generated query is ~ as performant as the one generated by features, and the calls to Bio::DB::Das::Chado::Segment->sub_SeqFeatures are avoided, but this doesn't lead to a huge performace boost.

If a further development increases the performances provided by this 2 level prefetch, we will need to refactor features and _features2level to avoid code duplication

get_all_SeqFeature, get_SeqFeatures, top_SeqFeatures, all_SeqFeatures

Title   : get_all_SeqFeature, get_SeqFeatures, top_SeqFeatures, all_SeqFeatures
Usage   : $s->get_all_SeqFeature()
Function: get the sequence string for this segment
Returns : a string
Args    : none
Status  : Public

Several aliases of features() for backward compatibility

dna

Title   : dna
Usage   : $s->dna
Function: get the dna string this segment
Returns : a string
Args    : none
Status  : Public

Returns the sequence for this segment as a string.

seq

Title   : seq
Usage   : $s->seq
Function: get a Bio::Seq object for this segment
Returns : a Bio::Seq object
Args    : none
Status  : Public

Returns the sequence for this segment as a Bio::Seq object.

factory

Title   : factory
Usage   : $factory = $s->factory
Function: return the segment factory
Returns : a Bio::DasI object
Args    : see below
Status  : Public

This method returns a Bio::DasI object that can be used to fetch more segments. This is typically the Bio::DasI object from which the segment was originally generated.

srcfeature_id

Title   : srcfeature_id
Usage   : $obj->srcfeature_id($newval)
Function: undocumented method by Scott Cain
Returns : value of srcfeature_id (a scalar)
Args    : on set, new value (a scalar or undef, optional)

source

Title   : source
Usage   : $obj->source($newval)
Function: Returns the source; sets with an argument
Returns : A string that is the source
Args    : A string to set the source

source_tag

Title   : source_tag
Function: aliased to source() for Bio::SeqFeatureI compatibility

alphabet

Title   : alphabet
Usage   : $obj->alphabet($newval)
Function: Returns the sequence "type", ie, dna
Returns : scalar 'dna'
Args    : None

display_id, display_name, accession_number, desc

Title   : display_id, display_name, accession_number, desc
Usage   : $s->display_name()
Function: Alias of name()
Returns : string
Args    : none

Several aliases for name; it may be that these could do something better than just giving back the name.

get_feature_stream

Title   : get_feature_stream
Usage   : $db->get_feature_stream(@args)
Function: creates a feature iterator
Returns : A Bio::DB::Das::ChadoIterator object
Args    : The same arguments as the feature method

get_feature_stream has an alias called get_seq_stream for backward compatability.

clone

Title   : clone
Usage   : $copy = $s->clone
Function: make a copy of this segment
Returns : a Bio::DB::GFF::Segment object
Args    : none
Status  : Public

sourceseq

Title   : sourceseq
Usage   : $obj->sourceseq($newval)
Function: undocumented method by Scott Cain
Returns : value of sourceseq (a scalar)
Args    : on set, new value (a scalar or undef, optional)

refseq

Title   : refseq
Usage   : $s->refseq
Function: get or set the reference sequence
Returns : a string
Args    : none
Status  : Public

Examine or change the reference sequence. This is an alias to sourceseq(), provided here for API compatibility with Bio::DB::GFF::RelSegment.

abs_ref

Title   : abs_ref
Usage   : $obj->abs_ref()
Function: Alias of sourceseq
Returns : value of sourceseq (a scalar)
Args    : none

Alias of sourceseq for backward compatibility

abs_start

Title   : abs_start
Usage   : $obj->abs_start()
Function: Alias of start
Returns : value of start (a scalar)
Args    : none

abs_end

Title   : abs_end
Usage   : $obj->abs_end()
Function: Alias of end
Returns : value of end (a scalar)
Args    : none

asString

Title   : asString
Usage   : $s->asString
Function: human-readable string for segment
Returns : a string
Args    : none
Status  : Public

Returns a human-readable string representing this sequence. Format is:

sourceseq:start,stop