Bio::DB::Das::Chado - DAS-style access to a chado database
# Open up a feature database $db = Bio::DB::Das::Chado->new( -dsn => 'dbi:Pg:dbname=gadfly;host=lajolla' -user => 'jimbo', -pass => 'supersecret', ); @segments = $db->segment(-name => '2L', -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 { ... } ); # 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;
Chado is the GMOD database schema, and chado is a specific instance of it. It is still somewhat of a moving target, so this package will probably require several updates over the coming months to keep it working.
This is alpha code and doesn't work very well
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : new Usage : $db = Bio::DB::Das::Chado( -dsn => 'dbi:Pg:dbname=gadfly;host=lajolla' -user => 'jimbo', -pass => 'supersecret', ); Function: Open up a Bio::DB::DasI interface to a Chado database Returns : a new Bio::DB::Das::Chado object Args :
Title : use_all_feature_names Usage : $obj->use_all_feature_names() Function: set or return flag indicating that all_feature_names view is present Returns : 1 if all_feature_names present, 0 if not Args : to return the flag, none; to set, 1
Title : organism_id Usage : $obj->organism_id() Function: set or return the organism_id Returns : the value of the id Args : to return the flag, none; to set, the common name of the organism
If -organism is set when the Chado feature is instantiated, this method queries the database with the common name to cache the organism_id.
Title : inferCDS Usage : $obj->inferCDS() Function: set or return the inferCDS flag Returns : the value of the inferCDS flag Args : to return the flag, none; to set, 1
Often, chado databases will be populated without CDS features, since they can be inferred from a union of exons and polypeptide features. Setting this flag tells the adaptor to do the inferrence to get those derived CDS features (at some small performance penatly).
Title : allow_obsolete Usage : $obj->allow_obsolete() Function: set or return the allow_obsolete flag Returns : the value of the allow_obsolete flag Args : to return the flag, none; to set, 1
The chado feature table has a flag column called 'is_obsolete'. Normally, these features should be ignored by GBrowse, but the -allow_obsolete method is provided to allow displaying obsolete features.
Title : sofa_id Usage : $obj->sofa_id() Function: get or return the ID to use for SO terms Returns : the cv.cv_id for the SO ontology to use Args : to return the id, none; to determine the id, 1
Title : recursivMapping Usage : $obj->recursivMapping($newval) Function: Flag for activating the recursive mapping (desactivated by default) Returns : value of recursivMapping (a scalar) Args : on set, new value (a scalar or undef, optional) Goal : When we have a clone mapped on a chromosome, the recursive mapping maps the features of the clone on the chromosome.
Title : srcfeatureslice Usage : $obj->srcfeatureslice Function: Flag for activating Returns : value of srcfeatureslice Args : on set, new value (a scalar or undef, optional) Desc : Allows to use a featureslice of type featureloc_slice(srcfeat_id, int, int) Important : this and recursivMapping are mutually exclusives
Title : do2Level Usage : $obj->do2Level Function: Flag for activating the fetching of 2levels in segment->features Returns : value of do2Level Args : on set, new value (a scalar or undef, optional)
Title : dbh Usage : $obj->dbh($newval) Function: Returns : value of dbh (a scalar) Args : on set, new value (a scalar or undef, optional)
Title : term2name Usage : $obj->term2name($newval) Function: When called with a hashref, sets cvterm.cvterm_id to cvterm.name mapping hashref; when called with an int, returns the name corresponding to that cvterm_id; called with no arguments, returns the hashref. Returns : see above Args : on set, a hashref; to retrieve a name, an int; to retrieve the hashref, none.
Note: should be replaced by Bio::GMOD::Util->term2name
Title : name2term Usage : $obj->name2term($newval) Function: When called with a hashref, sets cvterm.name to cvterm.cvterm_id mapping hashref; when called with a string, returns the cvterm_id corresponding to that name; called with no arguments, returns the hashref. Returns : see above Args : on set, a hashref; to retrieve a cvterm_id, a string; to retrieve the hashref, none.
Note: Should be replaced by Bio::GMOD::Util->name2term
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".
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
-type 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.
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.
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.
-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.
NOTE: This currently raises a "not-implemented" exception, as the BioSQL API does not appear to provide this functionality.
Title : get_features_by_alias Usage : $db->get_feature_by_alias(@args) Function: return list of feature whose name or synonyms match Returns : a list of Bio::Das::Chado::Segment::Feature objects Args : See below
This method finds features matching the criteria outlined by the supplied arguments. Wildcards (*) are allowed. Valid arguments are:
Title : get_features_by_name Usage : $db->get_features_by_name(@args) Function: return list of feature whose names match Returns : a list of Bio::Das::Chado::Segment::Feature objects Args : See below
Title : _by_alias_by_name Usage : $db->_by_alias_by_name(@args) Function: return list of feature whose names match Returns : a list of Bio::Das::Chado::Segment::Feature objects Args : See below
A private method that implements the get_features_by_name and get_features_by_alias methods. It accepts the same args as those methods, plus an addtional on (-operation) which is either 'by_alias' or 'by_name' to indicate what rule it is to use for finding features.
returns a srcfeature name given a srcfeature_id
Title : gff_source_db_id Function: caches the chado db_id from the chado db table
Gets dbxref_id for features that have a gff source associated
returns the source (string) when given a dbxref_id
Title : source_dbxref_list Usage : @all_dbxref_ids = $db->source_dbxref_list() Function: Gets a list of all dbxref_ids that are used for GFF sources Returns : a comma delimited string that is a list of dbxref_ids Args : none Status : public
This method queries the database for all dbxref_ids that are used to store GFF source terms.
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 (accession?), $description is a human-readable description such as a locus line, and $score is the match strength.
sub search_notes { my $self = shift; my ($search_string,$limit) = @_; my $limit_str; if (defined $limit) { $limit_str = " LIMIT $limit "; } else { $limit_str = ""; }
# so here's the plan: # if there is only 1 word, do 1-3 # 1. search for accessions like $string.'%'--if any are found, quit and return them # 2. search for feature.name like $string.'%'--if found, keep and continue # 3. search somewhere in analysis like $string.'%'--if found, keep and continue # if there is more than one word, don't search accessions # 4. search each word anded together like '%'.$string.'%' --if found, keep and continue # 5. search somewhere in analysis like '%'.$string.'%'
# $self->dbh->trace(1);
my @search_str = split /\s+/, $search_string; my $qsearch_term = $self->dbh->quote($search_str[0]); my $like_str = "( (dbx.accession ~* $qsearch_term OR \n" ." f.name ~* $qsearch_term) "; for (my $i=1;$i<(scalar @search_str);$i++) { $qsearch_term = $self->dbh->quote($search_str[$i]); $like_str .= "and \n"; $like_str .= " (dbx.accession ~* $qsearch_term OR \n" ." f.name ~* $qsearch_term) "; } $like_str .= ")"; my $sth = $self->dbh->prepare(" select dbx.accession,f.name,0 from feature f, dbxref dbx, feature_dbxref fd where f.feature_id = fd.feature_id and fd.dbxref_id = dbx.dbxref_id and $like_str $limit_str "); $sth->execute or throw ("couldn't execute keyword query"); my @results; while (my ($acc, $name, $score) = $sth->fetchrow_array) { $score = sprintf("%.2f",$score); push @results, [$acc, $name, $score]; } @results; }
Title : attributes Usage : @attributes = $db->attributes($id,$name) Function: get the "attributes" on a particular feature Returns : an array of string Args : feature ID [, attribute name] Status : public
This method is intended as a "work-alike" to Bio::DB::GFF's attributes method, which has the following returns:
Called in list context, it returns a list. If called in a scalar context, it returns the first value of the attribute if an attribute name is provided, otherwise it returns a hash reference in which the keys are attribute names and the values are anonymous arrays containing the values.
Title : _segclass Usage : $class = $db->_segclass Function: returns the perl class that we use for segment() calls Returns : a string containing the segment class Args : none Status : reserved for subclass use
Title : chado_reference_class Usage : $obj->chado_reference_class() Function: get or return the ID to use for Gbrowse map reference class using cvtermprop table, value = MAP_REFERENCE_TYPE Returns : the cvterm.name Args : to return the id, none; to determine the id, 1 See also: default_class, refclass_feature_id Optionally test that user/config supplied ref class is indeed a proper chado feature type.
Title : refclass_feature_id Usage : $self->refclass_srcfeature_id() Function: Used to store the feature_id of the reference class feature we are working on (e.g. contig, supercontig) With this feature we can filter out all the request to be sure we are extracting a feature located on the reference class feature. Returns : A scalar Args : The feature_id on setting
these methods should probably be declared in an interface class that Bio::DB::GFF implements. for instance, the aggregator methods could be described in Bio::SeqFeature::AggregatorI
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