Bio::D...oracle(3pm)

💖 Bio::D...oracle(3pm) 💖

okay so bestie, this is the Bio::DB::GFF::Adaptor::dbi::oracle page from the User Contributed Perl Documentation set, and it's genuinely a whole vibe. it's the database adaptor for a specific oracle schema. sit down, grab a strawberry, we're doing this 🍓

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✨ NAME ✨

Bio::DB::GFF::Adaptor::dbi::oracle — Database adaptor for a specific oracle schema. that's it, that's the name, she's serving exactly what it says on the tin 💅

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🦋 SYNOPSIS 🦋

See Bio::DB::GFF.

(no fr, that's the whole synopsis. iconic brevity. she said "go read the parent module" and honestly? respect 🫶)

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🌈 DESCRIPTION 🌈

This adaptor implements a specific oracle database schema that is compatible with Bio::DB::GFF. And the family tree? she inherits from Bio::DB::GFF::Adaptor::dbi, which itself inherits from Bio::DB::GFF. three generations of iconic 💜

The schema uses several tables, and bestie we are going to meet ALL of them:

🧚 fdata 🧚

This is the feature data table, the main character. 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
gid            group ID (integer)
ftarget_start  for similarity features, the target start position (integer)
ftarget_stop   for similarity features, the target stop position (integer)

lowkey important note: it would be desirable to normalize the reference sequence name, since there are usually many features that share the same reference feature. BUT. in the current schema, query performance suffers dramatically when this additional join is added. so they didn't. and that's the tea 🫖

🌸 fgroup 🌸

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, she's versatile. 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, aka the receipts:

sql> select * from fgroup where gname='sjj_2L52.1';
+-------+-------------+------------+
| gid   | gclass      | gname      |
+-------+-------------+------------+
| 69736 | PCR_product | sjj_2L52.1 |
+-------+-------------+------------+
1 row in set (0.70 sec)

sql> 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)

🦋 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:

sql> 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)

🎀 fdna 🎀

This table holds the raw DNA of the reference sequences. She 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. chunked and organized, we love to see it ✨

💜 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? yeah bestie, weird 😭).

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)

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💅 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. so she does both jobs. girlboss 🫶

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🍓 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:oracle" is added to the database DSN identifier automatically if it is not there already. auto-prefix, no cap 💅

Argument       Description
--------       -----------

-dsn           the DBI data source, e.g. 'dbi:mysql:ens0040' or "ens0040"

-user          username for authentication

-pass          the password for authentication

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🌟 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. it's giving construction permit 🏗️

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🧁 do_initialize 🧁

Title   : do_initialize
Usage   : $success = $db->do_initialize($drop_all)
Function: initialize the database
Returns : a boolean indicating the success of the operation
Args    : a boolean indicating whether to delete existing data
Status  : protected

This method will load the schema into the database. If $drop_all is true, then any existing data in the tables known to the schema will be deleted. be so serious before you pass that flag, bestie 😭

Internally, this method calls schema() to get the schema data.

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💀 drop_all 💀

Title   : drop_all
Usage   : $db->drop_all
Function: empty the database
Returns : void
Args    : none
Status  : protected

This method drops the tables known to this module. Internally it calls the abstract tables() method. yeah. she's the destructive one. periodt 💀

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🦄 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. prep work, main character energy 👑

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🌈 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

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🔥 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. (mysql bestie, we still love you, but 😬)

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🎀 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.
• column 4 — A Bio::DB::GFF::Typename object

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🧚 make_meta_set_query 🧚

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. she's on her "no thoughts, head empty" arc and that is by design 🙈

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okay bestie, that's the whole page, every table, every column, every method, every flag, zero skips, no crumbs left 💖

this was the Bio::D...oracle(3pm) page from the User Contributed Perl Documentation, and the footer energy is: perl v5.30.0, dated 2020-01-13. so like, vintage but still serving. slay, take care, hydrate, and always pass your -dsn correctly 🫶💅✨