Bio::DB::GFF::Adaptor::dbi::mysql -- Database adaptor for a specific mysql schema
See Bio::DB::GFF
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 gid group ID (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. Columns:
gid the group ID (integer) gclass the class of the group (string) gname 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 fgroup.gid field joins with the fdata.gid field.
Examples:
mysql> select * from fgroup where gname='sjj_2L52.1'; +-------+-------------+------------+ | gid | gclass | gname | +-------+-------------+------------+ | 69736 | PCR_product | sjj_2L52.1 | +-------+-------------+------------+ 1 row in set (0.70 sec) mysql> select fref,fstart,fstop from fdata,fgroup where gclass='PCR_product' and gname = 'sjj_2L52.1' and fdata.gid=fgroup.gid; +---------------+--------+-------+ | 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,fgroup,ftype where gclass='PCR_product' and gname = 'sjj_2L52.1' and fdata.gid=fgroup.gid 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 : make_abscoord_query Usage : $sth = $db->make_abscoord_query($name,$class); Function: create query that finds the reference sequence coordinates given a landmark & classa Returns : a DBI statement handle Args : name and class of landmark Status : protected
The statement handler should return rows containing five fields:
1. reference sequence name 2. reference sequence class 3. start position 4. stop position 5. strand ("+" or "-")
This query always returns "Sequence" as the class of the reference sequence.
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_by_id_where_part Usage : $db->make_features_by_id_where_part($ids) Function: create the SQL fragment needed to select a set of features by their ids Returns : a SQL fragment and bind arguments Args : arrayref of IDs Status : Protected
Title : make_features_by_id_where_part Usage : $db->make_features_by_gid_where_part($ids) Function: create the SQL fragment needed to select a set of features by their ids Returns : a SQL fragment and bind arguments Args : arrayref of IDs Status : Protected
Title : make_features_select_part Usage : $string = $db->make_features_select_part() Function: make select 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 SELECT keyword.
Title : make_features_from_part Usage : $string = $db->make_features_from_part() Function: make from 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 FROM keyword.
Title : make_features_join_part Usage : $string = $db->make_features_join_part() Function: make join part of the features query Returns : a string Args : none Status : protected
This method creates the part of the features query that immediately follows the WHERE keyword.
Title : make_features_order_by_part Usage : ($query,@args) = $db->make_features_order_by_part() Function: make the ORDER BY part of the features() query Returns : a SQL fragment and bind arguments, if any Args : none Status : protected
This method creates the part of the features query that immediately follows the ORDER BY part of the query issued by features() and related methods.
Title : make_features_group_by_part Usage : ($query,@args) = $db->make_features_group_by_part() Function: make the GROUP BY part of the features() query Returns : a SQL fragment and bind arguments, if any Args : none Status : protected
This method creates the part of the features query that immediately follows the GROUP BY part of the query issued by features() and related methods.
Title : refseq_query Usage : ($query,@args) = $db->refseq_query($name,$class) Function: create SQL fragment that selects the desired reference sequence Returns : a list containing the query and bind arguments Args : reference sequence name and class Status : protected
This method is called by make_features_by_range_where_part() to construct the part of the select WHERE section that selects a particular reference sequence. It returns a mult-element list in which the first element is the SQL fragment and subsequent elements are bind values.
The current schema does not distinguish among different classes of reference sequence.
Title : attributes Usage : @attributes = $db->attributes($id,$name) Function: get the attributes 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=>value pairs. This lets you do:
%attributes = $db->attributes($id);
Normally, attributes() will be called by the feature:
@notes = $feature->attributes('Note');
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 : overlap_query Usage : ($query,@args) = $db->overlap_query($start,$stop) Function: create SQL fragment that selects the desired features by range Returns : a list containing the query and bind arguments Args : the start and stop of a range, inclusive Status : protected
This method is called by make_features_byrange_where_part() to construct the part of the select WHERE section that selects a set of features that overlap a range. It returns a multi-element list in which the first element is the SQL fragment and subsequent elements are bind values.
Title : contains_query Usage : ($query,@args) = $db->contains_query($start,$stop) Function: create SQL fragment that selects the desired features by range Returns : a list containing the query and bind arguments Args : the start and stop of a range, inclusive Status : protected
This method is called by make_features_byrange_where_part() to construct the part of the select WHERE section that selects a set of features entirely enclosed by a range. It returns a multi-element list in which the first element is the SQL fragment and subsequent elements are bind values.
Title : contained_in_query Usage : ($query,@args) = $db->contained_in_query($start,$stop) Function: create SQL fragment that selects the desired features by range Returns : a list containing the query and bind arguments Args : the start and stop of a range, inclusive Status : protected
This method is called by make_features_byrange_where_part() to construct the part of the select WHERE section that selects a set of features entirely enclosed by a range. It returns a multi-element list in which the first element is the SQL fragment and subsequent elements are bind values
Title : types_query Usage : ($query,@args) = $db->types_query($types) Function: create SQL fragment that selects the desired features by type Returns : a list containing the query and bind arguments Args : an array reference containing the types Status : protected
This method is called by make_features_byrange_where_part() to construct the part of the select WHERE section that selects a set of features based on their type. It returns a multi-element list in which the first element is the SQL fragment and subsequent elements are bind values. The argument is an array reference containing zero or more [$method,$source] pairs.
Title : make_types_select_part Usage : ($string,@args) = $db->make_types_select_part(@args) Function: create the select portion of the SQL for fetching features type list Returns : query string and bind arguments Args : see below Status : protected
This method is called by get_types() to generate the query fragment and bind arguments for the SELECT part of the query that retrieves lists of feature types. The four positional arguments are as follows:
$refseq reference sequence name $start start of region $stop end of region $want_count true to return the count of this feature type
If $want_count is false, the SQL fragment returned must produce a list of feature types in the format (method, source).
If $want_count is true, the returned fragment must produce a list of feature types in the format (method, source, count).
Title : make_types_from_part Usage : ($string,@args) = $db->make_types_from_part(@args) Function: create the FROM portion of the SQL for fetching features type lists Returns : query string and bind arguments Args : see below Status : protected
This method is called by get_types() to generate the query fragment and bind arguments for the FROM part of the query that retrieves lists of feature types. The four positional arguments are as follows:
Title : make_types_join_part Usage : ($string,@args) = $db->make_types_join_part(@args) Function: create the JOIN portion of the SQL for fetching features type lists Returns : query string and bind arguments Args : see below Status : protected
This method is called by get_types() to generate the query fragment and bind arguments for the JOIN part of the query that retrieves lists of feature types. The four positional arguments are as follows:
Title : make_types_where_part Usage : ($string,@args) = $db->make_types_where_part(@args) Function: create the WHERE portion of the SQL for fetching features type lists Returns : query string and bind arguments Args : see below Status : protected
This method is called by get_types() to generate the query fragment and bind arguments for the WHERE part of the query that retrieves lists of feature types. The four positional arguments are as follows:
Title : make_types_group_part Usage : ($string,@args) = $db->make_types_group_part(@args) Function: create the GROUP BY portion of the SQL for fetching features type lists Returns : query string and bind arguments Args : see below Status : protected
This method is called by get_types() to generate the query fragment and bind arguments for the GROUP BY part of the query that retrieves lists of feature types. The four positional arguments are as follows:
Title : tables Usage : @tables = $db->tables Function: return list of tables that belong to this module Returns : list of tables Args : none Status : protected
This method lists the tables known to the module, namely qw(fdata fref fgroup ftype fdna fnote fmeta).
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 : 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=>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.
Title : make_meta_set_query Usage : $sql = $db->make_meta_set_query Function: return SQL fragment for setting a meta parameter Returns : SQL fragment Args : none Status : public
By default this does nothing; meta parameters are not stored or retrieved.
Title : make_meta_get_query Usage : $sql = $db->make_meta_get_query Function: return SQL fragment for getting a meta parameter Returns : SQL fragment 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 : finish_load Usage : $db->finish_load Function: called after load_gff_line() Returns : number of records loaded Args : none Status : protected
This method performs schema-specific cleanup after loading a set of GFF records. It finishes each of the statement handlers prepared by setup_load().
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 : 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.
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.