Class: Exodb::Isoform

Inherits:
Object
  • Object
show all
Includes:
XrefsField, Mongoid::Document
Defined in:
lib/exodb/datamodel/reference.rb

Instance Method Summary collapse

Methods included from XrefsField

#get_xref

Instance Method Details

#get_cds_join(position = 0) ⇒ Object 



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# File 'lib/exodb/datamodel/reference.rb', line 301

def get_cds_join(position = 0)
	get_join_str(self[:cds], position)
end

#get_cds_seq(position = 0) ⇒ Bio::Sequence

Get spliced coding region sequence

Parameters:

  • end (Integer) —

    position to get sequence

Returns:

  • (Bio::Sequence) —

    an coding region sequence



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# File 'lib/exodb/datamodel/reference.rb', line 326

def get_cds_seq(position = 0)
	
	parent =  self.generef
	if parent.strand == '+'
		join = self.get_cds_join(position)
		return !join.empty? ? parent.to_seq.splicing("join(#{join})") : ""
	else
		join = self.get_cds_join(-position)
		return !join.empty? ? parent.to_seq.splicing("join(#{join})") : ""
	end
	
end

#get_codon(codon_pos) ⇒ Bio::Sequence

Get the codon sequence at the giving position base on position of amino acid

Parameters:

  • codon (Integer) —

    position

Returns:

  • (Bio::Sequence) —

    the codon at given position



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# File 'lib/exodb/datamodel/reference.rb', line 365

def get_codon(codon_pos)
	return self.get_cds_seq().subseq(((codon_pos - 1) * 3) + 1 , ((codon_pos - 1) * 3) + 3)
end

#get_dna_seq ⇒ Bio::Sequence

Get spliced DNA sequence

Returns:

  • (Bio::Sequence) —

    an DNA sequence



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# File 'lib/exodb/datamodel/reference.rb', line 308

def get_dna_seq
	parent =  self.generef
	return parent.strand == '+' ? parent.to_seq.splicing("join(#{self.get_exon_join})") : parent.to_seq.splicing("complement(join(#{self.get_exon_join}))")
end

#get_exon_join(position = 0) ⇒ Object 



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# File 'lib/exodb/datamodel/reference.rb', line 297

def get_exon_join(position = 0)
	get_join_str(self[:exon], position)
end

#get_join_str(arr, position = 0) ⇒ String

join exon or cds position into a string

Parameters:

  • input (Array) —

    array exon or cds

  • Position (Interger) —

    to stop positive value for forward read negative value for complement

Returns:

  • (String) —

    a string in start..end,start..end,…



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# File 'lib/exodb/datamodel/reference.rb', line 250

def get_join_str(arr, position = 0)
	
	reducer = self.generef.start - 1
	tmparr = []
	found = false
	
	if position > 0
		add = true
		arr.each do |e|
			
			if e[0] <= position && position <= e[1]
				tmparr.push([e[0], position])
				add = false
				found = true
			else
				tmparr.push(e) if add
			end
			
		end
	elsif position < 0
		position = position.abs
		add = false
		arr.each do |e|
			
			if e[0] <= position && position <= e[1]
				tmparr.push([position, e[1]])
				add = true
				found = true
			else
				tmparr.push(e) if add
			end
			
		end
	else
		tmparr = arr
	end
	
	tmparr = [] if !found && position != 0
	str = []
	
	tmparr.each do |e|
		str.push("#{e[0] - reducer}..#{e[1] - reducer}")
	end
	return str.join(',')
	
end

#get_mrna_seq ⇒ Bio::Sequence

Get spliced RNA sequence

Returns:

  • (Bio::Sequence) —

    an RNA sequence



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# File 'lib/exodb/datamodel/reference.rb', line 316

def get_mrna_seq
	parent =  self.generef
	return parent.strand == '+' ? parent.to_seq.splicing("join(#{self.get_exon_join})").rna : parent.to_seq.splicing("complement(join(#{self.get_exon_join}))").rna
end

#get_prot_pos(pos) ⇒ Array

convert genomic position to codon position

Parameters:

  • genomic (Integer) —

    position

Returns:

  • (Array) —

    Return all information of codon at given position



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# File 'lib/exodb/datamodel/reference.rb', line 373

def get_prot_pos(pos)
	
	seqlen = self.get_cds_seq(pos).length
	if seqlen != 0
		return [((seqlen - 1) / 3) + 1, ((seqlen - 1) % 3) + 1]
	else
		return []
	end
	
end

#get_prot_seq ⇒ Bio::Sequence

Get spliced protein sequence

Returns:

  • (Bio::Sequence) —

    an protein sequence



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# File 'lib/exodb/datamodel/reference.rb', line 342

def get_prot_seq
	parent =  self.generef
	return parent.strand == '+' ? parent.to_seq.splicing("join(#{self.get_cds_join})").translate : parent.to_seq.splicing("complement(join(#{self.get_cds_join}))").translate
end

#prot_len ⇒ Integer

get length of protein product

Returns:

  • (Integer) —

    length of protein product



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# File 'lib/exodb/datamodel/reference.rb', line 357

def prot_len
	return self.get_prot_seq.length
end

#rna_len ⇒ Integer

get length of spliced RNA

Returns:

  • (Integer) —

    length of spliced RNA



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# File 'lib/exodb/datamodel/reference.rb', line 350

def rna_len
	return self.get_mrna_seq.length
end