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.IX Title "Bio::DB::SeqFeature::Store::DBI::mysql 3pm"
.TH Bio::DB::SeqFeature::Store::DBI::mysql 3pm "2018-10-27" "perl v5.26.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
Bio::DB::SeqFeature::Store::DBI::mysql \-\- Mysql implementation of Bio::DB::SeqFeature::Store
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&  use Bio::DB::SeqFeature::Store;
\&
\&  # Open the sequence database
\&  my $db = Bio::DB::SeqFeature::Store\->new(\-adaptor => \*(AqDBI::mysql\*(Aq,
\&                                          \-dsn     => \*(Aqdbi:mysql:test\*(Aq);
\&
\&  # get a feature from somewhere
\&  my $feature = Bio::SeqFeature::Generic\->new(...);
\&
\&  # store it
\&  $db\->store($feature) or die "Couldn\*(Aqt 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\*(Aqt update!";
\&
\&  # searching...
\&  # ...by id
\&  my @features = $db\->fetch_many(@list_of_ids);
\&
\&  # ...by name
\&  @features = $db\->get_features_by_name(\*(AqZK909\*(Aq);
\&
\&  # ...by alias
\&  @features = $db\->get_features_by_alias(\*(Aqsma\-3\*(Aq);
\&
\&  # ...by type
\&  @features = $db\->get_features_by_name(\*(Aqgene\*(Aq);
\&
\&  # ...by location
\&  @features = $db\->get_features_by_location(\-seq_id=>\*(AqChr1\*(Aq,\-start=>4000,\-end=>600000);
\&
\&  # ...by attribute
\&  @features = $db\->get_features_by_attribute({description => \*(Aqprotein kinase\*(Aq})
\&
\&  # ...by the GFF "Note" field
\&  @result_list = $db\->search_notes(\*(Aqkinase\*(Aq);
\&
\&  # ...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(\*(AqChr1\*(Aq,5000=>6000);
\&  my @features = $segment\->features(\-type=>[\*(AqmRNA\*(Aq,\*(Aqmatch\*(Aq]);
\&
\&  # getting & storing sequence information
\&  # Warning: this returns a string, and not a PrimarySeq object
\&  $db\->insert_sequence(\*(AqChr1\*(Aq,\*(AqGATCCCCCGGGATTCCAAAA...\*(Aq);
\&  my $sequence = $db\->fetch_sequence(\*(AqChr1\*(Aq,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 => \*(AqmRNA\*(Aq,
\&                                 \-seq_id      => \*(Aqchr3\*(Aq,
\&                                 \-start      => 10000,
\&                                 \-end        => 11000);
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
Bio::DB::SeqFeature::Store::mysql is the Mysql adaptor for
Bio::DB::SeqFeature::Store. You will not create it directly, but
instead use Bio::DB::SeqFeature::Store\->\fInew()\fR to do so.
.PP
See Bio::DB::SeqFeature::Store for complete usage instructions.
.SS "Using the Mysql adaptor"
.IX Subsection "Using the Mysql adaptor"
Before you can use the adaptor, you must use the mysqladmin tool to
create a database and establish a user account with write
permission. In order to use \*(L"fast\*(R" loading, the user account must have
\&\*(L"file\*(R" privileges.
.PP
To establish a connection to the database, call
Bio::DB::SeqFeature::Store\->new(\-adaptor=>'DBI::mysql',@more_args). The
additional arguments are as follows:
.PP
.Vb 2
\&  Argument name       Description
\&  \-\-\-\-\-\-\-\-\-\-\-\-\-       \-\-\-\-\-\-\-\-\-\-\-
\&
\& \-dsn              The database name. You can abbreviate 
\&                   "dbi:mysql:foo" as "foo" if you wish.
\&
\& \-user             Username for authentication.
\&
\& \-pass             Password for authentication.
\&
\& \-namespace        A prefix to attach to each table. This allows you
\&                   to have several virtual databases in the same
\&                   physical database.
\&
\& \-temp             Boolean flag. If true, a temporary database
\&                   will be created and destroyed as soon as
\&                   the Store object goes out of scope. (synonym \-temporary)
\&
\& \-autoindex        Boolean flag. If true, features in the database will be
\&                   reindexed every time they change. This is the default.
\&
\&
\& \-tmpdir           Directory in which to place temporary files during "fast" loading.
\&                   Defaults to File::Spec\->tmpdir(). (synonyms \-dump_dir, \-dumpdir, \-tmp)
\&
\& \-dbi_options      A hashref to pass to DBI\->connect\*(Aqs 4th argument, the "attributes."
\&                   (synonyms \-options, \-dbi_attr)
\&
\& \-write            Pass true to open database for writing or updating.
.Ve
.PP
If successful, a new instance of
Bio::DB::SeqFeature::Store::DBI::mysql will be returned.
.PP
In addition to the standard methods supported by all well-behaved
Bio::DB::SeqFeature::Store databases, several following
adaptor-specific methods are provided. These are described in the next
sections.
.SS "types"
.IX Subsection "types"
.Vb 6
\& 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
.Ve
.SS "toplevel_types"
.IX Subsection "toplevel_types"
.Vb 6
\& 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
.Ve
.PP
This is similar to \fItypes()\fR but only returns the types of
\&\s-1INDEXED\s0 (toplevel) features.