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

💖 Bio::D...ariaDB(3pm) 💖

okay bestie, so this is the manpage for Bio::DB::SeqFeature::Store::DBI::MariaDB — she's part of the User Contributed Perl Documentation, and the manual herself goes by Bio::D...ariaDB(3pm). grab a lil snack, we're getting into it 🍓

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✨ NAME ✨

Bio::DB::SeqFeature::Store::DBI::MariaDB — the MariaDB implementation of Bio::DB::SeqFeature::Store. no cap, that's literally her whole job 💅

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🌸 SYNOPSIS 🌸

vibe check, here's the whole flow, verbatim, don't @ me:

  use Bio::DB::SeqFeature::Store;

  # Open the sequence database
  my $db = Bio::DB::SeqFeature::Store->new(-adaptor => 'DBI::MariaDB',
                                          -dsn     => 'dbi:MariaDB:test');

  # get a feature from somewhere
  my $feature = Bio::SeqFeature::Generic->new(...);

  # store it
  $db->store($feature) or die "Couldn't store!";

  # primary ID of the feature is changed to indicate its primary ID
  # in the database...
  my $id = $feature->primary_id;

  # get the feature back out
  my $f  = $db->fetch($id);

  # change the feature and update it
  $f->start(100);
  $f->update($f) or die "Couldn't update!";

  # searching...
  # ...by id
  my @features = $db->fetch_many(@list_of_ids);

  # ...by name
  @features = $db->get_features_by_name('ZK909');

  # ...by alias
  @features = $db->get_features_by_alias('sma-3');

  # ...by type
  @features = $db->get_features_by_name('gene');

  # ...by location
  @features = $db->get_features_by_location(-seq_id=>'Chr1',-start=>4000,-end=>600000);

  # ...by attribute
  @features = $db->get_features_by_attribute({description => 'protein kinase'})

  # ...by the GFF "Note" field
  @result_list = $db->search_notes('kinase');

  # ...by arbitrary combinations of selectors
  @features = $db->features(-name => $name,
                            -type => $types,
                            -seq_id => $seqid,
                            -start  => $start,
                            -end    => $end,
                            -attributes => $attributes);

  # ...using an iterator
  my $iterator = $db->get_seq_stream(-name => $name,
                                     -type => $types,
                                     -seq_id => $seqid,
                                     -start  => $start,
                                     -end    => $end,
                                     -attributes => $attributes);

  while (my $feature = $iterator->next_seq) {
    # do something with the feature
  }

  # ...limiting the search to a particular region
  my $segment  = $db->segment('Chr1',5000=>6000);
  my @features = $segment->features(-type=>['mRNA','match']);

  # getting & storing sequence information
  # Warning: this returns a string, and not a PrimarySeq object
  $db->insert_sequence('Chr1','GATCCCCCGGGATTCCAAAA...');
  my $sequence = $db->fetch_sequence('Chr1',5000=>6000);

  # what feature types are defined in the database?
  my @types    = $db->types;

  # create a new feature in the database
  my $feature = $db->new_feature(-primary_tag => 'mRNA',
                                 -seq_id      => 'chr3',
                                 -start      => 10000,
                                 -end        => 11000);

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🦋 DESCRIPTION 🦋

Bio::DB::SeqFeature::Store::MariaDB is the MariaDB adaptor for Bio::DB::SeqFeature::Store. and listen — you do not create it directly, okay? that's not the move. instead you use Bio::DB::SeqFeature::Store->new() and let her do her thing. main character energy, but off-screen 💅

for the complete usage instructions, go read Bio::DB::SeqFeature::Store. she's the blueprint, fr fr.

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🎀 Using the MariaDB adaptor 🎀

before you can even think about using this adaptor, you have to use the mariadb-admin tool to create a database and set up a user account with write permission. that's step one, non-negotiable. and if you wanna use "fast" loading? then that user account also needs "file" privileges. periodt.

to establish a connection to the database, call Bio::DB::SeqFeature::Store->new(-adaptor=>'DBI::MariaDB',@more_args).

and the additional arguments are as follows, bestie — every single one, no skipping:

• -dsn — the database name. you can abbreviate "dbi:mariadb:foo" as "foo" if you want, cute little shortcut ✨
• -user — username for authentication.
• -pass — password for authentication.
• -namespace — a prefix to attach to each table. this is how you get several virtual databases living inside the same physical database. iconic, honestly.
• -temp — boolean flag. if true, a temporary database gets created and destroyed as soon as the Store object goes out of scope. (synonym -temporary)
• -autoindex — boolean flag. if true, features in the database get reindexed every time they change. and yes, this is the default. the grind never stops 🫶
• -tmpdir — directory where temporary files go during "fast" loading. defaults to File::Spec->tmpdir(). (synonyms -dump_dir, -dumpdir, -tmp)
• -dbi_options — a hashref you pass to DBI->connect's 4th argument, the "attributes." (synonyms -options, -dbi_attr)
• -write — pass true to open the database for writing or updating.

if all goes well, you get back a brand new instance of Bio::DB::SeqFeature::Store::DBI::MariaDB. slay.

on top of the standard methods that every well-behaved Bio::DB::SeqFeature::Store database supports, there are also a few adaptor-specific methods. those are the next sections, keep scrolling 💜

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⭐ types ⭐

• Title: types
• Usage: @type_list = $db->types
• Function: get all the types in the database
• Returns: array of Bio::DB::GFF::Typename objects
• Args: none
• Status: public

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🌈 toplevel_types 🌈

• Title: toplevel_types
• Usage: @type_list = $db->toplevel_types
• Function: get the toplevel types in the database
• Returns: array of Bio::DB::GFF::Typename objects
• Args: none
• Status: public

this one is similar to types() but it only returns the types of INDEXED (toplevel) features. so like, the VIP section of the type list 👑

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okay that's the whole page, you made it, I'm so proud of you 🥹

and that's a wrap on Bio::D...ariaDB(3pm) — this version is straight from perl v5.40.0, dated 2024-10-11. go forth and store your features, bestie, you've got this 💖✨🦋