Raw content of Bio::DB::GFF # $Id: GFF.pm,v 1.71.2.2 2003/09/12 13:29:32 lstein Exp $ =head1 NAME Bio::DB::GFF -- Storage and retrieval of sequence annotation data =head1 SYNOPSIS use Bio::DB::GFF; # Open the sequence database my $db = Bio::DB::GFF->new( -adaptor => 'dbi::mysqlopt', -dsn => 'dbi:mysql:elegans', -fasta => '/usr/local/fasta_files' ); # fetch a 1 megabase segment of sequence starting at landmark "ZK909" my $segment = $db->segment('ZK909', 1 => 1000000); # pull out all transcript features my @transcripts = $segment->features('transcript'); # for each transcript, total the length of the introns my %totals; for my $t (@transcripts) { my @introns = $t->Intron; $totals{$t->name} += $_->length foreach @introns; } # Sort the exons of the first transcript by position my @exons = sort {$a->start <=> $b->start} $transcripts[0]->Exon; # Get a region 1000 bp upstream of first exon my $upstream = $exons[0]->segment(-1000,0); # get its DNA my $dna = $upstream->dna; # and get all curated polymorphisms inside it @polymorphisms = $upstream->contained_features('polymorphism:curated'); # get all feature types in the database my @types = $db->types; # count all feature types in the segment my %type_counts = $segment->types(-enumerate=>1); # get an iterator on all curated features of type 'exon' or 'intron' my $iterator = $db->get_seq_stream(-type => ['exon:curated','intron:curated']); while (my $s = $iterator->next_seq) { print $s,"\n"; } # find all transcripts annotated as having function 'kinase' my $iterator = $db->get_seq_stream(-type=>'transcript', -attributes=>{Function=>'kinase'}); while (my $s = $iterator->next_seq) { print $s,"\n"; } =head1 DESCRIPTION Bio::DB::GFF provides fast indexed access to a sequence annotation database. It supports multiple database types (ACeDB, relational), and multiple schemas through a system of adaptors and aggregators. The following operations are supported by this module: - retrieving a segment of sequence based on the ID of a landmark - retrieving the DNA from that segment - finding all annotations that overlap with the segment - finding all annotations that are completely contained within the segment - retrieving all annotations of a particular type, either within a segment, or globally - conversion from absolute to relative coordinates and back again, using any arbitrary landmark for the relative coordinates - using a sequence segment to create new segments based on relative offsets The data model used by Bio::DB::GFF is compatible with the GFF flat file format (http://www.sanger.ac.uk/localsw/GFF). The module can load a set of GFF files into the database, and serves objects that have methods corresponding to GFF fields. The objects returned by Bio::DB::GFF are compatible with the SeqFeatureI interface, allowing their use by the Bio::Graphics and Bio::DAS modules. =head2 Auxiliary Scripts The bioperl distribution includes several scripts that make it easier to work with Bio::DB::GFF databases. They are located in the scripts directory under a subdirectory named Bio::DB::GFF: =over 4 =item bp_load_gff.pl This script will load a Bio::DB::GFF database from a flat GFF file of sequence annotations. Only the relational database version of Bio::DB::GFF is supported. It can be used to create the database from scratch, as well as to incrementally load new data. This script takes a --fasta argument to load raw DNA into the database as well. However, GFF databases do not require access to the raw DNA for most of their functionality. load_gff.pl also has a --upgrade option, which will perform a non-destructive upgrade of older schemas to newer ones. =item bp_bulk_load_gff.pl This script will populate a Bio::DB::GFF database from a flat GFF file of sequence annotations. Only the MySQL database version of Bio::DB::GFF is supported. It uses the "LOAD DATA INFILE" query in order to accelerate loading considerably; however, it can only be used for the initial load, and not for updates. This script takes a --fasta argument to load raw DNA into the database as well. However, GFF databases do not require access to the raw DNA for most of their functionality. =item bp_fast_load_gff.pl This script is as fast as bp_bulk_load_gff.pl but uses Unix pipe tricks to allow for incremental updates. It only supports the MySQL database version of Bio::DB::GFF and is guaranteed not to work on non-Unix platforms. Arguments are the same as bp_load_gff.pl =item gadfly_to_gff.pl This script will convert the GFF-like format used by the Berkeley Drosophila Sequencing project into a format suitable for use with this module. =item sgd_to_gff.pl This script will convert the tab-delimited feature files used by the Saccharomyces Genome Database into a format suitable for use with this module. =back =head2 GFF Fundamentals The GFF format is a flat tab-delimited file, each line of which corresponds to an annotation, or feature. Each line has nine columns and looks like this: Chr1 curated CDS 365647 365963 . + 1 Transcript "R119.7" The 9 columns are as follows: =over 4 =item 1. reference sequence This is the ID of the sequence that is used to establish the coordinate system of the annotation. In the example above, the reference sequence is "Chr1". =item 2. source The source of the annotation. This field describes how the annotation was derived. In the example above, the source is "curated" to indicate that the feature is the result of human curation. The names and versions of software programs are often used for the source field, as in "tRNAScan-SE/1.2". =item 3. method The annotation method. This field describes the type of the annotation, such as "CDS". Together the method and source describe the annotation type. =item 4. start position The start of the annotation relative to the reference sequence. =item 5. stop position The stop of the annotation relative to the reference sequence. Start is always less than or equal to stop. =item 6. score For annotations that are associated with a numeric score (for example, a sequence similarity), this field describes the score. The score units are completely unspecified, but for sequence similarities, it is typically percent identity. Annotations that don't have a score can use "." =item 7. strand For those annotations which are strand-specific, this field is the strand on which the annotation resides. It is "+" for the forward strand, "-" for the reverse strand, or "." for annotations that are not stranded. =item 8. phase For annotations that are linked to proteins, this field describes the phase of the annotation on the codons. It is a number from 0 to 2, or "." for features that have no phase\. =item 9. group GFF provides a simple way of generating annotation hierarchies ("is composed of" relationships) by providing a group field. The group field contains the class and ID of an annotation which is the logical parent of the current one. In the example given above, the group is the Transcript named "R119.7". The group field is also used to store information about the target of sequence similarity hits, and miscellaneous notes. See the next section for a description of how to describe similarity targets. The format of the group fields is "Class ID" with a single space (not a tab) separating the class from the ID. It is VERY IMPORTANT to follow this format, or grouping will not work properly. =back The sequences used to establish the coordinate system for annotations can correspond to sequenced clones, clone fragments, contigs or super-contigs. Thus, this module can be used throughout the lifecycle of a sequencing project. In addition to a group ID, the GFF format allows annotations to have a group class. For example, in the ACeDB representation, RNA interference experiments have a class of "RNAi" and an ID that is unique among the RNAi experiments. Since not all databases support this notion, the class is optional in all calls to this module, and defaults to "Sequence" when not provided. Double-quotes are sometimes used in GFF files around components of the group field. Strictly, this is only necessary if the group name or class contains whitespace. =head2 Making GFF files work with this module Some annotations do not need to be individually named. For example, it is probably not useful to assign a unique name to each ALU repeat in a vertebrate genome. Others, such as predicted genes, correspond to named biological objects; you probably want to be able to fetch the positions of these objects by referring to them by name. To accomodate named annotations, the GFF format places the object class and name in the group field. The name identifies the object, and the class prevents similarly-named objects, for example clones and sequences, from collding. A named object is shown in the following excerpt from a GFF file: Chr1 curated transcript 939627 942410 . + . Transcript Y95B8A.2 This object is a predicted transcript named Y95BA.2. In this case, the group field is used to identify the class and name of the object, even though no other annotation belongs to that group. It now becomes possible to retrieve the region of the genome covered by transcript Y95B8A.2 using the segment() method: $segment = $db->segment(-class=>'Transcript',-name=>'Y95B8A.2'); It is not necessary for the annotation's method to correspond to the object class, although this is commonly the case. As explained above, each annotation in a GFF file refers to a reference sequence. It is important that each reference sequence also be identified by a line in the GFF file. This allows the Bio::DB::GFF module to determine the length and class of the reference sequence, and makes it possible to do relative arithmetic. For example, if "Chr1" is used as a reference sequence, then it should have an entry in the GFF file similar to this one: Chr1 assembly chromosome 1 14972282 . + . Sequence Chr1 This indicates that the reference sequence named "Chr1" has length 14972282 bp, method "chromosome" and source "assembly". In addition, as indicated by the group field, Chr1 has class "Sequence" and name "Chr1". The object class "Sequence" is used by default when the class is not specified in the segment() call. This allows you to use a shortcut form of the segment() method: $segment = $db->segment('Chr1'); # whole chromosome $segment = $db->segment('Chr1',1=>1000); # first 1000 bp For your convenience, if, during loading a GFF file, Bio::DB::GFF encounters a line like the following: ##sequence-region Chr1 1 14972282 It will automatically generate the following entry: Chr1 reference Component 1 14972282 . + . Sequence Chr1 This is sufficient to use Chr1 as a reference point. The ##sequence-region line is frequently found in the GFF files distributed by annotation groups. =head2 Sequence alignments There are two cases in which an annotation indicates the relationship between two sequences. The first case is a similarity hit, where the annotation indicates an alignment. The second case is a map assembly, in which the annotation indicates that a portion of a larger sequence is built up from one or more smaller ones. Both cases are indicated by using the B<Target> tag in the group field. For example, a typical similarity hit will look like this: Chr1 BLASTX similarity 76953 77108 132 + 0 Target Protein:SW:ABL_DROME 493 544 The group field contains the Target tag, followed by an identifier for the biological object referred to. The GFF format uses the notation I<Class>:I<Name> for the biological object, and even though this is stylistically inconsistent, that's the way it's done. The object identifier is followed by two integers indicating the start and stop of the alignment on the target sequence. Unlike the main start and stop columns, it is possible for the target start to be greater than the target end. The previous example indicates that the the section of Chr1 from 76,953 to 77,108 aligns to the protein SW:ABL_DROME starting at position 493 and extending to position 544. A similar notation is used for sequence assembly information as shown in this example: Chr1 assembly Link 10922906 11177731 . . . Target Sequence:LINK_H06O01 1 254826 LINK_H06O01 assembly Cosmid 32386 64122 . . . Target Sequence:F49B2 6 31742 This indicates that the region between bases 10922906 and 11177731 of Chr1 are composed of LINK_H06O01 from bp 1 to bp 254826. The region of LINK_H0601 between 32386 and 64122 is, in turn, composed of the bases 5 to 31742 of cosmid F49B2. =head2 Attributes While not intended to serve as a general-purpose sequence database (see bioperl-db for that), GFF allows you to tag features with arbitrary attributes. Attributes appear in the Group field following the initial class/name pair. For example: Chr1 cur trans 939 942 . + . Transcript Y95B8A.2 ; Gene sma-3 ; Alias sma3 This line tags the feature named Transcript Y95B8A.2 as being "Gene" named sma-3 and having the Alias "sma3". Features having these attributes can be looked up using the fetch_feature_by_attribute() method. Two attributes have special meaning: "Note" is for backward compatibility and is used for unstructured text remarks. "Alias" is considered as a synonym for the feature name and will be consulted when looking up a feature by its name. =head2 Adaptors and Aggregators This module uses a system of adaptors and aggregators in order to make it adaptable to use with a variety of databases. =over 4 =item Adaptors The core of the module handles the user API, annotation coordinate arithmetic, and other common issues. The details of fetching information from databases is handled by an adaptor, which is specified during Bio::DB::GFF construction. The adaptor encapsulates database-specific information such as the schema, user authentication and access methods. Currently there are two adaptors: 'dbi::mysql' and 'dbi::mysqlopt'. The former is an interface to a simple Mysql schema. The latter is an optimized version of dbi::mysql which uses a binning scheme to accelerate range queries and the Bio::DB::Fasta module for rapid retrieval of sequences. Note the double-colon between the words. =item Aggregators The GFF format uses a "group" field to indicate aggregation properties of individual features. For example, a set of exons and introns may share a common transcript group, and multiple transcripts may share the same gene group. Aggregators are small modules that use the group information to rebuild the hierarchy. When a Bio::DB::GFF object is created, you indicate that it use a set of one or more aggregators. Each aggregator provides a new composite annotation type. Before the database query is generated each aggregator is called to "disaggregate" its annotation type into list of component types contained in the database. After the query is generated, each aggregator is called again in order to build composite annotations from the returned components. For example, during disaggregation, the standard "processed_transcript" aggregator generates a list of component feature types including "UTR", "CDS", and "polyA_site". Later, it aggregates these features into a set of annotations of type "processed_transcript". During aggregation, the list of aggregators is called in reverse order. This allows aggregators to collaborate to create multi-level structures: the transcript aggregator assembles transcripts from introns and exons; the gene aggregator then assembles genes from sets of transcripts. Three default aggregators are provided: transcript assembles transcripts from features of type exon, CDS, 5'UTR, 3'UTR, TSS, and PolyA clone assembles clones from Clone_left_end, Clone_right_end and Sequence features. alignment assembles gapped alignments from features of type "similarity". In addition, this module provides the optional "wormbase_gene" aggregator, which accomodates the WormBase representation of genes. This aggregator aggregates features of method "exon", "CDS", "5'UTR", "3'UTR", "polyA" and "TSS" into a single object. It also expects to find a single feature of type "Sequence" that spans the entire gene. The existing aggregators are easily customized. Note that aggregation will not occur unless you specifically request the aggregation type. For example, this call: @features = $segment->features('alignment'); will generate an array of aggregated alignment features. However, this call: @features = $segment->features(); will return a list of unaggregated similarity segments. For more informnation, see the manual pages for Bio::DB::GFF::Aggregator::processed_transcript, Bio::DB::GFF::Aggregator::clone, etc. =back =head1 API The following is the API for Bio::DB::GFF. =cut package Bio::DB::GFF; use strict; use Bio::DB::GFF::Util::Rearrange; use Bio::DB::GFF::RelSegment; use Bio::DB::GFF::Feature; use Bio::DB::GFF::Aggregator; use Bio::DasI; use Bio::Root::Root; use vars qw(@ISA $VERSION); @ISA = qw(Bio::Root::Root Bio::DasI); $VERSION = '1.2003'; my %valid_range_types = (overlaps => 1, contains => 1, contained_in => 1); =head1 Querying GFF Databases =head2 new Title : new Usage : my $db = new Bio::DB::GFF(@args); Function: create a new Bio::DB::GFF object Returns : new Bio::DB::GFF object Args : lists of adaptors and aggregators Status : Public These are the arguments: -adaptor Name of the adaptor module to use. If none provided, defaults to "dbi::mysqlopt". -aggregator Array reference to a list of aggregators to apply to the database. If none provided, defaults to ['processed_transcript','alignment']. <other> Any other named argument pairs are passed to the adaptor for processing. The adaptor argument must correspond to a module contained within the Bio::DB::GFF::Adaptor namespace. For example, the Bio::DB::GFF::Adaptor::dbi::mysql adaptor is loaded by specifying 'dbi::mysql'. By Perl convention, the adaptors names are lower case because they are loaded at run time. The aggregator array may contain a list of aggregator names, a list of initialized aggregator objects, or a string in the form "aggregator_name{subpart1,subpart2,subpart3/main_method}" (the /main_method part is optional). For example, if you wish to change the components aggregated by the transcript aggregator, you could pass it to the GFF constructor this way: my $transcript = Bio::DB::Aggregator::transcript->new(-sub_parts=>[qw(exon intron utr polyA spliced_leader)]); my $db = Bio::DB::GFF->new(-aggregator=>[$transcript,'clone','alignment], -adaptor => 'dbi::mysql', -dsn => 'dbi:mysql:elegans42'); Alternatively, you could create an entirely new transcript aggregator this way: my $new_agg = 'transcript{exon,intron,utr,polyA,spliced_leader}'; my $db = Bio::DB::GFF->new(-aggregator=>[$new_agg,'clone','alignment], -adaptor => 'dbi::mysql', -dsn => 'dbi:mysql:elegans42'); See L<Bio::DB::GFF::Aggregator> for more details. The commonly used 'dbi::mysql' adaptor recognizes the following adaptor-specific arguments: Argument Description -------- ----------- -dsn the DBI data source, e.g. 'dbi:mysql:ens0040' If a partial name is given, such as "ens0040", the "dbi:mysql:" prefix will be added automatically. -user username for authentication -pass the password for authentication -refclass landmark Class; defaults to "Sequence" The commonly used 'dbi::mysqlopt' adaptor also recogizes the following arguments. Argument Description -------- ----------- -fasta path to a directory containing FASTA files for the DNA contained in this database (e.g. "/usr/local/share/fasta") -acedb an acedb URL to use when converting features into ACEDB objects (e.g. sace://localhost:2005) =cut #' sub new { my $package = shift; my ($adaptor,$aggregators,$args,$refclass); if (@_ == 1) { # special case, default to dbi::mysqlopt $adaptor = 'dbi::mysqlopt'; $args = {DSN => shift}; } else { ($adaptor,$aggregators,$refclass,$args) = rearrange([ [qw(ADAPTOR FACTORY)], [qw(AGGREGATOR AGGREGATORS)], 'REFCLASS', ],@_); } $adaptor ||= 'dbi::mysqlopt'; my $class = "Bio::DB::GFF::Adaptor::\L${adaptor}\E"; eval "require $class" unless $class->can('new'); $package->throw("Unable to load $adaptor adaptor: $@") if $@; my $self = $class->new($args); $self->default_class($refclass) if defined $refclass; # handle the aggregators. # aggregators are responsible for creating complex multi-part features # from the GFF "group" field. If none are provided, then we provide a # list of the two used in WormBase. # Each aggregator can be a scalar or a ref. In the former case # it is treated as a class name to call new() on. In the latter # the aggreator is treated as a ready made object. $aggregators = $self->default_aggregators unless defined $aggregators; my @a = ref($aggregators) eq 'ARRAY' ? @$aggregators : $aggregators; for my $a (@a) { $self->add_aggregator($a); } # default settings go here..... $self->automerge(1); # set automerge to true $self; } =head2 types Title : types Usage : $db->types(@args) Function: return list of feature types in range or database Returns : a list of Bio::DB::GFF::Typename objects Args : see below Status : public This routine returns a list of feature types known to the database. The list can be database-wide or restricted to a region. It is also possible to find out how many times each feature occurs. For range queries, it is usually more convenient to create a Bio::DB::GFF::Segment object, and then invoke it's types() method. Arguments are as follows: -ref ID of reference sequence -class class of reference sequence -start start of segment -stop stop of segment -enumerate if true, count the features The returned value will be a list of Bio::DB::GFF::Typename objects, which if evaluated in a string context will return the feature type in "method:source" format. This object class also has method() and source() methods for retrieving the like-named fields. If -enumerate is true, then the function returns a hash (not a hash reference) in which the keys are type names in "method:source" format and the values are the number of times each feature appears in the database or segment. The argument -end is a synonum for -stop, and -count is a synonym for -enumerate. =cut sub types { my $self = shift; my ($refseq,$start,$stop,$enumerate,$refclass,$types) = rearrange ([ [qw(REF REFSEQ)], qw(START), [qw(STOP END)], [qw(ENUMERATE COUNT)], [qw(CLASS SEQCLASS)], [qw(TYPE TYPES)], ],@_); $types = $self->parse_types($types) if defined $types; $self->get_types($refseq,$refclass,$start,$stop,$enumerate,$types); } =head2 classes Title : classes Usage : $db->classes Function: return list of landmark classes in database Returns : a list of classes Args : none Status : public This routine returns the list of reference classes known to the database, or empty if classes are not used by the database. Classes are distinct from types, being essentially qualifiers on the reference namespaces. =cut sub classes { my $self = shift; return (); } =head2 segment Title : segment Usage : $db->segment(@args); Function: create a segment object Returns : segment object(s) Args : numerous, see below Status : public This method generates a segment object, which is a Perl object subclassed from Bio::DB::GFF::Segment. The segment can be used to find overlapping features and the raw DNA. 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 extent of the landmark is used to generate the segment. You may also provide the ID of a "reference" sequence, which will set the coordinate system and orientation used for all features contained within the segment. The reference sequence can be changed later. If no reference sequence is provided, then the coordinate system is based on the landmark. Arguments: -name ID of the landmark sequence. -class Database object class for the landmark sequence. "Sequence" assumed if not specified. This is irrelevant for databases which do not recognize object classes. -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 Stop of the segment relative to the landmark. If not specified, defaults to the end of the landmark. -stop Same as -end. -offset For those who prefer 0-based indexing, the offset specifies the position of the new segment relative to the start of the landmark. -length For those who prefer 0-based indexing, the length specifies the length of the new segment. -refseq Specifies the ID of the reference landmark used to establish the coordinate system for the newly-created segment. -refclass Specifies the class of the reference landmark, for those databases that distinguish different object classes. Defaults to "Sequence". -absolute Return features in absolute coordinates rather than relative to the parent segment. -nocheck Don't check the database for the coordinates and length of this feature. Construct a segment using the indicated name as the reference, a start coordinate of 1, an undefined end coordinate, and a strand of +1. -force Same as -nocheck. -seq,-sequence,-sourceseq Aliases for -name. -begin,-end Aliases for -start and -stop -off,-len Aliases for -offset and -length -seqclass Alias for -class Here's an example to explain how this works: my $db = Bio::DB::GFF->new(-dsn => 'dbi:mysql:human',-adaptor=>'dbi::mysql'); If successful, $db will now hold the database accessor object. We now try to fetch the fragment of sequence whose ID is A0000182 and class is "Accession." my $segment = $db->segment(-name=>'A0000182',-class=>'Accession'); If successful, $segment now holds the entire segment corresponding to this accession number. By default, the sequence is used as its own reference sequence, so its first base will be 1 and its last base will be the length of the accession. Assuming that this sequence belongs to a longer stretch of DNA, say a contig, we can fetch this information like so: my $sourceseq = $segment->sourceseq; and find the start and stop on the source like this: my $start = $segment->abs_start; my $stop = $segment->abs_stop; If we had another segment, say $s2, which is on the same contiguous piece of DNA, we can pass that to the refseq() method in order to establish it as the coordinate reference point: $segment->refseq($s2); Now calling start() will return the start of the segment relative to the beginning of $s2, accounting for differences in strandedness: my $rel_start = $segment->start; IMPORTANT NOTE: This method can be used to return the segment spanned by an arbitrary named annotation. However, if the annotation appears at multiple locations on the genome, for example an EST that maps to multiple locations, then, provided that all locations reside on the same physical segment, the method will return a segment that spans the minimum and maximum positions. If the reference sequence occupies ranges on different physical segments, then it returns them all in an array context, and raises a "multiple segment exception" exception in a scalar context. =cut #' sub segment { my $self = shift; my @segments = Bio::DB::GFF::RelSegment->new(-factory => $self, $self->setup_segment_args(@_)); foreach (@segments) { $_->absolute(1) if $self->absolute; } $self->_multiple_return_args(@segments); } sub _multiple_return_args { my $self = shift; my @args = @_; if (@args == 0) { return; } elsif (@args == 1) { return $args[0]; } elsif (wantarray) { # more than one reference sequence return @args; } else { $self->error($args[0]->name, " has more than one reference sequence in database. Please call in a list context to retrieve them all."); $self->throw('multiple segment exception'); return; } } # backward compatibility -- don't use! # (deliberately undocumented too) sub abs_segment { my $self = shift; return $self->segment($self->setup_segment_args(@_),-absolute=>1); } sub setup_segment_args { my $self = shift; return @_ if defined $_[0] && $_[0] =~ /^-/; return (-name=>$_[0],-start=>$_[1],-stop=>$_[2]) if @_ == 3; return (-class=>$_[0],-name=>$_[1]) if @_ == 2; return (-name=>$_[0]) if @_ == 1; } =head2 features Title : features Usage : $db->features(@args) Function: get all features, possibly filtered by type Returns : a list of Bio::DB::GFF::Feature 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 method and source. Arguments are as follows: -types List of feature types to return. Argument is an array reference containing strings of the format "method:source" -merge Whether to apply aggregators to the generated features. -rare Turn on optimizations suitable for a relatively rare feature type, where it makes more sense to filter by feature type first, and then by position. -attributes A hash reference containing attributes to match. -iterator Whether to return an iterator across the features. -binsize A true value will create a set of artificial features whose start and stop positions indicate bins of the given size, and whose scores are the number of features in the bin. The class and method of the feature will be set to "bin", its source to "method:source", and its group to "bin:method:source". This is a handy way of generating histograms of feature density. If -iterator is true, then the method returns a single scalar value consisting of a Bio::SeqIO object. You can call next_seq() repeatedly on this object to fetch each of the features in turn. If iterator is false or absent, then all the features are returned as a list. Currently aggregation is disabled when iterating over a series of features. Types are indicated using the nomenclature "method:source". Either of these fields can be omitted, in which case a wildcard is used for the missing field. Type names without the colon (e.g. "exon") are interpreted as the method name and a source wild card. Regular expressions are allowed in either field, as in: "similarity:BLAST.*". 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. =cut sub features { my $self = shift; my ($types,$automerge,$sparse,$iterator,$other); if (defined $_[0] && $_[0] =~ /^-/) { ($types,$automerge,$sparse,$iterator,$other) = rearrange([ [qw(TYPE TYPES)], [qw(MERGE AUTOMERGE)], [qw(RARE SPARSE)], 'ITERATOR' ],@_); } else { $types = \@_; } # for whole database retrievals, we probably don't want to automerge! $automerge = $self->automerge unless defined $automerge; $other ||= {}; $self->_features({ rangetype => 'contains', types => $types, }, { sparse => $sparse, automerge => $automerge, iterator =>$iterator, %$other, } ); } =head2 get_seq_stream Title : get_seq_stream Usage : my $seqio = $self->get_seq_sream(@args) Function: Performs a query and returns an iterator over it Returns : a Bio::SeqIO stream capable of producing sequence 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: This is also called get_feature_stream(), since that's what it really does. =cut sub get_seq_stream { my $self = shift; my @args = !defined($_[0]) || $_[0] =~ /^-/ ? (@_,-iterator=>1) : (-types=>\@_,-iterator=>1); $self->features(@args); } *get_feature_stream = \&get_seq_stream; =head2 get_feature_by_name Title : get_feature_by_name Usage : $db->get_feature_by_name($class => $name) Function: fetch features by their name Returns : a list of Bio::DB::GFF::Feature 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. GFF annotations are named using the group class and name fields, so for features that belong to a group of size one, this method can be used to retrieve that group (and is equivalent to the segment() method). Any Alias attributes are also searched for matching names. An alternative syntax allows you to search for features by name within a circumscribed region: @f = $db->get_feature_by_name(-class => $class,-name=>$name, -ref => $sequence_name, -start => $start, -end => $end); This method may return zero, one, or several Bio::DB::GFF::Feature objects. Aggregation is performed on features as usual. NOTE: At various times, this function was called fetch_group(), fetch_feature(), fetch_feature_by_name() and segments(). These names are preserved for backward compatibility. =cut sub get_feature_by_name { my $self = shift; my ($gclass,$gname,$automerge,$ref,$start,$end); if (@_ == 1) { $gclass = $self->default_class; $gname = shift; } else { ($gclass,$gname,$automerge,$ref,$start,$end) = rearrange(['CLASS','NAME','AUTOMERGE', ['REF','REFSEQ'], 'START',['STOP','END'] ],@_); $gclass ||= $self->default_class; } $automerge = $self->automerge unless defined $automerge; # we need to refactor this... It's repeated code (see below)... my @aggregators; if ($automerge) { for my $a ($self->aggregators) { push @aggregators,$a if $a->disaggregate([],$self); } } my %groups; # cache the groups we create to avoid consuming too much unecessary memory my $features = []; my $callback = sub { push @$features,$self->make_feature(undef,\%groups,@_) }; my $location = [$ref,$start,$end] if defined $ref; $self->_feature_by_name($gclass,$gname,$location,$callback); warn "aggregating...\n" if $self->debug; foreach my $a (@aggregators) { # last aggregator gets first shot $a->aggregate($features,$self) or next; } @$features; } # horrible indecision regarding proper names! *fetch_group = *fetch_feature = *fetch_feature_by_name = \&get_feature_by_name; *segments = \&segment; =head2 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::DB::GFF::Feature 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. =cut sub get_feature_by_target { shift->get_feature_by_name(@_); } =head2 get_feature_by_attribute Title : get_feature_by_attribute Usage : $db->get_feature_by_attribute(attribute1=>value1,attribute2=>value2) Function: fetch segments by combinations of attribute values Returns : a list of Bio::DB::GFF::Feature 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=E<gt>value pairs. They will be logically ANDED together. =cut sub get_feature_by_attribute { my $self = shift; my %attributes = ref($_[0]) ? %{$_[0]} : @_; # we need to refactor this... It's repeated code (see above)... my @aggregators; if ($self->automerge) { for my $a ($self->aggregators) { unshift @aggregators,$a if $a->disaggregate([],$self); } } my %groups; # cache the groups we create to avoid consuming too much unecessary memory my $features = []; my $callback = sub { push @$features,$self->make_feature(undef,\%groups,@_) }; $self->_feature_by_attribute(\%attributes,$callback); warn "aggregating...\n" if $self->debug; foreach my $a (@aggregators) { # last aggregator gets first shot $a->aggregate($features,$self) or next; } @$features; } # more indecision... *fetch_feature_by_attribute = \&get_feature_by_attribute; =head2 get_feature_by_id Title : get_feature_by_id Usage : $db->get_feature_by_id($id) Function: fetch segments by feature ID Returns : a Bio::DB::GFF::Feature object Args : the feature ID Status : public This method can be used to fetch a feature from the database using its ID. Not all GFF databases support IDs, so be careful with this. =cut sub get_feature_by_id { my $self = shift; my $id = ref($_[0]) eq 'ARRAY' ? $_[0] : \@_; my %groups; # cache the groups we create to avoid consuming too much unecessary memory my $features = []; my $callback = sub { push @$features,$self->make_feature(undef,\%groups,@_) }; $self->_feature_by_id($id,'feature',$callback); return wantarray ? @$features : $features->[0]; } *fetch_feature_by_id = \&get_feature_by_id; =head2 get_feature_by_gid Title : get_feature_by_gid Usage : $db->get_feature_by_gid($id) Function: fetch segments by feature ID Returns : a Bio::DB::GFF::Feature object Args : the feature ID Status : public This method can be used to fetch a feature from the database using its group ID. Not all GFF databases support IDs, so be careful with this. The group ID is often more interesting than the feature ID, since groups can be complex objects containing subobjects. =cut sub get_feature_by_gid { my $self = shift; my $id = ref($_[0]) eq 'ARRAY' ? $_[0] : \@_; my %groups; # cache the groups we create to avoid consuming too much unecessary memory my $features = []; my $callback = sub { push @$features,$self->make_feature(undef,\%groups,@_) }; $self->_feature_by_id($id,'group',$callback); return wantarray ? @$features : $features->[0]; } *fetch_feature_by_gid = \&get_feature_by_gid; =head2 delete_features Title : delete_features Usage : $db->delete_features(@ids_or_features) Function: delete one or more features Returns : count of features deleted Args : list of features or feature ids Status : public Pass this method a list of numeric feature ids or a set of features. It will attempt to remove the features from the database and return a count of the features removed. NOTE: This method is also called delete_feature(). Also see delete_groups(). =cut *delete_feature = \&delete_features; sub delete_features { my $self = shift; my @features_or_ids = @_; my @ids = map {UNIVERSAL::isa($_,'Bio::DB::GFF::Feature') ? $_->id : $_} @features_or_ids; return unless @ids; $self->_delete_features(@ids); } =head2 delete_groups Title : delete_groups Usage : $db->delete_groups(@ids_or_features) Function: delete one or more feature groups Returns : count of features deleted Args : list of features or feature group ids Status : public Pass this method a list of numeric group ids or a set of features. It will attempt to recursively remove the features and ALL members of their group from the database. It returns a count of the number of features (not groups) returned. NOTE: This method is also called delete_group(). Also see delete_features(). =cut *delete_group = \&delete_groupss; sub delete_groups { my $self = shift; my @features_or_ids = @_; my @ids = map {UNIVERSAL::isa($_,'Bio::DB::GFF::Feature') ? $_->group_id : $_} @features_or_ids; return unless @ids; $self->_delete_groups(@ids); } =head2 delete Title : delete Usage : $db->delete(@args) Function: delete features Returns : count of features deleted -- if available Args : numerous, see below Status : public This method deletes all features that overlap the specified region or are of a particular type. If no arguments are provided and the -force argument is true, then deletes ALL features. Arguments: -name ID of the landmark sequence. -ref ID of the landmark sequence (synonym for -name). -class Database object class for the landmark sequence. "Sequence" assumed if not specified. This is irrelevant for databases which do not recognize object classes. -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 Stop of the segment relative to the landmark. If not specified, defaults to the end of the landmark. -offset Zero-based addressing -length Length of region -type,-types Either a single scalar type to be deleted, or an reference to an array of types. -force Force operation to be performed even if it would delete entire feature table. -range_type Control the range type of the deletion. One of "overlaps" (default) "contains" or "contained_in" Examples: $db->delete(-type=>['intron','repeat:repeatMasker']); # remove all introns & repeats $db->delete(-name=>'chr3',-start=>1,-end=>1000); # remove annotations on chr3 from 1 to 1000 $db->delete(-name=>'chr3',-type=>'exon'); # remove all exons on chr3 The short form of this call, as described in segment() is also allowed: $db->delete("chr3",1=>1000); $db->delete("chr3"); IMPORTANT NOTE: This method only deletes features. It does *NOT* delete the names of groups that contain the deleted features. Group IDs will be reused if you later load a feature with the same group name as one that was previously deleted. NOTE ON FEATURE COUNTS: The DBI-based versions of this call return the result code from the SQL DELETE operation. Some dbd drivers return the count of rows deleted, while others return 0E0. Caveat emptor. =cut sub delete { my $self = shift; my @args = $self->setup_segment_args(@_); my ($name,$class,$start,$end,$offset,$length,$type,$force,$range_type) = rearrange([['NAME','REF'],'CLASS','START',[qw(END STOP)],'OFFSET', 'LENGTH',[qw(TYPE TYPES)],'FORCE','RANGE_TYPE'],@args); $offset = 0 unless defined $offset; $start = $offset+1 unless defined $start; $end = $start+$length-1 if !defined $end and $length; $class ||= $self->default_class; my $types = $self->parse_types($type); # parse out list of types $range_type ||= 'overlaps'; $self->throw("range type must be one of {". join(',',keys %valid_range_types). "}\n") unless $valid_range_types{lc $range_type}; my @segments; if (defined $name && $name ne '') { my @args = (-name=>$name,-class=>$class); push @args,(-start=>$start) if defined $start; push @args,(-end =>$end) if defined $end; @segments = $self->segment(@args); return unless @segments; } $self->_delete({segments => \@segments, types => $types, range_type => $range_type, force => $force} ); } =head2 absolute Title : absolute Usage : $abs = $db->absolute([$abs]); Function: gets/sets absolute mode Returns : current setting of absolute mode boolean Args : new setting for absolute mode boolean Status : public $db-E<gt>absolute(1) will turn on absolute mode for the entire database. All segments retrieved will use absolute coordinates by default, rather than relative coordinates. You can still set them to use relative coordinates by calling $segment-E<gt>absolute(0). Note that this is not the same as calling abs_segment(); it continues to allow you to look up groups that are not used directly as reference sequences. =cut sub absolute { my $self = shift; my $d = $self->{absolute}; $self->{absolute} = shift if @_; $d; } =head2 strict_bounds_checking Title : strict_bounds_checking Usage : $flag = $db->strict_bounds_checking([$flag]) Function: gets/sets strict bounds checking Returns : current setting of bounds checking flag Args : new setting for bounds checking flag Status : public This flag enables extra checks for segment requests that go beyond the ends of their reference sequences. If bounds checking is enabled, then retrieved segments will be truncated to their physical length, and their truncated() methods will return true. If the flag is off (the default), then the module will return segments that appear to extend beyond their physical boundaries. Requests for features beyond the end of the segment will, however, return empty. =cut sub strict_bounds_checking { my $self = shift; my $d = $self->{strict}; $self->{strict} = shift if @_; $d; } =head2 get_Seq_by_id Title : get_Seq_by_id Usage : $seq = $db->get_Seq_by_id('ROA1_HUMAN') Function: Gets a Bio::Seq object by its name Returns : a Bio::Seq object Args : the id (as a string) of a sequence Throws : "id does not exist" exception NOTE: Bio::DB::RandomAccessI compliant method =cut sub get_Seq_by_id { my $self = shift; my $id = shift; my $stream = $self->get_Stream_by_id($id); return $stream->next_seq; } =head2 get_Seq_by_accession Title : get_Seq_by_accession Usage : $seq = $db->get_Seq_by_accession('AL12234') Function: Gets a Bio::Seq object by its accession Returns : a Bio::Seq object Args : the id (as a string) of a sequence Throws : "id does not exist" exception NOTE: Bio::DB::RandomAccessI compliant method =cut sub get_Seq_by_accession { my $self = shift; my $id = shift; my $stream = $self->get_Stream_by_accession($id); return $stream->next_seq; } =head2 get_Stream_by_acc () =cut =head2 get_Seq_by_acc Title : get_Seq_by_acc Usage : $seq = $db->get_Seq_by_acc('X77802'); Function: Gets a Bio::Seq object by accession number Returns : A Bio::Seq object Args : accession number (as a string) Throws : "acc does not exist" exception NOTE: Bio::DB::RandomAccessI compliant method =cut sub get_Stream_by_name { my $self = shift; my @ids = @_; my $id = ref($ids[0]) ? $ids[0] : \@ids; Bio::DB::GFF::ID_Iterator->new($self,$id,'name'); } =head2 get_Stream_by_id Title : get_Stream_by_id Usage : $seq = $db->get_Stream_by_id(@ids); Function: Retrieves a stream of Seq objects given their ids Returns : a Bio::SeqIO stream object Args : an array of unique ids/accession numbers, or an array reference NOTE: This is also called get_Stream_by_batch() =cut sub get_Stream_by_id { my $self = shift; my @ids = @_; my $id = ref($ids[0]) ? $ids[0] : \@ids; Bio::DB::GFF::ID_Iterator->new($self,$id,'feature'); } =head2 get_Stream_by_batch () Title : get_Stream_by_batch Usage : $seq = $db->get_Stream_by_batch(@ids); Function: Retrieves a stream of Seq objects given their ids Returns : a Bio::SeqIO stream object Args : an array of unique ids/accession numbers, or an array reference NOTE: This is the same as get_Stream_by_id(). =cut *get_Stream_by_batch = \&get_Stream_by_id; =head2 get_Stream_by_group () Bioperl compatibility. =cut sub get_Stream_by_group { my $self = shift; my @ids = @_; my $id = ref($ids[0]) ? $ids[0] : \@ids; Bio::DB::GFF::ID_Iterator->new($self,$id,'group'); } =head2 all_seqfeatures Title : all_seqfeatures Usage : @features = $db->all_seqfeatures(@args) Function: fetch all the features in the database Returns : an array of features, or an iterator Args : See below Status : public This is equivalent to calling $db-E<gt>features() without any types, and will return all the features in the database. The -merge and -iterator arguments are recognized, and behave the same as described for features(). =cut sub all_seqfeatures { my $self = shift; my ($automerge,$iterator)= rearrange([ [qw(MERGE AUTOMERGE)], 'ITERATOR' ],@_); my @args; push @args,(-merge=>$automerge) if defined $automerge; push @args,(-iterator=>$iterator) if defined $iterator; $self->features(@args); } =head1 Creating and Loading GFF Databases =head2 initialize Title : initialize Usage : $db->initialize(-erase=>$erase,-option1=>value1,-option2=>value2); Function: initialize a GFF database Returns : true if initialization successful Args : a set of named parameters Status : Public This method can be used to initialize an empty database. It takes the following named arguments: -erase A boolean value. If true the database will be wiped clean if it already contains data. Other named arguments may be recognized by subclasses. They become database meta values that control various settable options. As a shortcut (and for backward compatibility) a single true argument is the same as initialize(-erase=E<gt>1). =cut sub initialize { my $self = shift; #$self->do_initialize(1) if @_ == 1 && $_[0]; #why was this line (^) here? I can't see that it actually does anything #one option would be to execute the line and return, but I don't know #why you would want to do that either. my ($erase,$meta) = rearrange(['ERASE'],@_); $meta ||= {}; # initialize (possibly erasing) return unless $self->do_initialize($erase); my @default = $self->default_meta_values; # this is an awkward way of uppercasing the # even-numbered values (necessary for case-insensitive SQL databases) for (my $i=0; $i<@default; $i++) { $default[$i] = uc $default[$i] if !($i % 2); } my %values = (@default,%$meta); foreach (keys %values) { $self->meta($_ => $values{$_}); } 1; } =head2 load_gff Title : load_gff Usage : $db->load_gff($file|$directory|$filehandle); Function: load GFF data into database Returns : count of records loaded Args : a directory, a file, a list of files, or a filehandle Status : Public This method takes a single overloaded argument, which can be any of: =over 4 =item 1. a scalar corresponding to a GFF file on the system A pathname to a local GFF file. Any files ending with the .gz, .Z, or .bz2 suffixes will be transparently decompressed with the appropriate command-line utility. =item 2. an array reference containing a list of GFF files on the system For example ['/home/gff/gff1.gz','/home/gff/gff2.gz'] =item 3. directory path The indicated directory will be searched for all files ending in the suffixes .gff, .gff.gz, .gff.Z or .gff.bz2. =item 4. filehandle An open filehandle from which to read the GFF data. Tied filehandles now work as well. =item 5. a pipe expression A pipe expression will also work. For example, a GFF file on a remote web server can be loaded with an expression like this: $db->load_gff("lynx -dump -source http://stein.cshl.org/gff_test |"); =back If successful, the method will return the number of GFF lines successfully loaded. NOTE:this method used to be called load(), but has been changed. The old method name is also recognized. =cut sub load_gff { my $self = shift; my $file_or_directory = shift || '.'; return $self->do_load_gff($file_or_directory) if ref($file_or_directory) && tied *$file_or_directory; my $tied_stdin = tied(*STDIN); open SAVEIN,"<&STDIN" unless $tied_stdin; local @ARGV = $self->setup_argv($file_or_directory,'gff') or return; # to play tricks with reader my $result = $self->do_load_gff('ARGV'); open STDIN,"<&SAVEIN" unless $tied_stdin; # restore STDIN return $result; } *load = \&load_gff; =head2 load_fasta Title : load_fasta Usage : $db->load_fasta($file|$directory|$filehandle); Function: load FASTA data into database Returns : count of records loaded Args : a directory, a file, a list of files, or a filehandle Status : Public This method takes a single overloaded argument, which can be any of: =over 4 =item 1. scalar corresponding to a FASTA file on the system A pathname to a local FASTA file. Any files ending with the .gz, .Z, or .bz2 suffixes will be transparently decompressed with the appropriate command-line utility. =item 2. array reference containing a list of FASTA files on the system For example ['/home/fasta/genomic.fa.gz','/home/fasta/genomic.fa.gz'] =item 3. path to a directory The indicated directory will be searched for all files ending in the suffixes .fa, .fa.gz, .fa.Z or .fa.bz2. a=item 4. filehandle An open filehandle from which to read the FASTA data. =item 5. pipe expression A pipe expression will also work. For example, a FASTA file on a remote web server can be loaded with an expression like this: $db->load_gff("lynx -dump -source http://stein.cshl.org/fasta_test.fa |"); =back =cut sub load_fasta { my $self = shift; my $file_or_directory = shift || '.'; return $self->load_sequence($file_or_directory) if ref($file_or_directory) && tied *$file_or_directory; my $tied = tied(*STDIN); open SAVEIN,"<&STDIN" unless $tied; local @ARGV = $self->setup_argv($file_or_directory,'fa','dna','fasta') or return; # to play tricks with reader my $result = $self->load_sequence('ARGV'); open STDIN,"<&SAVEIN" unless $tied; # restore STDIN return $result; } =head2 load_sequence_string Title : load_sequence_string Usage : $db->load_sequence_string($id,$dna) Function: load a single DNA entry Returns : true if successfully loaded Args : a raw sequence string (DNA, RNA, protein) Status : Public =cut sub load_sequence_string { my $self = shift; my ($acc,$seq) = @_; my $offset = 0; $self->insert_sequence_chunk($acc,\$offset,\$seq) or return; $self->insert_sequence($acc,$offset,$seq) or return; 1; } sub setup_argv { my $self = shift; my $file_or_directory = shift; my @suffixes = @_; no strict 'refs'; # so that we can call fileno() on the argument my @argv; if (-d $file_or_directory) { @argv = map { glob("$file_or_directory/*.{$_,$_.gz,$_.Z,$_.bz2}")} @suffixes; }elsif (my $fd = fileno($file_or_directory)) { open STDIN,"<&=$fd" or $self->throw("Can't dup STDIN"); @argv = '-'; } elsif (ref $file_or_directory) { @argv = @$file_or_directory; } else { @argv = $file_or_directory; } foreach (@argv) { if (/\.gz$/) { $_ = "gunzip -c $_ |"; } elsif (/\.Z$/) { $_ = "uncompress -c $_ |"; } elsif (/\.bz2$/) { $_ = "bunzip2 -c $_ |"; } } @argv; } =head2 lock_on_load Title : lock_on_load Usage : $lock = $db->lock_on_load([$lock]) Function: set write locking during load Returns : current value of lock-on-load flag Args : new value of lock-on-load-flag Status : Public This method is honored by some of the adaptors. If the value is true, the tables used by the GFF modules will be locked for writing during loads and inaccessible to other processes. =cut sub lock_on_load { my $self = shift; my $d = $self->{lock}; $self->{lock} = shift if @_; $d; } =head2 meta Title : meta Usage : $value = $db->meta($name [,$newval]) Function: get or set a meta variable Returns : a string Args : meta variable name and optionally value Status : abstract Get or set a named metavalues for the database. Metavalues can be used for database-specific settings. By default, this method does nothing! =cut sub meta { my $self = shift; my ($name,$value) = @_; return; } =head2 default_meta_values Title : default_meta_values Usage : %values = $db->default_meta_values Function: empty the database Returns : a list of tag=>value pairs Args : none Status : protected This method returns a list of tag=E<gt>value pairs that contain default meta information about the database. It is invoked by initialize() to write out the default meta values. The base class version returns an empty list. For things to work properly, meta value names must be UPPERCASE. =cut sub default_meta_values { my $self = shift; return (); } =head2 error Title : error Usage : $db->error( [$new error] ); Function: read or set error message Returns : error message Args : an optional argument to set the error message Status : Public This method can be used to retrieve the last error message. Errors are not reset to empty by successful calls, so contents are only valid immediately after an error condition has been detected. =cut sub error { my $self = shift; my $g = $self->{error}; $self->{error} = join '',@_ if @_; $g; } =head2 debug Title : debug Usage : $db->debug( [$flag] ); Function: read or set debug flag Returns : current value of debug flag Args : new debug flag (optional) Status : Public This method can be used to turn on debug messages. The exact nature of those messages depends on the adaptor in use. =cut sub debug { my $self = shift; my $g = $self->{debug}; $self->{debug} = shift if @_; $g; } =head2 automerge Title : automerge Usage : $db->automerge( [$new automerge] ); Function: get or set automerge value Returns : current value (boolean) Args : an optional argument to set the automerge value Status : Public By default, this module will use the aggregators to merge groups into single composite objects. This default can be changed to false by calling automerge(0). =cut sub automerge { my $self = shift; my $g = $self->{automerge}; $self->{automerge} = shift if @_; $g; } =head2 attributes Title : attributes Usage : @attributes = $db->attributes($id,$name) Function: get the "attributres" on a particular feature Returns : an array of string Args : feature ID Status : public Some GFF version 2 files use the groups column to store a series of attribute/value pairs. In this interpretation of GFF, the first such pair is treated as the primary group for the feature; subsequent pairs are treated as attributes. Two attributes have special meaning: "Note" is for backward compatibility and is used for unstructured text remarks. "Alias" is considered as a synonym for the feature name. If no name is provided, then attributes() returns a flattened hash, of attribute=E<gt>value pairs. This lets you do: %attributes = $db->attributes($id); Normally, attributes() will be called by the feature: @notes = $feature->attributes('Note'); In a scalar context, attributes() returns the first value of the attribute if a tag is present, otherwise a hash reference in which the keys are attribute names and the values are anonymous arrays containing the values. =cut sub attributes { my $self = shift; my ($id,$tag) = @_; my @result = $self->do_attributes($id,$tag) or return; return @result if wantarray; # what to do in an array context return $result[0] if $tag; my %result; while (my($key,$value) = splice(@result,0,2)) { push @{$result{$key}},$value; } return \%result; } =head2 fast_queries Title : fast_queries Usage : $flag = $db->fast_queries([$flag]) Function: turn on and off the "fast queries" option Returns : a boolean Args : a boolean flag (optional) Status : public The mysql database driver (and possibly others) support a "fast" query mode that caches results on the server side. This makes queries come back faster, particularly when creating iterators. The downside is that while iterating, new queries will die with a "command synch" error. This method turns the feature on and off. For databases that do not support a fast query, this method has no effect. =cut # override this method in order to set the mysql_use_result attribute, which is an obscure # but extremely powerful optimization for both performance and memory. sub fast_queries { my $self = shift; my $d = $self->{fast_queries}; $self->{fast_queries} = shift if @_; $d; } =head2 add_aggregator Title : add_aggregator Usage : $db->add_aggregator($aggregator) Function: add an aggregator to the list Returns : nothing Args : an aggregator Status : public This method will append an aggregator to the end of the list of registered aggregators. Three different argument types are accepted: 1) a Bio::DB::GFF::Aggregator object -- will be added 2) a string in the form "aggregator_name{subpart1,subpart2,subpart3/main_method}" -- will be turned into a Bio::DB::GFF::Aggregator object (the /main_method part is optional). 3) a valid Perl token -- will be turned into a Bio::DB::GFF::Aggregator subclass, where the token corresponds to the subclass name. =cut sub add_aggregator { my $self = shift; my $aggregator = shift; my $list = $self->{aggregators} ||= []; if (ref $aggregator) { # an object @$list = grep {$_->get_method ne $aggregator->get_method} @$list; push @$list,$aggregator; } elsif ($aggregator =~ /^(\w+)\{([^\/\}]+)\/?(.*)\}$/) { my($agg_name,$subparts,$mainpart) = ($1,$2,$3); my @subparts = split /,\s*/,$subparts; my @args = (-method => $agg_name, -sub_parts => \@subparts); push @args,(-main_method => $mainpart) if $mainpart; warn "making an aggregator with (@args), subparts = @subparts" if $self->debug; push @$list,Bio::DB::GFF::Aggregator->new(@args); } else { my $class = "Bio::DB::GFF::Aggregator::\L${aggregator}\E"; eval "require $class"; $self->throw("Unable to load $aggregator aggregator: $@") if $@; push @$list,$class->new(); } } =head2 aggregators Title : aggregators Usage : $db->aggregators([@new_aggregators]); Function: retrieve list of aggregators Returns : list of aggregators Args : a list of aggregators to set (optional) Status : public This method will get or set the list of aggregators assigned to the database. If 1 or more arguments are passed, the existing set will be cleared. =cut sub aggregators { my $self = shift; my $d = $self->{aggregators}; if (@_) { $self->clear_aggregators; $self->add_aggregator($_) foreach @_; } return unless $d; return @$d; } =head2 clear_aggregators Title : clear_aggregators Usage : $db->clear_aggregators Function: clears list of aggregators Returns : nothing Args : none Status : public This method will clear the aggregators stored in the database object. Use aggregators() or add_aggregator() to add some back. =cut sub clear_aggregators { shift->{aggregators} = [] } =head1 Methods for use by Subclasses The following methods are chiefly of interest to subclasses and are not intended for use by end programmers. =head2 abscoords Title : abscoords Usage : $db->abscoords($name,$class,$refseq) Function: finds position of a landmark in reference coordinates Returns : ($ref,$class,$start,$stop,$strand) Args : name and class of landmark Status : public This method is called by Bio::DB::GFF::RelSegment to obtain the absolute coordinates of a sequence landmark. The arguments are the name and class of the landmark. If successful, abscoords() returns the ID of the reference sequence, its class, its start and stop positions, and the orientation of the reference sequence's coordinate system ("+" for forward strand, "-" for reverse strand). If $refseq is present in the argument list, it forces the query to search for the landmark in a particular reference sequence. =cut sub abscoords { my $self = shift; my ($name,$class,$refseq) = @_; $class ||= $self->{default_class}; $self->get_abscoords($name,$class,$refseq); } =head1 Protected API The following methods are not intended for public consumption, but are intended to be overridden/implemented by adaptors. =head2 default_aggregators Title : default_aggregators Usage : $db->default_aggregators; Function: retrieve list of aggregators Returns : array reference containing list of aggregator names Args : none Status : protected This method (which is intended to be overridden by adaptors) returns a list of standard aggregators to be applied when no aggregators are specified in the constructor. =cut sub default_aggregators { my $self = shift; return ['processed_transcript','alignment']; } =head2 do_load_gff Title : do_load_gff Usage : $db->do_load_gff($handle) Function: load a GFF input stream Returns : number of features loaded Args : A filehandle. Status : protected This method is called to load a GFF data stream. The method will read GFF features from E<lt>E<gt> and load them into the database. On exit the method must return the number of features loaded. Note that the method is responsible for parsing the GFF lines. This is to allow for differences in the interpretation of the "group" field, which are legion. You probably want to use load_gff() instead. It is more flexible about the arguments it accepts. =cut # load from <> sub do_load_gff { my $self = shift; my $io_handle = shift; local $self->{gff3_flag} = 0; $self->setup_load(); my $fasta_sequence_id; while (<$io_handle>) { chomp; $self->{gff3_flag}++ if /^\#\#gff-version\s+3/; if (/^>(\S+)/) { # uh oh, sequence coming $fasta_sequence_id = $1; last; } if (/^\#\#\s*sequence-region\s+(\S+)\s+(\d+)\s+(\d+)/i) { # header line $self->load_gff_line( { ref => $1, class => 'Sequence', source => 'reference', method => 'Component', start => $2, stop => $3, score => undef, strand => undef, phase => undef, gclass => 'Sequence', gname => $1, tstart => undef, tstop => undef, attributes => [], } ); next; } next if /^\#/; my ($ref,$source,$method,$start,$stop,$score,$strand,$phase,$group) = split "\t"; next unless defined($ref) && defined($method) && defined($start) && defined($stop); foreach (\$score,\$strand,\$phase) { undef $$_ if $$_ eq '.'; } my ($gclass,$gname,$tstart,$tstop,$attributes) = $self->split_group($group,$self->{gff3_flag}); # no standard way in the GFF file to denote the class of the reference sequence -- drat! # so we invoke the factory to do it my $class = $self->refclass($ref); # call subclass to do the dirty work if ($start > $stop) { ($start,$stop) = ($stop,$start); if ($strand eq '+') { $strand = '-'; } elsif ($strand eq '-') { $strand = '+'; } } $self->load_gff_line({ref => $ref, class => $class, source => $source, method => $method, start => $start, stop => $stop, score => $score, strand => $strand, phase => $phase, gclass => $gclass, gname => $gname, tstart => $tstart, tstop => $tstop, attributes => $attributes} ); } my $result = $self->finish_load(); $result += $self->load_sequence($io_handle,$fasta_sequence_id) if defined $fasta_sequence_id; $result; } =head2 load_sequence Title : load_sequence Usage : $db->load_sequence($handle [,$id]) Function: load a FASTA data stream Returns : number of sequences Args : a filehandle and optionally the ID of the first sequence in the stream. Status : protected You probably want to use load_fasta() instead. The $id argument is a hack used to switch from GFF loading to FASTA loading when load_gff() discovers FASTA data hiding at the bottom of the GFF file (as Artemis does). =cut sub load_sequence { my $self = shift; my $io_handle = shift; my $id = shift; # hack for GFF files that contain fasta data # read fasta file(s) from ARGV my ($seq,$offset,$loaded) = (undef,0,0); while (<$io_handle>) { chomp; if (/^>(\S+)/) { $self->insert_sequence($id,$offset,$seq) if $id; $id = $1; $offset = 0; $seq = ''; $loaded++; } else { $seq .= $_; $self->insert_sequence_chunk($id,\$offset,\$seq); } } $self->insert_sequence($id,$offset,$seq) if $id; $loaded+0; } sub insert_sequence_chunk { my $self = shift; my ($id,$offsetp,$seqp) = @_; if (my $cs = $self->dna_chunk_size) { while (length($$seqp) >= $cs) { my $chunk = substr($$seqp,0,$cs); $self->insert_sequence($id,$$offsetp,$chunk); $$offsetp += length($chunk); substr($$seqp,0,$cs) = ''; } } return 1; # the calling routine may expect success or failure } # used to store big pieces of DNA in itty bitty pieces sub dna_chunk_size { return 0; } sub insert_sequence { my $self = shift; my($id,$offset,$seq) = @_; $self->throw('insert_sequence(): must be defined in subclass'); } # This is the default class for reference points. Defaults to Sequence. sub default_class { my $self = shift; my $d = exists($self->{default_class}) ? $self->{default_class} : 'Sequence'; $self->{default_class} = shift if @_; $d; } # gets name of the reference sequence, and returns its class # currently just calls default_class sub refclass { my $self = shift; my $name = shift; return $self->default_class; } =head2 setup_load Title : setup_load Usage : $db->setup_load Function: called before load_gff_line() Returns : void Args : none Status : abstract This abstract method gives subclasses a chance to do any schema-specific initialization prior to loading a set of GFF records. It must be implemented by a subclass. =cut sub setup_load { # default, do nothing } =head2 finish_load Title : finish_load Usage : $db->finish_load Function: called after load_gff_line() Returns : number of records loaded Args : none Status :abstract This method gives subclasses a chance to do any schema-specific cleanup after loading a set of GFF records. =cut sub finish_load { # default, do nothing } =head2 load_gff_line Title : load_gff_line Usage : $db->load_gff_line(@args) Function: called to load one parsed line of GFF Returns : true if successfully inserted Args : see below Status : abstract This abstract method is called once per line of the GFF and passed a hashref containing parsed GFF fields. The fields are: {ref => $ref, class => $class, source => $source, method => $method, start => $start, stop => $stop, score => $score, strand => $strand, phase => $phase, gclass => $gclass, gname => $gname, tstart => $tstart, tstop => $tstop, attributes => $attributes} =cut sub load_gff_line { shift->throw("load_gff_line(): must be implemented by an adaptor"); } =head2 do_initialize Title : do_initialize Usage : $db->do_initialize([$erase]) Function: initialize and possibly erase database Returns : true if successful Args : optional erase flag Status : protected This method implements the initialize() method described above, and takes the same arguments. =cut sub do_initialize { shift->throw('do_initialize(): must be implemented by an adaptor'); } =head2 dna Title : dna Usage : $db->dna($id,$start,$stop,$class) Function: return the raw DNA string for a segment Returns : a raw DNA string Args : id of the sequence, its class, start and stop positions Status : public This method is invoked by Bio::DB::GFF::Segment to fetch the raw DNA sequence. Arguments: -name sequence name -start start position -stop stop position -class sequence class If start and stop are both undef, then the entire DNA is retrieved. So to fetch the whole dna, call like this: $db->dna($name_of_sequence); or like this: $db->dna(-name=>$name_of_sequence,-class=>$class_of_sequence); NOTE: you will probably prefer to create a Segment and then invoke its dna() method. =cut # call to return the DNA string for the indicated region # real work is done by get_dna() sub dna { my $self = shift; my ($id,$start,$stop,$class) = rearrange([ [qw(NAME ID REF REFSEQ)], qw(START), [qw(STOP END)], 'CLASS', ],@_); # return unless defined $start && defined $stop; $self->get_dna($id,$start,$stop,$class); } sub features_in_range { my $self = shift; my ($range_type,$refseq,$class,$start,$stop,$types,$parent,$sparse,$automerge,$iterator,$other) = rearrange([ [qw(RANGE_TYPE)], [qw(REF REFSEQ)], qw(CLASS), qw(START), [qw(STOP END)], [qw(TYPE TYPES)], qw(PARENT), [qw(RARE SPARSE)], [qw(MERGE AUTOMERGE)], 'ITERATOR' ],@_); $other ||= {}; $automerge = $types && $self->automerge unless defined $automerge; $self->throw("range type must be one of {". join(',',keys %valid_range_types). "}\n") unless $valid_range_types{lc $range_type}; $self->_features({ rangetype => lc $range_type, refseq => $refseq, refclass => $class, start => $start, stop => $stop, types => $types }, { sparse => $sparse, automerge => $automerge, iterator => $iterator, %$other, }, $parent); } =head2 get_dna Title : get_dna Usage : $db->get_dna($id,$start,$stop,$class) Function: get DNA for indicated segment Returns : the dna string Args : sequence ID, start, stop and class Status : protected If start E<gt> stop and the sequence is nucleotide, then this method should return the reverse complement. The sequence class may be ignored by those databases that do not recognize different object types. =cut sub get_dna { my $self = shift; my ($id,$start,$stop,$class,) = @_; $self->throw("get_dna() must be implemented by an adaptor"); } =head2 get_features Title : get_features Usage : $db->get_features($search,$options,$callback) Function: get list of features for a region Returns : count of number of features retrieved Args : see below Status : protected The first argument is a hash reference containing search criteria for retrieving features. It contains the following keys: rangetype One of "overlaps", "contains" or "contained_in". Indicates the type of range query requested. refseq ID of the landmark that establishes the absolute coordinate system. refclass Class of this landmark. Can be ignored by implementations that don't recognize such distinctions. start Start of the range, inclusive. stop Stop of the range, inclusive. types Array reference containing the list of annotation types to fetch from the database. Each annotation type is an array reference consisting of [source,method]. The second argument is a hash reference containing certain options that affect the way information is retrieved: sort_by_group A flag. If true, means that the returned features should be sorted by the group that they're in. sparse A flag. If true, means that the expected density of the features is such that it will be more efficient to search by type rather than by range. If it is taking a long time to fetch features, give this a try. binsize A true value will create a set of artificial features whose start and stop positions indicate bins of the given size, and whose scores are the number of features in the bin. The class of the feature will be set to "bin", and its name to "method:source". This is a handy way of generating histograms of feature density. The third argument, the $callback, is a code reference to which retrieved features are passed. It is described in more detail below. This routine is responsible for getting arrays of GFF data out of the database and passing them to the callback subroutine. The callback does the work of constructing a Bio::DB::GFF::Feature object out of that data. The callback expects a list of 13 fields: $refseq The reference sequence $start feature start $stop feature stop $source feature source $method feature method $score feature score $strand feature strand $phase feature phase $groupclass group class (may be undef) $groupname group ID (may be undef) $tstart target start for similarity hits (may be undef) $tstop target stop for similarity hits (may be undef) $feature_id A unique feature ID (may be undef) These fields are in the same order as the raw GFF file, with the exception that the group column has been parsed into group class and group name fields. The feature ID, if provided, is a unique identifier of the feature line. The module does not depend on this ID in any way, but it is available via Bio::DB::GFF-E<gt>id() if wanted. In the dbi::mysql and dbi::mysqlopt adaptor, the ID is a unique row ID. In the acedb adaptor it is not used. =cut sub get_features{ my $self = shift; my ($search,$options,$callback) = @_; $self->throw("get_features() must be implemented by an adaptor"); } =head2 _feature_by_name Title : _feature_by_name Usage : $db->_feature_by_name($class,$name,$location,$callback) Function: get a list of features by name and class Returns : count of number of features retrieved Args : name of feature, class of feature, and a callback Status : abstract This method is used internally. The callback arguments are the same as those used by make_feature(). This method must be overidden by subclasses. =cut sub _feature_by_name { my $self = shift; my ($class,$name,$location,$callback) = @_; $self->throw("_feature_by_name() must be implemented by an adaptor"); } sub _feature_by_attribute { my $self = shift; my ($attributes,$callback) = @_; $self->throw("_feature_by_name() must be implemented by an adaptor"); } =head2 _feature_by_id Title : _feature_by_id Usage : $db->_feature_by_id($ids,$type,$callback) Function: get a feature based Returns : count of number of features retrieved Args : arrayref to feature IDs to fetch Status : abstract This method is used internally to fetch features either by their ID or their group ID. $ids is a arrayref containing a list of IDs, $type is one of "feature" or "group", and $callback is a callback. The callback arguments are the same as those used by make_feature(). This method must be overidden by subclasses. =cut sub _feature_by_id { my $self = shift; my ($ids,$type,$callback) = @_; $self->throw("_feature_by_id() must be implemented by an adaptor"); } =head2 overlapping_features Title : overlapping_features Usage : $db->overlapping_features(@args) Function: get features that overlap the indicated range Returns : a list of Bio::DB::GFF::Feature objects Args : see below Status : public This method is invoked by Bio::DB::GFF::Segment-E<gt>features() to find the list of features that overlap a given range. It is generally preferable to create the Segment first, and then fetch the features. This method takes set of named arguments: -refseq ID of the reference sequence -class Class of the reference sequence -start Start of the desired range in refseq coordinates -stop Stop of the desired range in refseq coordinates -types List of feature types to return. Argument is an array reference containing strings of the format "method:source" -parent A parent Bio::DB::GFF::Segment object, used to create relative coordinates in the generated features. -rare Turn on an optimization suitable for a relatively rare feature type, where it will be faster to filter by feature type first and then by position, rather than vice versa. -merge Whether to apply aggregators to the generated features. -iterator Whether to return an iterator across the features. If -iterator is true, then the method returns a single scalar value consisting of a Bio::SeqIO object. You can call next_seq() repeatedly on this object to fetch each of the features in turn. If iterator is false or absent, then all the features are returned as a list. Currently aggregation is disabled when iterating over a series of features. Types are indicated using the nomenclature "method:source". Either of these fields can be omitted, in which case a wildcard is used for the missing field. Type names without the colon (e.g. "exon") are interpreted as the method name and a source wild card. Regular expressions are allowed in either field, as in: "similarity:BLAST.*". =cut # call to return the features that overlap the named region # real work is done by get_features sub overlapping_features { my $self = shift; $self->features_in_range(-range_type=>'overlaps',@_); } =head2 contained_features Title : contained_features Usage : $db->contained_features(@args) Function: get features that are contained within the indicated range Returns : a list of Bio::DB::GFF::Feature objects Args : see overlapping_features() Status : public This call is similar to overlapping_features(), except that it only retrieves features whose end points are completely contained within the specified range. Generally you will want to fetch a Bio::DB::GFF::Segment object and call its contained_features() method rather than call this directly. =cut # The same, except that it only returns features that are completely contained within the # range (much faster usually) sub contained_features { my $self = shift; $self->features_in_range(-range_type=>'contains',@_); } =head2 contained_in Title : contained_in Usage : @features = $s->contained_in(@args) Function: get features that contain this segment Returns : a list of Bio::DB::GFF::Feature objects Args : see features() Status : Public This is identical in behavior to features() except that it returns only those features that completely contain the segment. =cut sub contained_in { my $self = shift; $self->features_in_range(-range_type=>'contained_in',@_); } =head2 get_abscoords Title : get_abscoords Usage : $db->get_abscoords($name,$class,$refseq) Function: get the absolute coordinates of sequence with name & class Returns : ($absref,$absstart,$absstop,$absstrand) Args : name and class of the landmark Status : protected Given the name and class of a genomic landmark, this function returns a four-element array consisting of: $absref the ID of the reference sequence that contains this landmark $absstart the position at which the landmark starts $absstop the position at which the landmark stops $absstrand the strand of the landmark, relative to the reference sequence If $refseq is provided, the function searches only within the specified reference sequence. =cut sub get_abscoords { my $self = shift; my ($name,$class,$refseq) = @_; $self->throw("get_abscoords() must be implemented by an adaptor"); } =head2 get_types Title : get_types Usage : $db->get_types($absref,$class,$start,$stop,$count) Function: get list of all feature types on the indicated segment Returns : list or hash of Bio::DB::GFF::Typename objects Args : see below Status : protected Arguments are: $absref the ID of the reference sequence $class the class of the reference sequence $start the position to start counting $stop the position to end counting $count a boolean indicating whether to count the number of occurrences of each feature type If $count is true, then a hash is returned. The keys of the hash are feature type names in the format "method:source" and the values are the number of times a feature of this type overlaps the indicated segment. Otherwise, the call returns a set of Bio::DB::GFF::Typename objects. If $start or $stop are undef, then all features on the indicated segment are enumerated. If $absref is undef, then the call returns all feature types in the database. =cut sub get_types { my $self = shift; my ($refseq,$class,$start,$stop,$count,$types) = @_; $self->throw("get_types() must be implemented by an adaptor"); } =head2 make_feature Title : make_feature Usage : $db->make_feature(@args) Function: Create a Bio::DB::GFF::Feature object from string data Returns : a Bio::DB::GFF::Feature object Args : see below Status : internal This takes 14 arguments (really!): $parent A Bio::DB::GFF::RelSegment object $group_hash A hashref containing unique list of GFF groups $refname The name of the reference sequence for this feature $refclass The class of the reference sequence for this feature $start Start of feature $stop Stop of feature $source Feature source field $method Feature method field $score Feature score field $strand Feature strand $phase Feature phase $group_class Class of feature group $group_name Name of feature group $tstart For homologies, start of hit on target $tstop Stop of hit on target The $parent argument, if present, is used to establish relative coordinates in the resulting Bio::DB::Feature object. This allows one feature to generate a list of other features that are relative to its coordinate system (for example, finding the coordinates of the second exon relative to the coordinates of the first). The $group_hash allows the group_class/group_name strings to be turned into rich database objects via the make_obect() method (see above). Because these objects may be expensive to create, $group_hash is used to uniquefy them. The index of this hash is the composite key {$group_class,$group_name,$tstart,$tstop}. Values are whatever object is returned by the make_object() method. The remainder of the fields are taken from the GFF line, with the exception that "Target" features, which contain information about the target of a homology search, are parsed into their components. =cut # This call is responsible for turning a line of GFF into a # feature object. # The $parent argument is a Bio::DB::GFF::Segment object and is used # to establish the coordinate system for the new feature. # The $group_hash argument is an hash ref that holds previously- # generated group objects. # Other arguments are taken right out of the GFF table. sub make_feature { my $self = shift; my ($parent,$group_hash, # these arguments provided by generic mechanisms $srcseq, # the rest is provided by adaptor $start,$stop, $source,$method, $score,$strand,$phase, $group_class,$group_name, $tstart,$tstop, $db_id,$group_id) = @_; return unless $srcseq; # return undef if called with no arguments. This behavior is used for # on-the-fly aggregation. my $group; # undefined if (defined $group_class && defined $group_name) { $tstart ||= ''; $tstop ||= ''; if ($group_hash) { $group = $group_hash->{$group_class,$group_name,$tstart,$tstop} ||= $self->make_object($group_class,$group_name,$tstart,$tstop); } else { $group = $self->make_object($group_class,$group_name,$tstart,$tstop); } } # fix for some broken GFF files # unfortunately - has undesired side effects # if (defined $tstart && defined $tstop && !defined $strand) { # $strand = $tstart <= $tstop ? '+' : '-'; # } if (ref $parent) { # note that the src sequence is ignored return Bio::DB::GFF::Feature->new_from_parent($parent,$start,$stop, $method,$source, $score,$strand,$phase, $group,$db_id,$group_id, $tstart,$tstop); } else { return Bio::DB::GFF::Feature->new($self,$srcseq, $start,$stop, $method,$source, $score,$strand,$phase, $group,$db_id,$group_id, $tstart,$tstop); } } sub make_aggregated_feature { my $self = shift; my ($accumulated_features,$parent,$aggregators) = splice(@_,0,3); my $feature = $self->make_feature($parent,undef,@_); return [$feature] if $feature && !$feature->group; # if we have accumulated features and either: # (1) make_feature() returned undef, indicated very end or # (2) the current group is different from the previous one local $^W = 0; # irritating uninitialized value warning in next statement if (@$accumulated_features && (!defined($feature) || ($accumulated_features->[-1]->group ne $feature->group))) { foreach my $a (@$aggregators) { # last aggregator gets first shot $a->aggregate($accumulated_features,$self) or next; } my @result = @$accumulated_features; @$accumulated_features = $feature ? ($feature) : (); return unless @result; return \@result ; } push @$accumulated_features,$feature; return; } =head2 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. =cut # turn feature types in the format "method:source" into a list of [method,source] refs sub parse_types { my $self = shift; return [] if !@_ or !defined($_[0]); return $_[0] if ref $_[0] eq 'ARRAY' && ref $_[0][0]; my @types = ref($_[0]) ? @{$_[0]} : @_; my @type_list = map { [split(':',$_,2)] } @types; return \@type_list; } =head2 make_match_sub Title : make_match_sub Usage : $db->make_match_sub($types) Function: creates a subroutine used for filtering features Returns : a code reference Args : a list of parsed type names Status : protected This method is used internally to generate a code subroutine that will accept or reject a feature based on its method and source. It takes an array of parsed type names in the format returned by parse_types(), and generates an anonymous subroutine. The subroutine takes a single Bio::DB::GFF::Feature object and returns true if the feature matches one of the desired feature types, and false otherwise. =cut # a subroutine that matches features indicated by list of types sub make_match_sub { my $self = shift; my $types = shift; return sub { 1 } unless ref $types && @$types; my @expr; for my $type (@$types) { my ($method,$source) = @$type; $method ||= '.*'; $source = $source ? ":$source" : "(?::.+)?"; push @expr,"${method}${source}"; } my $expr = join '|',@expr; return $self->{match_subs}{$expr} if $self->{match_subs}{$expr}; my $sub =<<END; sub { my \$feature = shift or return; return \$feature->type =~ /^($expr)\$/i; } END warn "match sub: $sub\n" if $self->debug; my $compiled_sub = eval $sub; $self->throw($@) if $@; return $self->{match_subs}{$expr} = $compiled_sub; } =head2 make_object Title : make_object Usage : $db->make_object($class,$name,$start,$stop) Function: creates a feature object Returns : a feature object Args : see below Status : protected This method is called to make an object from the GFF "group" field. By default, all Target groups are turned into Bio::DB::GFF::Homol objects, and everything else becomes a Bio::DB::GFF::Featname. However, adaptors are free to override this method to generate more interesting objects, such as true BioPerl objects, or Acedb objects. Arguments are: $name database ID for object $class class of object $start for similarities, start of match inside object $stop for similarities, stop of match inside object =cut # abstract call to turn a feature into an object, given its class and name sub make_object { my $self = shift; my ($class,$name,$start,$stop) = @_; return Bio::DB::GFF::Homol->new($self,$class,$name,$start,$stop) if defined $start and length $start; return Bio::DB::GFF::Featname->new($class,$name); } =head2 do_attributes Title : do_attributes Usage : $db->do_attributes($id [,$tag]); Function: internal method to retrieve attributes given an id and tag Returns : a list of Bio::DB::GFF::Feature objects Args : a feature id and a attribute tag (optional) Status : protected This method is overridden by subclasses in order to return a list of attributes. If called with a tag, returns the value of attributes of that tag type. If called without a tag, returns a flattened array of (tag=E<gt>value) pairs. A particular tag can be present multiple times. =cut sub do_attributes { my $self = shift; my ($id,$tag) = @_; return (); } =head1 Internal Methods The following methods are internal to Bio::DB::GFF and are not guaranteed to remain the same. =head2 _features Title : _features Usage : $db->_features($search,$options,$parent) Function: internal method Returns : a list of Bio::DB::GFF::Feature objects Args : see below Status : internal This is an internal method that is called by overlapping_features(), contained_features() and features() to create features based on a parent segment's coordinate system. It takes three arguments, a search options hashref, an options hashref, and a parent segment. The search hashref contains the following keys: rangetype One of "overlaps", "contains" or "contained_in". Indicates the type of range query requested. refseq reference sequence ID refclass reference sequence class start start of range stop stop of range types arrayref containing list of types in "method:source" form The options hashref contains zero or more of the following keys: sparse turn on optimizations for a rare feature automerge if true, invoke aggregators to merge features iterator if true, return an iterator The $parent argument is a scalar object containing a Bio::DB::GFF::RelSegment object or descendent. =cut #' sub _features { my $self = shift; my ($search,$options,$parent) = @_; (@{$search}{qw(start stop)}) = (@{$search}{qw(stop start)}) if defined($search->{start}) && $search->{start} > $search->{stop}; my $types = $self->parse_types($search->{types}); # parse out list of types my @aggregated_types = @$types; # keep a copy # allow the aggregators to operate on the original my @aggregators; if ($options->{automerge}) { for my $a ($self->aggregators) { $a = $a->clone if $options->{iterator}; unshift @aggregators,$a if $a->disaggregate(\@aggregated_types,$self); } } if ($options->{iterator}) { my @accumulated_features; my $callback = $options->{automerge} ? sub { $self->make_aggregated_feature(\@accumulated_features,$parent,\@aggregators,@_) } : sub { [$self->make_feature($parent,undef,@_)] }; return $self->get_features_iterator({ %$search, types => \@aggregated_types }, { %$options, sort_by_group => $options->{automerge} }, $callback ); } my %groups; # cache the groups we create to avoid consuming too much unecessary memory my $features = []; my $callback = sub { push @$features,$self->make_feature($parent,\%groups,@_) }; $self->get_features({ %$search, types => \@aggregated_types }, $options, $callback); if ($options->{automerge}) { warn "aggregating...\n" if $self->debug; foreach my $a (@aggregators) { # last aggregator gets first shot warn "Aggregator $a:\n" if $self->debug; $a->aggregate($features,$self); } } @$features; } =head2 get_features_iterator Title : get_features_iterator Usage : $db->get_features_iterator($search,$options,$callback) Function: get an iterator on a features query Returns : a Bio::SeqIO object Args : as per get_features() Status : Public This method takes the same arguments as get_features(), but returns an iterator that can be used to fetch features sequentially, as per Bio::SeqIO. Internally, this method is simply a front end to range_query(). The latter method constructs and executes the query, returning a statement handle. This routine passes the statement handle to the constructor for the iterator, along with the callback. =cut sub get_features_iterator { my $self = shift; my ($search,$options,$callback) = @_; $self->throw('feature iteration is not implemented in this adaptor'); } =head2 split_group Title : split_group Usage : $db->split_group($group_field,$gff3_flag) Function: parse GFF group field Returns : ($gclass,$gname,$tstart,$tstop,$attributes) Args : the gff group column and a flag indicating gff3 compatibility Status : internal This is a method that is called by load_gff_line to parse out the contents of one or more group fields. It returns the class of the group, its name, the start and stop of the target, if any, and an array reference containing any attributes that were stuck into the group field, in [attribute_name,attribute_value] format. =cut sub split_group { my $self = shift; my ($group,$gff3) = @_; if ($gff3) { my @groups = split /[;&]/,$group; # so easy! return $self->_split_gff3_group(@groups); } else { # handle group parsing # protect embedded semicolons in the group; there must be faster/more elegant way # to do this. $group =~ s/\\;/$;/g; while ($group =~ s/( \"[^\"]*);([^\"]*\")/$1$;$2/) { 1 } my @groups = split(/\s*;\s*/,$group); foreach (@groups) { s/$;/;/g } return $self->_split_gff2_group(@groups); } } =head2 _split_gff2_group This is an internal method called by split_group(). =cut sub _split_gff2_group { my $self = shift; my @groups = @_; my ($gclass,$gname,$tstart,$tstop,@attributes); for (@groups) { my ($tag,$value) = /^(\S+)(?:\s+(.+))?/; $value ||= ''; if ($value =~ /^\"(.+)\"$/) { #remove quotes $value = $1; } $value =~ s/\\t/\t/g; $value =~ s/\\r/\r/g; # Any additional groups become part of the attributes hash # For historical reasons, the tag "Note" is treated as an # attribute, even if it is the only group. $tag ||= ''; if ($tag eq 'Note' or ($gclass && $gname)) { push @attributes,[$tag => $value]; } # if the tag eq 'Target' then the class name is embedded in the ID # (the GFF format is obviously screwed up here) elsif ($tag eq 'Target' && /([^:\"\s]+):([^\"\s]+)/) { ($gclass,$gname) = ($1,$2); ($tstart,$tstop) = / (\d+) (\d+)/; } elsif (!$value) { push @attributes,[Note => $tag]; # e.g. "Confirmed_by_EST" } # otherwise, the tag and value correspond to the # group class and name else { ($gclass,$gname) = ($tag,$value); } } return ($gclass,$gname,$tstart,$tstop,\@attributes); } =head2 _split_gff3_group This is called internally from split_group(). =cut sub _split_gff3_group { my $self = shift; my @groups = @_; my ($gclass,$gname,$tstart,$tstop,@attributes); for my $group (@groups) { my ($tag,$value) = split /=/,$group; $tag = unescape($tag); my @values = map {unescape($_)} split /,/,$value; if ($tag eq 'Parent') { $gclass = 'Sequence'; $gname = shift @values; } elsif ($tag eq 'ID') { $gclass = 'Sequence'; $gname = shift @values; } elsif ($tag eq 'Target') { $gclass = 'Sequence'; ($gname,$tstart,$tstop) = split /\s+/,shift @values; } push @attributes,[$tag=>$_] foreach @values; } return ($gclass,$gname,$tstart,$tstop,\@attributes); } =head2 _delete_features(), _delete_groups(),_delete() Title : _delete_features(), _delete_groups(),_delete() Usage : $count = $db->_delete_features(@feature_ids) $count = $db->_delete_groups(@group_ids) $count = $db->_delete(\%delete_spec) Function: low-level feature/group deleter Returns : count of groups removed Args : list of feature or group ids removed Status : for implementation by subclasses These methods need to be implemented in adaptors. For _delete_features and _delete_groups, the arguments are a list of feature or group IDs to remove. For _delete(), the argument is a hashref with the three keys 'segments', 'types' and 'force'. The first contains an arrayref of Bio::DB::GFF::RelSegment objects to delete (all FEATURES within the segment are deleted). The second contains an arrayref of [method,source] feature types to delete. The two are ANDed together. If 'force' has a true value, this forces the operation to continue even if it would delete all features. =cut sub _delete_features { my $self = shift; my @feature_ids = @_; $self->throw('_delete_features is not implemented in this adaptor'); } sub _delete_groups { my $self = shift; my @group_ids = @_; $self->throw('_delete_groups is not implemented in this adaptor'); } sub _delete { my $self = shift; my $delete_options = shift; $self->throw('_delete is not implemented in this adaptor'); } sub unescape { my $v = shift; $v =~ tr/+/ /; $v =~ s/%([0-9a-fA-F]{2})/chr hex($1)/ge; return $v; } package Bio::DB::GFF::ID_Iterator; use strict; use Bio::Root::Root; use vars '@ISA'; @ISA = 'Bio::Root::Root'; sub new { my $class = shift; my ($db,$ids,$type) = @_; return bless {ids=>$ids,db=>$db,type=>$type},$class; } sub next_seq { my $self = shift; my $next = shift @{$self->{ids}}; return unless $next; my $name = ref($next) eq 'ARRAY' ? Bio::DB::GFF::Featname->new(@$next) : $next; my $segment = $self->{type} eq 'name' ? $self->{db}->segment($name) : $self->{type} eq 'feature' ? $self->{db}->fetch_feature_by_id($name) : $self->{type} eq 'group' ? $self->{db}->fetch_feature_by_gid($name) : $self->throw("Bio::DB::GFF::ID_Iterator called to fetch an unknown type of identifier"); $self->throw("id does not exist") unless $segment; return $segment; } 1; __END__ =head1 BUGS Features can only belong to a single group at a time. This must be addressed soon. Start coordinate can be greater than stop coordinate for relative addressing. This breaks strict BioPerl compatibility and must be fixed. =head1 SEE ALSO L<bioperl>, L<Bio::DB::GFF::RelSegment>, L<Bio::DB::GFF::Aggregator>, L<Bio::DB::GFF::Feature>, L<Bio::DB::GFF::Adaptor::dbi::mysqlopt>, L<Bio::DB::GFF::Adaptor::dbi::oracle>, L<Bio::DB::GFF::Adaptor::memory> =head1 AUTHOR Lincoln Stein E<lt>lstein@cshl.orgE<gt>. Copyright (c) 2001 Cold Spring Harbor Laboratory. This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut