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Bio-ToolBox-1.30
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/ Bio::ToolBox::Data::Feature

NAME

Bio::ToolBox::Data::Feature - Objects representing rows in a data table

DESCRIPTION

A Bio::ToolBox::Data::Feature is an object representing a row in the data table. Usually, this in turn represents an annotated feature or segment in the genome. As such, this object provides convenient methods for accessing and manipulating the values in a row, as well as methods for working with the represented genomic feature.

This class should not be used directly by the user. Rather, Feature objects are generated from a Bio::ToolBox::Data::Iterator object (generated itself from the row_stream function in Bio::ToolBox::Data), or the iterate function in Bio::ToolBox::Data. Please see the respective documentation for more information.

Example of working with a stream object.

  my $Data = Bio::ToolBox::Data->new(file => $file);
  
  # stream method
  my $stream = $Data->row_stream;
  while (my $row = $stream->next_row) {
	 # each $row is a Bio::ToolBox::Data::Feature object
	 # representing the row in the data table
	 my $value = $row->value($index);
	 # do something with $value
  }
  
  # iterate method
  $Data->iterate( sub {
     my $row = shift;
     my $number = $row->value($index);
     my $log_number = log($number);
     $row->value($index, $log_number);
  } );

METHODS

General information methods

row_index

Returns the index position of the current data row within the data table. Useful for knowing where you are at within the data table.

feature_type

Returns one of three specific values describing the contents of the data table inferred by the presence of specific column names. This provides a clue as to whether the table features represent genomic regions (defined by coordinate positions) or named database features. The return values include:

coordinate: Table includes at least chromosome and start
named: Table includes name, type, and/or Primary_ID
unknown: unrecognized

Methods to access row feature attributes

These methods return the corresponding value, if present in the data table, based on the column header name. If the row represents a named database object, try calling the feature() method first. This will retrieve the database SeqFeature object, and the attributes can then be retrieved using the methods below or on the actual database SeqFeature object.

These methods do not set attribute values. If you need to change the values in a table, use the value() method below.

seq_id

The name of the chromosome the feature is on.

start
end
stop

The coordinates of the feature or segment. Coordinates from known 0-based file formats, e.g. BED, are returned as 1-based. Coordinates must be integers to be returned. Zero or negative start coordinates are assumed to be accidents or poor programming and transformed to 1. Zero or negative stop coordinates are just ignored. Use the value() method if you don't want this to happen.

strand

The strand of the feature or segment. Returns -1, 0, or 1. Default is 0, or unstranded.

name
display_name

The name of the feature.

type

The type of feature. Typically either primary_tag or primary_tag:source_tag. In a GFF3 file, this represents columns 3 and 2, respectively. In annotation databases such as Bio::DB::SeqFeature::Store, the type is used to restrict to one of many different types of features, e.g. gene, mRNA, or exon.

id

Here, this represents the primary_ID in the database. Note that this number is unique to a specific database, and not portable between databases.

length

The length of the feature or segment.

Accessing and setting values in the row.

value($index)
value($index, $new_value)

Returns or sets the value at a specific column index in the current data row.

row_values

Returns an array or array reference representing all the values in the current data row.

Convenience Methods to database functions

The next three functions are convenience methods for using the attributes in the current data row to interact with databases. They are wrappers to methods in the <Bio::ToolBox::db_helper> module.

feature

Returns a SeqFeature object from the database using the name and type values in the current Data table row. The SeqFeature object is requested from the database named in the general metadata. If an alternate database is desired, you should change it first using the $Data->database() method. If the feature name or type is not present in the table, then nothing is returned.

See <Bio::DB::SeqFeature> and Bio::SeqFeatureI for more information about working with these objects.

segment

Returns a database Segment object corresponding to the coordinates defined in the Data table row. If a named feature and type are present instead of coordinates, then the feature is first automatically retrieved and a Segment returned based on its coordinates. The database named in the general metadata is used to establish the Segment object. If a different database is desired, it should be changed first using the general database() method.

See Bio::DB::SeqFeature::Segment and Bio::RangeI for more information about working with Segment objects.

get_score(%args)

This is a convenience method for the get_chromo_region_score method. It will return a single score value for the region defined by the coordinates or typed named feature in the current data row. If the Data table has coordinates, then those will be automatically used. If the Data table has typed named features, then the coordinates will automatically be looked up for you by requesting a SeqFeature object from the database.

The name of the dataset from which to collect the data must be provided. This may be a GFF type in a SeqFeature database, a BigWig member in a BigWigSet database, or a path to a BigWig, BigBed, Bam, or USeq file. Additional parameters may also be specified; please see the Bio::ToolBox::db_helper for full details.

If you wish to override coordinates that are present in the Data table, for example to extend or shift the given coordinates by some amount, then simply pass the new start and end coordinates as options to this method.

Here is an example of collecting mean values from a BigWig and adding the scores to the Data table.

my $index = $Data->add_column('MyData');
my $stream = $Data->row_stream;
while (my $row = $stream->next_row) {
   my $score = $row->get_score(
      'method'    => 'mean',
      'dataset'   => '/path/to/MyData.bw',
   );
   $row->value($index, $score);
}
get_position_scores(%args)

This is a convenience method for the get_region_dataset_hash method. It will return a hash of positions => scores over the region defined by the coordinates or typed named feature in the current data row. The coordinates for the interrogated region will be automatically provided.

Just like the get_score method, the dataset from which to collect the scores must be provided, along with any other optional arguments.

If you wish to override coordinates that are present in the Data table, for example to extend or shift the given coordinates by some amount, then simply pass the new start and end coordinates as options to this method.

Here is an example for collecting positioned scores around the 5 prime end of a feature from a BigWigSet directory.

my $stream = $Data->row_stream;
while (my $row = $stream->next_row) {
   my %position2score = $row->get_position_scores(
      'ddb'       => '/path/to/BigWigSet/',
      'dataset'   => 'MyData',
      'position'  => 5,
   )
   # do something with %position2score
}

Feature Export

These methods allow the feature to be exported in industry standard formats, including the BED format and the GFF format. Both methods return a formatted tab-delimited text string suitable for printing to file. The string does not include a line ending character.

These methods rely on coordinates being present in the source table. If the row feature represents a database item, the feature() method should be called prior to these methods, allowing the feature to be retrieved from the database and coordinates obtained.

bed_string(%args)

Returns a BED formatted string. By default, a 6-element string is generated, unless otherwise specified. Pass an array of key values to control how the string is generated. The following arguments are supported.

bed => <integer>

Specify the number of BED elements to include. The number of elements correspond to the number of columns in the BED file specification. A minimum of 3 (chromosome, start, stop) is required, and maximum of 6 is allowed (chromosome, start, stop, name, score, strand).

chromo => <text>
seq_id => <text>
start => <integer>
stop => <integer>
end => <integer>
strand => $strand

Provide alternate values from those defined or missing in the current row Feature. Note that start values are automatically converted to 0-base by subtracting 1.

name => <text>

Provide alternate or missing name value to be used as text in the 4th column. If no name is provided or available, a default name is generated.

score => <number>

Provide a numerical value to be included as the score. BED files typically use integer values ranging from 1..1000.

gff_string(%args)

Returns a GFF3 formatted string. Pass an array of key values to control how the string is generated. The following arguments are supported.

chromo => <text>
seq_id => <text>
start => <integer>
stop => <integer>
end => <integer>
strand => $strand

Provide alternate values from those defined or missing in the current row Feature.

source => <text>

Provide a text string to be used as the source_tag value in the 2nd column. The default value is null ".".

primary_tag => <text>

Provide a text string to be used as the primary_tag value in the 3rd column. The default value is null ".".

type => <text>

Provide a text string. This can be either a "primary_tag:source_tag" value as used by GFF based BioPerl databases, or "primary_tag" alone.

score => <number>

Provide a numerical value to be included as the score. The default value is null ".".

name => <text>

Provide alternate or missing name value to be used as the display_name. If no name is provided or available, a default name is generated.

attributes => [index],

Provide an anonymous array reference of one or more row Feature indices to be used as GFF attributes. The name of the column is used as the GFF attribute key.

AUTHOR

Timothy J. Parnell, PhD
Dept of Oncological Sciences
Huntsman Cancer Institute
University of Utah
Salt Lake City, UT, 84112

This package is free software; you can redistribute it and/or modify it under the terms of the Artistic License 2.0.