Provided by: libbio-db-gff-perl_1.7.4-1_all 
NAME
Bio::DB::GFF::Adaptor::dbi::mysqlcmap -- Database adaptor for an integraded CMap/GBrowse
mysql schema
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 position 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 :
BUGS
none ;-)
SEE ALSO
Bio::DB::GFF, bioperl
AUTHOR
Ben Faga <faga@cshl.org>.
Modified from mysql.pm by:
Lincoln Stein <lstein@cshl.org>.
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.