Linux Certif

Toute la documentation sur la certification Linux LPI

Bio::DasI.3pm

NAME

Bio::DasI - DAS-style access to a feature database

SYNOPSIS

   # Open up a feature database somehow...
   $db = Bio::DasI->new(@args);
 
   @segments = $db->segment(-name  => 'NT_29921.4',
                            -start => 1,
                            -end   => 1000000);
 
   # segments are Bio::Das::SegmentI - compliant objects
 
   # fetch a list of features
   @features = $db->features(-type=>['type1','type2','type3']);
 
   # invoke a callback over features
   $db->features(-type=>['type1','type2','type3'],
                 -callback => sub { ... }
                 );
 
   $stream   = $db->get_seq_stream(-type=>['type1','type2','type3']);
   while (my $feature = $stream->next_seq) {
      # each feature is a Bio::SeqFeatureI-compliant object
   }
 
   # get all feature types
   @types   = $db->types;
 
   # count types
   %types   = $db->types(-enumerate=>1);
 
   @feature = $db->get_feature_by_name($class=>$name);
   @feature = $db->get_feature_by_target($target_name);
   @feature = $db->get_feature_by_attribute($att1=>$value1,$att2=>$value2);
   $feature = $db->get_feature_by_id($id);
 
   $error = $db->error;
 
 

DESCRIPTION

Bio::DasI is a simplified alternative interface to sequence annotation databases used by the distributed annotation system (see Bio::Das). In this scheme, the genome is represented as a series of features, a subset of which are named. Named features can be used as reference points for retrieving ``segments'' (see Bio::Das::SegmentI), and these can, in turn, be used as the basis for exploring the genome further.

In addition to a name, each feature has a ``class'', which is essentially a namespace qualifier and a ``type'', which describes what type of feature it is. Das uses the GO consortium's ontology of feature types, and so the type is actually an object of class Bio::Das::FeatureTypeI (see Bio::Das::FeatureTypeI). Bio::DasI provides methods for interrogating the database for the types it contains and the counts of each type.

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@bioperl.org
 
 

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

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 the web:

   http://bugzilla.open-bio.org/
 
 

AUTHOR - Lincoln Stein

Email lstein@cshl.org

APPENDIX

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

new

  Title   : new
  Usage   : Bio::DasI->new(@args)
  Function: Create new Bio::DasI object
  Returns : a Bio::DasI object
  Args    : see below
 
 

The new() method creates a new object. The argument list is either a single argument consisting of a connection string, or the following list of -name=>value arguments:

    Argument        Description
    --------        -----------
 
    -dsn            Connection string for database
    -adaptor        Name of an adaptor class to use when connecting
    -aggregator     Array ref containing list of aggregators
                      "semantic mappers" to apply to database
    -user           Authentication username
    -pass           Authentication password
 
 

Implementors of DasI may add other arguments.

types

  Title   : types
  Usage   : $db->types(@args)
  Function: return list of feature types in database
  Returns : a list of Bio::Das::FeatureTypeI objects
  Args    : see below
 
 

This routine returns a list of feature types known to the database. It is also possible to find out how many times each feature occurs.

Arguments are -option=>value pairs as follows:

   -enumerate  if true, count the features
 
 

The returned value will be a list of Bio::Das::FeatureTypeI objects (see Bio::Das::FeatureTypeI.

If -enumerate is true, then the function returns a hash (not a hash reference) in which the keys are the stringified versions of Bio::Das::FeatureTypeI and the values are the number of times each feature appears in the database.

parse_types

  Title   : parse_types
  Usage   : $db->parse_types(@args)
  Function: parses list of types
  Returns : an array ref containing ['method','source'] pairs
  Args    : a list of types in 'method:source' form
  Status  : internal
 
 

This method takes an array of type names in the format ``method:source'' and returns an array reference of ['method','source'] pairs. It will also accept a single argument consisting of an array reference with the list of type names.

segment

  Title   : segment
  Usage   : $db->segment(@args);
  Function: create a segment object
  Returns : segment object(s)
  Args    : see below
 
 

This method generates a Bio::Das::SegmentI object (see Bio::Das::SegmentI). The segment can be used to find overlapping features and the raw sequence.

When making the segment() call, you specify the ID of a sequence landmark (e.g. an accession number, a clone or contig), and a positional range relative to the landmark. If no range is specified, then the entire region spanned by the landmark is used to generate the segment.

Arguments are -option=>value pairs as follows:

  -name         ID of the landmark sequence.
 
  -class        A namespace qualifier.  It is not necessary for the
                database to honor namespace qualifiers, but if it
                does, this is where the qualifier is indicated.
 
  -version      Version number of the landmark.  It is not necessary for
                the database to honor versions, but if it does, this is
                where the version is indicated.
 
  -start        Start of the segment relative to landmark.  Positions
                follow standard 1-based sequence rules.  If not specified,
                defaults to the beginning of the landmark.
 
  -end          End of the segment relative to the landmark.  If not specified,
                defaults to the end of the landmark.
 
 

The return value is a list of Bio::Das::SegmentI objects. If the method is called in a scalar context and there are no more than one segments that satisfy the request, then it is allowed to return the segment. Otherwise, the method must throw a ``multiple segment exception''.

features

  Title   : features
  Usage   : $db->features(@args)
  Function: get all features, possibly filtered by type
  Returns : a list of Bio::SeqFeatureI objects
  Args    : see below
  Status  : public
 
 

This routine will retrieve features in the database regardless of position. It can be used to return all features, or a subset based on their type

Arguments are -option=>value pairs as follows:

   -types     List of feature types to return.  Argument is an array
              of Bio::Das::FeatureTypeI objects or a set of strings
              that can be converted into FeatureTypeI objects.
 
   -callback   A callback to invoke on each feature.  The subroutine
               will be passed each Bio::SeqFeatureI object in turn.
 
   -attributes A hash reference containing attributes to match.
 
 

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

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

Attribute matching is simple exact string matching, and multiple attributes are ANDed together. See Bio::DB::ConstraintsI for a more sophisticated take on this.

If one provides a callback, it will be invoked on each feature in turn. If the callback returns a false value, iteration will be interrupted. When a callback is provided, the method returns undef.

get_feature_by_name

  Title   : get_feature_by_name
  Usage   : $db->get_feature_by_name(-class=>$class,-name=>$name)
  Function: fetch features by their name
  Returns : a list of Bio::SeqFeatureI objects
  Args    : the class and name of the desired feature
  Status  : public
 
 

This method can be used to fetch named feature(s) from the database. The -class and -name arguments have the same meaning as in segment(), and the method also accepts the following short-cut forms:

   1) one argument: the argument is treated as the feature name
   2) two arguments: the arguments are treated as the class and name
      (note: this uses _rearrange() so the first argument must not
      begin with a hyphen or it will be interpreted as a named
      argument).
 
 

This method may return zero, one, or several Bio::SeqFeatureI objects. The implementor may allow the name to contain wildcards, in which case standard C-shell glob semantics are expected.

get_feature_by_target

  Title   : get_feature_by_target
  Usage   : $db->get_feature_by_target($class => $name)
  Function: fetch features by their similarity target
  Returns : a list of Bio::SeqFeatureI objects
  Args    : the class and name of the desired feature
  Status  : public
 
 

This method can be used to fetch a named feature from the database based on its similarity hit. The arguments are the same as get_feature_by_name(). If this is not implemented, the interface defaults to using get_feature_by_name().

get_feature_by_id

  Title   : get_feature_by_id
  Usage   : $db->get_feature_by_target($id)
  Function: fetch a feature by its ID
  Returns : a Bio::SeqFeatureI objects
  Args    : the ID of the feature
  Status  : public
 
 

If the database provides unique feature IDs, this can be used to retrieve a single feature from the database. If not overridden, this interface calls get_feature_by_name() and returns the first element.

get_feature_by_attribute

  Title   : get_feature_by_attribute
  Usage   : $db->get_feature_by_attribute(attribute1=>value1,attribute2=>value2)
  Function: fetch features by combinations of attribute values
  Returns : a list of Bio::SeqFeatureI objects
  Args    : the class and name of the desired feature
  Status  : public
 
 

This method can be used to fetch a set of features from the database. Attributes are a list of name=>value pairs. They will be logically ANDed together. If an attribute value is an array reference, the list of values in the array is treated as an alternative set of values to be ORed together.

search_notes

  Title   : search_notes
  Usage   : $db->search_notes($search_term,$max_results)
  Function: full-text search on features, ENSEMBL-style
  Returns : an array of [$name,$description,$score]
  Args    : see below
  Status  : public
 
 

This routine performs a full-text search on feature attributes (which attributes depend on implementation) and returns a list of [$name,$description,$score], where $name is the feature ID, $description is a human-readable description such as a locus line, and $score is the match strength.

Since this is a decidedly non-standard thing to do (but the generic genome browser uses it), the default method returns an empty list. You do not have to implement it.

get_seq_stream

  Title   : get_seq_stream
  Usage   : $seqio = $db->get_seq_stream(@args)
  Function: Performs a query and returns an iterator over it
  Returns : a Bio::SeqIO stream capable of returning Bio::SeqFeatureI objects
  Args    : As in features()
  Status  : public
 
 

This routine takes the same arguments as features(), but returns a Bio::SeqIO::Stream-compliant object. Use it like this:

   $stream = $db->get_seq_stream('exon');
   while (my $exon = $stream->next_seq) {
      print $exon,"\n";
   }
 
 

NOTE: In the interface this method is aliased to get_feature_stream(), as the name is more descriptive.

refclass

  Title   : refclass
  Usage   : $class = $db->refclass
  Function: returns the default class to use for segment() calls
  Returns : a string
  Args    : none
  Status  : public
 
 

For data sources which use namespaces to distinguish reference sequence accessions, this returns the default namespace (or ``class'') to use. This interface defines a default of ``Accession''.