Bio::DB::GFF::Adaptor::dbi::mysqlcmap -- Database adaptor for an integraded CMap/GBrowse mysql schema
This adaptor implements a specific mysql database schema that is compatible with Bio::DB::GFF. It inherits from Bio::DB::GFF::Adaptor::dbi, which itself inherits from Bio::DB::GFF.
The schema uses several tables:
This is the feature data table. Its columns are: - fid feature ID (integer) fref reference sequence name (string) fstart start position relative to reference (integer) fstop stop postion relative to reference (integer) ftypeid feature type ID (integer) fscore feature score (float); may be null fstrand strand; one of "+" or "-"; may be null fphase phase; one of 0, 1 or 2; may be null feature_id group ID used to be 'gid' (integer) ftarget_start for similarity features, the target start position (integer) ftarget_stop for similarity features, the target stop position (integer)
Note that it would be desirable to normalize the reference sequence name, since there are usually many features that share the same reference feature. However, in the current schema, query performance suffers dramatically when this additional join is added.
This is the group table. There is one row for each group. This is the shared table between CMap and GBrowse. There are many CMap related columns but only a few that GBrowse uses.
feature_id the group ID (integer) gclass the class of the group (string) feature_name the name of the group (string)
The group table serves multiple purposes. As you might expect, it is used to cluster features that logically belong together, such as the multiple exons of the same transcript. It is also used to assign a name and class to a singleton feature. Finally, the group table is used to identify the target of a similarity hit. This is consistent with the way in which the group field is used in the GFF version 2 format.
The cmap_feature.feature_id field joins with the fdata.feature_id field.
mysql> select * from cmap_feature where feature_name='sjj_2L52.1'; +--------------+-------------+--------------+ | feature_id | gclass | feature_name | +--------------+-------------+--------------+ | 69736 | PCR_product | sjj_2L52.1 | +--------------+-------------+--------------+ 1 row in set (0.70 sec) mysql> select fref,fstart,fstop from fdata,cmap_feature where gclass='PCR_product' and feature_name = 'sjj_2L52.1' and fdata.feature_id=cmap_feature.feature_id; +---------------+--------+-------+ | fref | fstart | fstop | +---------------+--------+-------+ | CHROMOSOME_II | 1586 | 2355 | +---------------+--------+-------+ 1 row in set (0.03 sec)
This table contains the feature types, one per row. Columns are:
ftypeid the feature type ID (integer) fmethod the feature type method name (string) fsource the feature type source name (string)
The ftype.ftypeid field joins with the fdata.ftypeid field. Example:
mysql> select fref,fstart,fstop,fmethod,fsource from fdata,cmap_feature,ftype where gclass='PCR_product' and feature_name = 'sjj_2L52.1' and fdata.feature_id=cmap_feature.feature_id and fdata.ftypeid=ftype.ftypeid; +---------------+--------+-------+-------------+-----------+ | fref | fstart | fstop | fmethod | fsource | +---------------+--------+-------+-------------+-----------+ | CHROMOSOME_II | 1586 | 2355 | PCR_product | GenePairs | +---------------+--------+-------+-------------+-----------+ 1 row in set (0.08 sec)
This table holds the raw DNA of the reference sequences. It has three columns:
fref reference sequence name (string) foffset offset of this sequence fdna the DNA sequence (longblob)
To overcome problems loading large blobs, DNA is automatically fragmented into multiple segments when loading, and the position of each segment is stored in foffset. The fragment size is controlled by the -clump_size argument during initialization.
This table holds "attributes", which are tag/value pairs stuffed into the GFF line. The first tag/value pair is treated as the group, and anything else is treated as an attribute (weird, huh?).
CHR_I assembly_tag Finished 2032 2036 . + . Note "Right: cTel33B" CHR_I assembly_tag Polymorphism 668 668 . + . Note "A->C in cTel33B"
The columns of this table are:
fid feature ID (integer) fattribute_id ID of the attribute (integer) fattribute_value text of the attribute (text)
The fdata.fid column joins with fattribute_to_feature.fid.
This table holds the normalized names of the attributes. Fields are:
fattribute_id ID of the attribute (integer) fattribute_name Name of the attribute (varchar)
In addition to implementing the abstract SQL-generating methods of Bio::DB::GFF::Adaptor::dbi, this module also implements the data loading functionality of Bio::DB::GFF.
Title : new Usage : $db = Bio::DB::GFF->new(@args) Function: create a new adaptor Returns : a Bio::DB::GFF object Args : see below Status : Public
The new constructor is identical to the "dbi" adaptor's new() method, except that the prefix "dbi:mysql" is added to the database DSN identifier automatically if it is not there already.
Argument Description -------- ----------- -dsn the DBI data source, e.g. 'dbi:mysql:ens0040' or "ens0040" -user username for authentication -pass the password for authentication
Title : get_dna Usage : $string = $db->get_dna($name,$start,$stop,$class) Function: get DNA string Returns : a string Args : name, class, start and stop of desired segment Status : Public
This method performs the low-level fetch of a DNA substring given its name, class and the desired range. This should probably be moved to the parent class.
Title : schema Usage : $schema = $db->schema Function: return the CREATE script for the schema Returns : a list of CREATE statemetns Args : none Status : protected
This method returns a list containing the various CREATE statements needed to initialize the database tables.
Title : make_classes_query Usage : ($query,@args) = $db->make_classes_query Function: return query fragment for generating list of reference classes Returns : a query and args Args : none Status : public
Title : setup_load Usage : $db->setup_load Function: called before load_gff_line() Returns : void Args : none Status : protected
This method performs schema-specific initialization prior to loading a set of GFF records. It prepares a set of DBI statement handlers to be used in loading the data.
Title : load_gff_line Usage : $db->load_gff_line($fields) Function: called to load one parsed line of GFF Returns : true if successfully inserted Args : hashref containing GFF fields Status : protected
This method is called once per line of the GFF and passed a series of parsed data items that are stored into the hashref $fields. The keys are:
ref reference sequence source annotation source method annotation method start annotation start stop annotation stop score annotation score (may be undef) strand annotation strand (may be undef) phase annotation phase (may be undef) group_class class of annotation's group (may be undef) group_name ID of annotation's group (may be undef) target_start start of target of a similarity hit target_stop stop of target of a similarity hit attributes array reference of attributes, each of which is a [tag=>value] array ref
Title : get_feature_id Usage : $integer = $db->get_feature_id($ref,$start,$stop,$typeid,$groupid) Function: get the ID of a feature Returns : an integer ID or undef Args : none Status : private
This internal method is called by load_gff_line to look up the integer ID of an existing feature. It is ony needed when replacing a feature with new information.
Title : get_table_id Usage : $integer = $db->get_table_id($table,@ids) Function: get the ID of a group or type Returns : an integer ID or undef Args : none Status : private
This internal method is called by load_gff_line to look up the integer ID of an existing feature type or group. The arguments are the name of the table, and two string identifiers. For feature types, the identifiers are the method and source. For groups, the identifiers are group name and class.
This method requires that a statement handler named lookup_$table, have been created previously by setup_load(). It is here to overcome deficiencies in mysql's INSERT syntax.
Title : make_features_by_name_where_part Usage : $db->make_features_by_name_where_part Function: create the SQL fragment needed to select a feature by its group name & class Returns : a SQL fragment and bind arguments Args : see below Status : Protected
Title : make_features_join_part Usage : $string = $db->make_features_join_part() Function: make join part of the features query Returns : a string Args : none Status : protected
This method creates the part of the features query that immediately follows the WHERE keyword.
Title : search_notes Usage : @search_results = $db->search_notes("full text search string",$limit) Function: Search the notes for a text string, using mysql full-text search Returns : array of results Args : full text search string, and an optional row limit Status : public
This is a mysql-specific method. Given a search string, it performs a full-text search of the notes table and returns an array of results. Each row of the returned array is a arrayref containing the following fields:
column 1 A Bio::DB::GFF::Featname object, suitable for passing to segment() column 2 The text of the note column 3 A relevance score.
Title : make_features_order_by_part Usage : ($query,@args) = $db->make_features_order_by_part() Function: make the ORDER BY part of the features() query Returns : a SQL fragment and bind arguments, if any Args : none Status : protected
This method creates the part of the features query that immediately follows the ORDER BY part of the query issued by features() and related methods.
Title : create_cmap_viewer_link Usage : $link_str = $db->create_cmap_viewer_link(data_source=>$ds,group_id=>$gid) Function: Returns : Args : Status :
Ben Faga <firstname.lastname@example.org>.
Modified from mysql.pm by:
Lincoln Stein <email@example.com>.
Copyright (c) 2002 Cold Spring Harbor Laboratory.
This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself.