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.\" ========================================================================
.\"
.IX Title "Bio::DB::SeqFeature::Store::Alias 3pm"
.TH Bio::DB::SeqFeature::Store::Alias 3pm "2018-10-03" "perl v5.26.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.nh
.SH "NAME"
Bio::DB::SeqFeature::Store::Alias \-\- override feature type, method, source and attribute fields
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 2
\& # override feature type, method, source and attribute fields
\& # with the contents of a simple text index file
\&
\& use Bio::DB::SeqFeature::Store::Alias;
\& use Bio::DB::SeqFeature::Store;
\& my $db = Bio::DB::SeqFeature::Store\->new(\-adaptor=>\*(AqDBI::mysql\*(Aq,
\&                                          \-dsn    =>\*(Aqtestdb\*(Aq);
\& my $meta = Bio::DB::SeqFeature::Store::Alias\->new(\-store => $db,
\&                                                    \-index => \*(Aq/usr/local/testdb/meta.index\*(Aq,
\&                                                    \-default_type => \*(Aqexample_feature\*(Aq,
\&    );
\& my @features = $meta\->get_seq_stream(\-seq_id => \*(AqI\*(Aq,
\&                                      \-attributes => {foo => \*(Aqbar\*(Aq});
.Ve
.PP
meta.index  has the following structure
.PP
.Vb 9
\& [feature_name_1]
\& :dbid        = f101
\& :selected    = 1
\& display_name = My First Feature
\& type         = some_type1
\& method       = my_method1
\& source       = my_source1
\& some_attribute    = value1
\& another_attribute = value2
\&
\& [feature_name_2]
\& :dbid        = f102
\& :selected    = 1
\& display_name = My Second Feature
\& type         = some_type2
\& method       = my_method2
\& source       = my_source2
\& some_attribute    = value3
\& another_attribute = value4
\&
\& [feature_name_3]
\& :dbid        = f103
\& type         = some_type2
\& method       = my_method2
\& source       = my_source2
\& some_attribute    = value5
\& another_attribute = value6
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This module can be used as a wrapper around any BioPerl database that
supports the \fIget_feature_by_name()\fR method. It allows you to
dynamically override the type, source, method and display name of each
feature, as well as to assign new metadata attributes to each one.
.PP
It is used by GBrowse to create subtracks for tracks that have a small
number of named features, primarily wiggle tracks.
.SS "Metadata Format"
.IX Subsection "Metadata Format"
The wrapper is associated with a text file that contains metadata
about each feature. You can use any name for the text file, but it
must follow this format:
.PP
.Vb 8
\& [feature_name_1]
\& :dbid        = f101
\& :selected    = 1
\& type         = some_type1
\& method       = my_method1
\& source       = my_source1
\& some_attribute    = value1
\& another_attribute = value2
\&
\& [feature_name_2]
\& :dbid        = f102
\& :selected    = 1
\& type         = some_type2
\& method       = my_method2
\& source       = my_source2
\& some_attribute    = value3
\& another_attribute = value4
\&
\& [feature_name_3]
\& :dbid        = f103
\& type         = some_type2
\& method       = my_method2
\& source       = my_source2
\& some_attribute    = value5
\& another_attribute = value6
.Ve
.PP
Each [stanza] begins with the name of a feature as it is represented
in the underlying database. A call to the database's
\&\fIget_feature_by_name()\fR method with the [stanza] heading contents
(e.g. \*(L"feature_name_2\*(R") and a genomic position should return one and
only one feature.
.PP
Below each [stanza] heading are a series of tag=value pairs. The
following tag names have special meaning:
.PP
.Vb 10
\& :dbid          Unique identifier for the feature, used by GBrowse to process
\&                  clicks on the feature.
\& :selected      If true, this subtrack is selected by default when the
\&                  containing track is turned on.
\& display_name   Display name for the feature. If not present, will
\&                  default to the feature\*(Aqs native display name
\&                  (i.e. the one in the [stanza]).
\& type           What is returned by calling the feature\*(Aqs type()
\&                  method.
\& method         What is returned by calling the feature\*(Aqs method()
\&                  method.
\& source         What is returned by calling the feature\*(Aqs source()
\&                  method.
\& score         What is returned by calling the feature\*(Aqs score() method.
.Ve
.PP
Any other tags become sortable attributes which are displayed by the
GBrowse subtrack selection dialog box. For this to work properly, each
tag must be present in each stanza. Tags that are present in some
stanzas and not others are ignored.
.SH "METHODS"
.IX Header "METHODS"
.ie n .SS "$aliasdb = Bio::DB::SeqFeature::Store::Alias\->new(\-metadata=>$path,\-store=>$db,\-type=>$type)"
.el .SS "\f(CW$aliasdb\fP = Bio::DB::SeqFeature::Store::Alias\->new(\-metadata=>$path,\-store=>$db,\-type=>$type)"
.IX Subsection "$aliasdb = Bio::DB::SeqFeature::Store::Alias->new(-metadata=>$path,-store=>$db,-type=>$type)"
\&\fInew()\fR creates the Alias database. The arguments are:
.PP
.Vb 5
\&  \-metadata       Full path to the metadata file.
\&  \-store          Previously opened handle to the feature database
\&                    (e.g. Bio::SeqFeature::Store, Bio::DB::GFF,
\&                     Bio::DB::Chado)
\&  \-type           Default type to use for features in this database.
.Ve
.ie n .SS "$type = $aliasdb\->default_type([$type])"
.el .SS "\f(CW$type\fP = \f(CW$aliasdb\fP\->default_type([$type])"
.IX Subsection "$type = $aliasdb->default_type([$type])"
Gets or sets the default type.
.ie n .SS "$store = $aliasdb\->store"
.el .SS "\f(CW$store\fP = \f(CW$aliasdb\fP\->store"
.IX Subsection "$store = $aliasdb->store"
Gets the underlying feature database specified during \fInew()\fR (immutable).
.ie n .SS "$index = $aliasdb\->index"
.el .SS "\f(CW$index\fP = \f(CW$aliasdb\fP\->index"
.IX Subsection "$index = $aliasdb->index"
Returns the path to the metadata description file.
.ie n .SS "$meta = $aliasdb\->metadata"
.el .SS "\f(CW$meta\fP = \f(CW$aliasdb\fP\->metadata"
.IX Subsection "$meta = $aliasdb->metadata"
Return a hashref in which the keys are the feature IDs (or an
arbitrary numeric value if :dbid was not specified), and the values
are a hashref of attribute/value pairs.
.ie n .SS "$f = $aliasdb\->get_feature($name)"
.el .SS "\f(CW$f\fP = \f(CW$aliasdb\fP\->get_feature($name)"
.IX Subsection "$f = $aliasdb->get_feature($name)"
Calls the underlying database's \fIget_feature_by_name()\fR method and
returns a list of response.
.ie n .SS "@f = $aliasdb\->features(@args)"
.el .SS "\f(CW@f\fP = \f(CW$aliasdb\fP\->features(@args)"
.IX Subsection "@f = $aliasdb->features(@args)"
Same as calling the underlying database's \fIfeatures()\fR method, except
that the values you specified in the metadata file for display_name,
type, method, source, score and other attributes will override the
original values.
.ie n .SS "$segment = $aliasdb\->segment(@args)"
.el .SS "\f(CW$segment\fP = \f(CW$aliasdb\fP\->segment(@args)"
.IX Subsection "$segment = $aliasdb->segment(@args)"
Creates a segment object (see Bio::DB::SeqFeature::Store\->\fIsegment()\fR),
which records a genomic range for use in further query refinement:
.PP
.Vb 2
\&  $chr1 = $aliasdb\->segment(\-seqid=>\*(Aqchr1\*(Aq);
\&  @f    = $chr1\->features;
.Ve
.ie n .SS "$iterator = $aliasdb\->get_seq_stream(@args)"
.el .SS "\f(CW$iterator\fP = \f(CW$aliasdb\fP\->get_seq_stream(@args)"
.IX Subsection "$iterator = $aliasdb->get_seq_stream(@args)"
This method is similar to the underlying database's \fIget_seq_stream()\fR
method, except that it wraps each feature. Example:
.PP
.Vb 4
\& $iterator = $aliasdb\->get_seq_stream(\-type=>\*(Aqsome_type2\*(Aq);
\& while (my $seq = $iterator\->next_seq) {
\&    # do something with the seq object.
\& }
.Ve
.ie n .SS "@f = $aliasdb\->get_features_by_location(@args)"
.el .SS "\f(CW@f\fP = \f(CW$aliasdb\fP\->get_features_by_location(@args)"
.IX Subsection "@f = $aliasdb->get_features_by_location(@args)"
This method is similar to the underlying database's \fIget_features_by_location()\fR
method.
.PP
.Vb 4
\& $iterator = $aliasdb\->get_seq_stream(\-type=>\*(Aqsome_type2\*(Aq);
\& while (my $seq = $iterator\->next_seq) {
\&    # do something with the seq object.
\& }
.Ve
.ie n .SS "@f = $aliasdb\->get_features_by_name(@args)"
.el .SS "\f(CW@f\fP = \f(CW$aliasdb\fP\->get_features_by_name(@args)"
.IX Subsection "@f = $aliasdb->get_features_by_name(@args)"
This method is similar to the underlying database's \fIget_features_by_location()\fR
method.
.ie n .SS "@f = $aliasdb\->get_features_by_name(@args)"
.el .SS "\f(CW@f\fP = \f(CW$aliasdb\fP\->get_features_by_name(@args)"
.IX Subsection "@f = $aliasdb->get_features_by_name(@args)"
This method is similar to the underlying database's \fIget_features_by_location()\fR
method.
.ie n .SS "@f = $aliasdb\->get_features_by_alias(@args);"
.el .SS "\f(CW@f\fP = \f(CW$aliasdb\fP\->get_features_by_alias(@args);"
.IX Subsection "@f = $aliasdb->get_features_by_alias(@args);"
This method is similar to the underlying database's \fIget_features_by_alias()\fR
method.
.ie n .SS "@f = $aliasdb\->get_features_by_attribute(@args);"
.el .SS "\f(CW@f\fP = \f(CW$aliasdb\fP\->get_features_by_attribute(@args);"
.IX Subsection "@f = $aliasdb->get_features_by_attribute(@args);"
This method is similar to the underlying database's \fIget_features_by_attribute()\fR
method.
.SH "BUGS"
.IX Header "BUGS"
Please report them.
.SH "SEE ALSO"
.IX Header "SEE ALSO"
Bio::SeqFeature::Store,
Bio::DB::GFF,
Bio::SeqI,
Bio::SeqFeatureI,
Bio::Das,
Bio::Graphics::Browser2
.SH "AUTHOR"
.IX Header "AUTHOR"
Copyright (c) 2012 Ontario Institute for Cancer Research
.PP
This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.  See \s-1DISCLAIMER\s0.txt for
disclaimers of warranty.