Class: Bio::Jaspar::Motif

Inherits:
Motifs::Motif
  • Object
show all
Defined in:
lib/bio-jaspar/jaspar.rb

Overview

Additional metadata information are stored if available. The metadata availability depends on the source of the JASPAR motif (a ‘pfm’ format file, a ‘jaspar’ format file or a JASPAR database).

A direct import of Bio.motifs.jaspar module in Biopython

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(matrix_id, name, opts = {}) ⇒ Motif

Construct a JASPAR Motif instance



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# File 'lib/bio-jaspar/jaspar.rb', line 43

def initialize(matrix_id, name, opts = {})
	opts = {
		:alphabet => DNA, 
		:instances => nil, 
		:counts => nil, 
		:collection => nil, 
		:tf_class => nil, 
		:tf_family => nil, 
		:species => nil, 
		:tax_group => nil, 
		:acc => nil, 
		:data_type => nil, 
		:medline => nil, 
		:pazar_id => nil, 
		:comment => nil
	}.merge(opts)

	super(opts[:alphabet], opts[:instances], opts[:counts])

	@name = name
	@matrix_id = matrix_id
	@collection = opts[:collection]
	@tf_class = opts[:tf_class]
	@tf_family = opts[:tf_family]
	@species = opts[:species]
	@tax_group = opts[:tax_group]
	@acc = opts[:acc]
	@data_type = opts[:data_type]
	@medline = opts[:medline]
	@pazar_id = opts[:pazar_id]
	@comment = opts[:comment]
end

Instance Attribute Details

#acc ⇒ Object

Returns the value of attribute acc.



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# File 'lib/bio-jaspar/jaspar.rb', line 38

def acc
  @acc
end

#collection ⇒ Object

Returns the value of attribute collection.



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# File 'lib/bio-jaspar/jaspar.rb', line 38

def collection
  @collection
end

#comment ⇒ Object

Returns the value of attribute comment.



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# File 'lib/bio-jaspar/jaspar.rb', line 38

def comment
  @comment
end

#data_type ⇒ Object

Returns the value of attribute data_type.



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# File 'lib/bio-jaspar/jaspar.rb', line 38

def data_type
  @data_type
end

#matrix_id ⇒ Object

Returns the value of attribute matrix_id.



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# File 'lib/bio-jaspar/jaspar.rb', line 38

def matrix_id
  @matrix_id
end

#medline ⇒ Object

Returns the value of attribute medline.



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# File 'lib/bio-jaspar/jaspar.rb', line 38

def medline
  @medline
end

#pazar_id ⇒ Object

Returns the value of attribute pazar_id.



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# File 'lib/bio-jaspar/jaspar.rb', line 38

def pazar_id
  @pazar_id
end

#species ⇒ Object

Returns the value of attribute species.



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# File 'lib/bio-jaspar/jaspar.rb', line 38

def species
  @species
end

#tax_group ⇒ Object

Returns the value of attribute tax_group.



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# File 'lib/bio-jaspar/jaspar.rb', line 38

def tax_group
  @tax_group
end

#tf_class ⇒ Object

Returns the value of attribute tf_class.



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# File 'lib/bio-jaspar/jaspar.rb', line 38

def tf_class
  @tf_class
end

#tf_family ⇒ Object

Returns the value of attribute tf_family.



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# File 'lib/bio-jaspar/jaspar.rb', line 38

def tf_family
  @tf_family
end

Instance Method Details

#==(other) ⇒ Object

Compare two JASPAR motifs for equality. Two motifs are equal if their matrix_ids match



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# File 'lib/bio-jaspar/jaspar.rb', line 150

def ==(other)
	return @matrix_id == other.matrix_id
end

#base_id ⇒ Object

Return the JASPAR base matrix ID



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# File 'lib/bio-jaspar/jaspar.rb', line 77

def base_id
	base_id, _ = Jaspar.split_jaspar_id(@matrix_id)
	return base_id
end

#hash ⇒ Object

Note: We assume the unicity of matrix IDs



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# File 'lib/bio-jaspar/jaspar.rb', line 144

def hash
	return @matrix_id.hash
end

#to_s ⇒ Object

We choose to provide only the filled metadata information.



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# File 'lib/bio-jaspar/jaspar.rb', line 91

def to_s
	tf_name_str = "TF name\t#{@name}\n"
	matrix_id_str = "Matrix ID\t#{@matrix_id}\n"
	the_string = tf_name_str + matrix_id_str

	if @collection
		collection_str = "Collection\t#{@collection}\n"
		the_string += collection_str
	end
     if @tf_class
       tf_class_str = "TF class\t#{@tf_class}\n"
       the_string += tf_class_str
     end
     if @tf_family
       tf_family_str = "TF family\t#{@tf_family}\n"
       the_string += tf_family_str
     end
     if @species
       species_str = "Species\t#{@species.join(",")}\n"
       the_string += species_str
     end
     if @tax_group
       tax_group_str = "Taxonomic group\t#{@tax_group}\n"
       the_string += tax_group_str
     end
     if @acc
       acc_str = "Accession\t#{@acc}\n"
       the_string += acc_str
     end
     if @data_type
       data_type_str = "Data type used\t#{@data_type}\n"
       the_string += data_type_str
     end
     if @medline
       medline_str = "Medline\t#{@medline}\n"
       the_string += medline_str
     end
     if @pazar_id
       pazar_id_str = "PAZAR ID\t#{@pazar_id}\n"
       the_string += pazar_id_str
     end
     if @comment
       comment_str = "Comments\t#{@comment}\n"
       the_string += comment_str
     end
     matrix_str = "Matrix:\n#{counts}\n\n"
     the_string += matrix_str
     return the_string
end

#version ⇒ Object

Return the JASPAR matrix version



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# File 'lib/bio-jaspar/jaspar.rb', line 83

def version
	_, version = Jaspar.split_jaspar_id(@matrix_id)
	return version
end