Class: Exodb::Isoform

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

Instance Method Summary collapse

Methods included from XrefsField

#get_xref

Instance Method Details

#cds_location ⇒ Bio::Locations

Get exon location

Returns:

  • (Bio::Locations) —

    of exon



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# File 'lib/exodb/datamodel/isoform.rb', line 63

def cds_location
	return Bio::Locations.new(genbank_loc(:cds, :abs))
end

#cds_seq ⇒ 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/isoform.rb', line 79

def cds_seq
	return self.generef.whole_seq.splice(genbank_loc(:cds, :trela))
end

#codon_at(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/isoform.rb', line 108

def codon_at(codon_pos)
	return self.cds_seq.subseq(((codon_pos - 1) * 3) + 1 , ((codon_pos - 1) * 3) + 3)
end

#effect_pred(position, alt) ⇒ array

predict efect of variants

SPL-D splice_donor_variant SO:0001575 SPL-A splice_acceptor_variant SO:0001574 SPL-R splice_region_variant SO:0001630 COD-SS COD-SN COD-DS COD-DN COD-IS COD-IN UTR-3 UTR-5 INT INI STO-L STO-G PRO TFB

Parameters:

  • list (array) —

    of variants

Returns:

  • (array) —

    list of predicted effect



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# File 'lib/exodb/datamodel/isoform.rb', line 204

def effect_pred(position, alt)
	
	results = []
	
	prot_pos = genomic2prot_pos(position)
	
	if prot_pos
		case alt
		when /^-([ATCG])+/
			results.push({vartype: $1.length % 3 == 0 ? 'COD-DS' : 'COD-DN'})
		when /^\+([ATCG])+/
			results.push({vartype: ($1.length - 1) % 3 == 0 ? 'COD-IS' : 'COD-IN'})
		else
			results.push({vartype: 'COD-SS'})
		end
	else
		#case
		#when test
		#	#code
		#when test
		#	#code
		#else
		#	results.push({vartype: 'INT'})
		#end
	end
	
	results.push({vartype: splice_rel_location[position]}) if splice_rel_location.has_key?(position)
	
	return results
	
end

#exon_location ⇒ Bio::Locations

Get exon location

Returns:

  • (Bio::Locations) —

    of exon



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# File 'lib/exodb/datamodel/isoform.rb', line 56

def exon_location
	return Bio::Locations.new(genbank_loc(:exon, :abs))
end

#genomic2cds_pos(pos) ⇒ Integer

convert genomic position to cds position

Parameters:

  • genomic (Integer) —

    position

Returns:

  • (Integer) —

    Return all information of cds at given position



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# File 'lib/exodb/datamodel/isoform.rb', line 116

def genomic2cds_pos(pos)
	cds_location.relative(pos)
end

#genomic2prot_pos(pos) ⇒ Array

convert genomic position to cds position

Parameters:

  • genomic (Integer) —

    position

Returns:

  • (Array) —

    Return [codon and position in codon]



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# File 'lib/exodb/datamodel/isoform.rb', line 124

def genomic2prot_pos(pos)
	cds_location.relative(pos, :aa)
end

#mrna_len ⇒ Integer

get length of spliced RNA

Returns:

  • (Integer) —

    length of spliced RNA



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# File 'lib/exodb/datamodel/isoform.rb', line 93

def mrna_len
	return self.exon_location.length
end

#mrna_seq ⇒ Bio::Sequence

Get spliced RNA sequence

Returns:

  • (Bio::Sequence) —

    an RNA sequence



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# File 'lib/exodb/datamodel/isoform.rb', line 70

def mrna_seq
	return self.return self.generef.whole_seq.splice(genbank_loc(:exon, :trela)).rna
end

#prot_len ⇒ Integer

get length of protein product

Returns:

  • (Integer) —

    length of protein product



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# File 'lib/exodb/datamodel/isoform.rb', line 100

def prot_len
	return self.cds_location.length
end

#prot_seq ⇒ Bio::Sequence

Get spliced protein sequence

Returns:

  • (Bio::Sequence) —

    an protein sequence



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# File 'lib/exodb/datamodel/isoform.rb', line 86

def prot_seq
	return self.cds_seq().translate
end

#splice_rel_location ⇒ Array

get splice related position 1-3 base into exon and 3-8 base into intron

SPL-D splice_donor_variant SO:0001575 SPL-A splice_acceptor_variant SO:0001574 SPL-R splice_region_variant SO:0001630

Returns:

  • (Array) —

    Return position of splice related site in array of [start, stop]



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# File 'lib/exodb/datamodel/isoform.rb', line 134

def splice_rel_location
	
	if @splice_location == nil
		
		results = {}
		right = nil
		
		self[:exon].each do |exon|
			if !right.blank?
				if self.generef.strand == '+'
					results[right + 1] = 'SPL-D'
					results[right + 2] = 'SPL-D'
					results[exon[0] - 1] = 'SPL-A'
					results[exon[0] - 2] = 'SPL-A'
				else
					results[right + 1] = 'SPL-A'
					results[right + 2] = 'SPL-A'
					results[exon[0] - 1] = 'SPL-D'
					results[exon[0] - 2] = 'SPL-D'
				end
				
				Range.new(right - 2, right).each {|e| results[e] = 'SPL-R'}
				Range.new(right + 3, right + 8).each {|e| results[e] = 'SPL-R'}
				Range.new(exon[0], exon[0] + 2).each {|e| results[e] = 'SPL-R'}
				Range.new(exon[0] - 3, exon[0] - 8).each {|e| results[e] = 'SPL-R'}
				
				right = exon[1]
			else
				right = exon[1]
			end
		end
		
		@splice_location = results
		return results
	else
		return @splice_location
	end
	
end

#utr3location ⇒ Object 



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# File 'lib/exodb/datamodel/isoform.rb', line 178

def utr3location
	return Bio::Locations.new(self.generef.strand == '+' ? "#{self[:cds][-1][1] + 1}..#{self[:exon][-1][1]}" : "complement(#{self[:exon][0][0]}..#{self[:cds][0][0] - 1})")
end

#utr5location ⇒ Object 



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# File 'lib/exodb/datamodel/isoform.rb', line 174

def utr5location
	return Bio::Locations.new(self.generef.strand == '+' ? "#{self[:exon][0][0]}..#{self[:cds][0][0] - 1}" : "complement(#{self[:cds][-1][1] + 1}..#{self[:exon][-1][1]})")
end