Sendu Bala
and 1 contributors

NAME

Bio::Graphics::FeatureFile -- A set of Bio::Graphics features, stored in a file

SYNOPSIS

 use Bio::Graphics::FeatureFile;
 my $data  = Bio::Graphics::FeatureFile->new(-file => 'features.txt');


 # create a new panel and render contents of the file onto it
 my $panel = $data->new_panel;
 my $tracks_rendered = $data->render($panel);

 # or do it all in one step
 my ($tracks_rendered,$panel) = $data->render;

 # for more control, render tracks individually
 my @feature_types = $data->types;
 for my $type (@feature_types) {
    my $features = $data->features($type);
    my %options  = $data->style($type);
    $panel->add_track($features,%options);  # assuming we have a Bio::Graphics::Panel
 }

 # get individual settings
 my $est_fg_color = $data->setting(EST => 'fgcolor');

 # or create the FeatureFile by hand

 # add a type
 $data->add_type(EST => {fgcolor=>'blue',height=>12});

 # add a feature
 my $feature = Bio::Graphics::Feature->new(
                                             # params
                                          ); # or some other SeqI
 $data->add_feature($feature=>'EST');

DESCRIPTION

The Bio::Graphics::FeatureFile module reads and parses files that describe sequence features and their renderings. It accepts both GFF format and a more human-friendly file format described below. Once a FeatureFile object has been initialized, you can interrogate it for its consistuent features and their settings, or render the entire file onto a Bio::Graphics::Panel.

This module is a precursor of Jason Stajich's Bio::Annotation::Collection class, and fulfills a similar function of storing a collection of sequence features. However, it also stores rendering information about the features, and does not currently follow the CollectionI interface.

The File Format

There are two types of entry in the file format: feature entries, and formatting entries. They can occur in any order. See the Appendix for a full example.

Feature entries can take several forms. At their simplest, they look like this:

 Gene   B0511.1 516-11208

This means that a feature of type "Gene" and name "B0511.1" occupies the range between bases 516 and 11208. A range can be specified equally well using a hyphen, or two dots as in 516..11208. Negative coordinates are allowed, such as -187..1000.

A discontinuous range ("split location") uses commas to separate the ranges. For example:

 Gene B0511.1  516-619,3185-3294,10946-11208

Alternatively, the locations can be split by repeating the features type and name on multiple adjacent lines:

 Gene   B0511.1 516-619
 Gene   B0511.1 3185-3294
 Gene   B0511.1 10946-11208

A comment can be added to features by adding a fourth column. These comments will be rendered as under-the-glyph descriptions by those glyphs that honor descriptions:

 Gene  B0511.1  516-619,3185-3294,10946-11208 "Putative primase"

Columns are separated using whitespace, not (necessarily) tabs. Embedded whitespace can be escaped using quote marks or backslashes in the same way as in the shell:

 'Putative Gene' my\ favorite\ gene 516-11208

Features can be grouped so that they are rendered by the "group" glyph (so far this has only been used to relate 5' and 3' ESTs). To start a group, create a two-column feature entry showing the group type and a name for the group. Follow this with a list of feature entries with a blank type. For example:

 EST    yk53c10
        yk53c10.3       15000-15500,15700-15800
        yk53c10.5       18892-19154

This example is declaring that the ESTs named yk53c10.3 and yk53c10.5 belong to the same group named yk53c10.

METHODS

$features = Bio::Graphics::FeatureFile->new(@args)

Create a new Bio::Graphics::FeatureFile using @args to initialize the object. Arguments are -name=>value pairs:

  Argument         Value
  --------         -----

   -file           Read data from a file path or filehandle.  Use
                   "-" to read from standard input.

   -text           Read data from a text scalar.

   -map_coords     Coderef containing a subroutine to use for remapping
                   all coordinates.

   -smart_features Flag indicating that the features created by this
                   module should be made aware of the FeatureFile
                   object by calling their configurator() method.

   -safe           Indicates that the contents of this file is trusted.
                   Any option value that begins with the string "sub {"
                   or \&subname will be evaluated as a code reference.

The -file and -text arguments are mutually exclusive, and -file will supersede the other if both are present.

-map_coords points to a coderef with the following signature:

  ($newref,[$start1,$end1],[$start2,$end2]....)
            = coderef($ref,[$start1,$end1],[$start2,$end2]...)

See the Bio::Graphics::Browser (part of the generic genome browser package) for an illustration of how to use this to do wonderful stuff.

The -smart_features flag is used by the generic genome browser to provide features with a way to access the link-generation code. See gbrowse for how this works.

If the file is trusted, and there is an option named "init_code" in the [GENERAL] section of the file, it will be evaluated as perl code immediately after parsing. You can use this to declare global variables and subroutines for use in option values.

($rendered,$panel) = $features->render([$panel, $position_to_insert, $options, $max_bump, $max_label, $selector])

Render features in the data set onto the indicated Bio::Graphics::Panel. If no panel is specified, creates one.

All arguments are optional.

$panel is a Bio::Graphics::Panel that has previously been created and configured.

$position_to_insert indicates the position at which to start inserting new tracks. The last current track on the panel is assumed.

$options is a scalar used to control automatic expansion of the tracks. 0=auto, 1=compact, 2=expanded, 3=expand and label, 4=hyperexpand, 5=hyperexpand and label.

$max_bump and $max_label indicate the maximum number of features before bumping and labeling are turned off.

$selector is a code ref that can be used to filter which features to render. It receives a feature and should return true to include the feature and false to exclude it.

In a scalar context returns the number of tracks rendered. In a list context, returns a three-element list containing the number of features rendered, the created panel, and a list of all the track objects created.

$error = $features->error([$error])

Get/set the current error message.

$smart_features = $features->smart_features([$flag]

Get/set the "smart_features" flag. If this is set, then any features added to the featurefile object will have their configurator() method called using the featurefile object as the argument.

$features->add_feature($feature [=>$type])

Add a new Bio::FeatureI object to the set. If $type is specified, the object will be added with the indicated type. Otherwise, the feature's primary_tag() method will be invoked to get the type.

$features->add_type($type=>$hashref)

Add a new feature type to the set. The type is a string, such as "EST". The hashref is a set of key=>value pairs indicating options to set on the type. Example:

  $features->add_type(EST => { glyph => 'generic', fgcolor => 'blue'})

When a feature of type "EST" is rendered, it will use the generic glyph and have a foreground color of blue.

$features->set($type,$tag,$value)

Change an individual option for a particular type. For example, this will change the foreground color of EST features to my favorite color:

  $features->set('EST',fgcolor=>'chartreuse')
$value = $features->setting($stanza => $option)

In the two-element form, the setting() method returns the value of an option in the configuration stanza indicated by $stanza. For example:

  $value = $features->setting(general => 'height')

will return the value of the "height" option in the [general] stanza.

Call with one element to retrieve all the option names in a stanza:

  @options = $features->setting('general');

Call with no elements to retrieve all stanza names:

  @stanzas = $features->setting;
$value = $features->code_setting($stanza=>$option);

This works like setting() except that it is also able to evaluate code references. These are options whose values begin with the characters "sub {". In this case the value will be passed to an eval() and the resulting codereference returned. Use this with care!

$flag = $features->safe([$flag]);

This gets or sets and "safe" flag. If the safe flag is set, then calls to setting() will invoke code_setting(), allowing values that begin with the string "sub {" to be interpreted as anonymous subroutines. This is a potential security risk when used with untrusted files of features, so use it with care.

@args = $features->style($type)

Given a feature type, returns a list of track configuration arguments suitable for suitable for passing to the Bio::Graphics::Panel->add_track() method.

$glyph = $features->glyph($type);

Return the name of the glyph corresponding to the given type (same as $features->setting($type=>'glyph')).

@types = $features->configured_types()

Return a list of all the feature types currently known to the feature file set. Roughly equivalent to:

  @types = grep {$_ ne 'general'} $features->setting;
@types = $features->types()

This is similar to the previous method, but will return *all* feature types, including those that are not configured with a stanza.

$features = $features->features($type)

Return a list of all the feature types of type "$type". If the featurefile object was created by parsing a file or text scalar, then the features will be of type Bio::Graphics::Feature (which follow the Bio::FeatureI interface). Otherwise the list will contain objects of whatever type you added with calls to add_feature().

Two APIs:

  1) original API:

      # Reference to an array of all features of type "$type"
      $features = $features-E<gt>features($type)

      # Reference to an array of all features of all types
      $features = $features-E<gt>features()

      # A list when called in a list context
      @features = $features-E<gt>features()

   2) Bio::Das::SegmentI API:

       @features = $features-E<gt>features(-type=>['list','of','types']);

       # variants
       $features = $features-E<gt>features(-type=>['list','of','types']);
       $features = $features-E<gt>features(-type=>'a type');
       $iterator = $features-E<gt>features(-type=>'a type',-iterator=>1);
@features = $features->features($type)

Return a list of all the feature types of type "$type". If the featurefile object was created by parsing a file or text scalar, then the features will be of type Bio::Graphics::Feature (which follow the Bio::FeatureI interface). Otherwise the list will contain objects of whatever type you added with calls to add_feature().

get_seq_stream

 Title   : get_seq_stream
 Usage   : $stream = $s->get_seq_stream(@args)
 Function: get a stream of features that overlap this segment
 Returns : a Bio::SeqIO::Stream-compliant stream
 Args    : see below
 Status  : Public

This is the same as feature_stream(), and is provided for Bioperl compatibility. Use like this:

 $stream = $s->get_seq_stream('exon');
 while (my $exon = $stream->next_seq) {
    print $exon->start,"\n";
 }

get_feature_by_name

 Usage   : $db->get_feature_by_name(-name => $name)
 Function: fetch features by their name
 Returns : a list of Bio::DB::GFF::Feature objects
 Args    : the name of the desired feature
 Status  : public

This method can be used to fetch a named feature from the file.

The full syntax is as follows. Features can be filtered by their reference, start and end positions

  @f = $db->get_feature_by_name(-name  => $name,
                                -ref   => $sequence_name,
                                -start => $start,
                                -end   => $end);

This method may return zero, one, or several Bio::Graphics::Feature objects.

search_notes

 Title   : search_notes
 Usage   : @search_results = $db->search_notes("full text search string",$limit)
 Function: Search the notes for a text string
 Returns : array of results
 Args    : full text search string, and an optional row limit
 Status  : public

Each row of the returned array is a arrayref containing the following fields:

  column 1     Display name of the feature
  column 2     The text of the note
  column 3     A relevance score.

get_feature_stream(), top_SeqFeatures(), all_SeqFeatures()

Provided for compatibility with older BioPerl and/or Bio::DB::GFF APIs.

@refs = $features->refs

Return the list of reference sequences referred to by this data file.

$min = $features->min

Return the minimum coordinate of the leftmost feature in the data set.

$max = $features->max

Return the maximum coordinate of the rightmost feature in the data set.

$mtime = $features->mtime
$atime = $features->atime
$ctime = $features->ctime
$size = $features->size

Returns stat() information about the data file, for featurefile objects created using the -file option. Size is in bytes. mtime, atime, and ctime are in seconds since the epoch.

$label = $features->feature2label($feature)

Given a feature, determines the configuration stanza that bests describes it. Uses the feature's type() method if it has it (DasI interface) or its primary_tag() method otherwise.

Given a feature, tries to generate a URL to link out from it. This uses the 'link' option, if one is present. This method is a convenience for the generic genome browser.

$citation = $features->citation($feature)

Given a feature, tries to generate a citation for it, using the "citation" option if one is present. This method is a convenience for the generic genome browser.

$name = $features->name([$feature])

Get/set the name of this feature set. This is a convenience method useful for keeping track of multiple feature sets.

Appendix -- Sample Feature File

 # file begins
 [general]
 pixels = 1024
 bases = 1-20000
 reference = Contig41
 height = 12

 [Cosmid]
 glyph = segments
 fgcolor = blue
 key = C. elegans conserved regions

 [EST]
 glyph = segments
 bgcolor= yellow
 connector = dashed
 height = 5;

 [FGENESH]
 glyph = transcript2
 bgcolor = green
 description = 1

 Cosmid B0511   516-619
 Cosmid B0511   3185-3294
 Cosmid B0511   10946-11208
 Cosmid B0511   13126-13511
 Cosmid B0511   11394-11539
 EST    yk260e10.5      15569-15724
 EST    yk672a12.5      537-618,3187-3294
 EST    yk595e6.5       552-618
 EST    yk595e6.5       3187-3294
 EST    yk846e07.3      11015-11208
 EST    yk53c10
        yk53c10.3       15000-15500,15700-15800
        yk53c10.5       18892-19154
 EST    yk53c10.5       16032-16105
 SwissProt      PECANEX 13153-13656     Swedish fish
 FGENESH        Predicted gene 1        1-205,518-616,661-735,3187-3365,3436-3846       Pfam domain
 FGENESH        Predicted gene 2        5513-6497,7968-8136,8278-8383,8651-8839,9462-9515,10032-10705,10949-11340,11387-11524,11765-12067,12876-13577,13882-14121,14169-14535,15006-15209,15259-15462,15513-15753,15853-16219   Mysterious
 FGENESH        Predicted gene 3        16626-17396,17451-17597
 FGENESH        Predicted gene 4        18459-18722,18882-19176,19221-19513,19572-19835 Transmembrane protein
 # file ends

SEE ALSO

Bio::Graphics::Panel, Bio::Graphics::Glyph, Bio::Graphics::Feature, Bio::Graphics::FeatureFile

AUTHOR

Lincoln Stein <lstein@cshl.org>.

Copyright (c) 2001 Cold Spring Harbor Laboratory

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See DISCLAIMER.txt for disclaimers of warranty.