SYNOPSIS

See Bio::DB::GFF

DESCRIPTION

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:

fdata

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.

cmap_feature (replaces fgroup)

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.

GBrowse Columns:

    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.

Examples:

  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)

ftype

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)

fdna

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.

fattribute_to_feature

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.

fattribute

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)

Data Loading Methods

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.

new

 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

get_dna

 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.

schema

 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.

make_classes_query

 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

setup_load

 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.

load_gff_line

 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

get_feature_id

 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.

get_table_id

 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.

make_features_by_name_where_part

 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

make_features_join_part

 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.

search_notes

 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.

make_features_order_by_part

 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.

create_cmap_viewer_link

 Title   : create_cmap_viewer_link
 Usage   : $link_str = $db->create_cmap_viewer_link(data_source=>$ds,group_id=>$gid)
 Function: 
 Returns : 
 Args    : 
 Status  :

AUTHOR

Ben Faga <[email protected]>.

Modified from mysql.pm by:

Lincoln Stein <[email protected]>.

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.