Class: Exodb::Generef

Inherits:
Reference show all
Includes:
GenomeLocationField
Defined in:
lib/exodb/datamodel/reference.rb

Instance Method Summary collapse

Methods included from GenomeLocationField

#begin, #chromosome, #end, #location_str, #parse_location, #start, #stop

Methods included from XrefsField

#get_xref

Instance Method Details

#can_translated? ⇒ Boolean

Check if Generef can translate

Returns:

  • (Boolean) —

    Return true if this can be translate



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# File 'lib/exodb/datamodel/reference.rb', line 212

def can_translated?()
	return self.has_sequence? && self.has_splices? && self.longest_splice != nil ? true : false
end

#dl_occurrent! ⇒ Object

Download incident data from TCGA



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

def dl_occurrent!
	
	if self.get_xref('urn:miriam:hgnc.symbol')
		
		cancerstudies = []
		
		open("http://www.cbioportal.org/public-portal/webservice.do?cmd=getCancerStudies") {|f|
			f.each_line {|line| cancerstudies.push(line.chomp.split("\t")[0])}
		}
		
		occurrents = {}
		totalcase = {}
		
		cancerstudies.each do |study|
			
			totalcase[study] = 0 if !totalcase.has_key?(study)
			
			open("http://www.cbioportal.org/public-portal/webservice.do?cmd=getCaseLists&cancer_study_id=#{study}") do |f|
				f.each_line do |line|
					totalcase[study] += line.chomp.split(/\t/)[4].split(' ').length if line =~ /\tSequenced Tumors\t/
				end
			end
			
			occurrents[study] = {} if !occurrents.has_key?(study)
			
			open("http://www.cbioportal.org/public-portal/webservice.do?cmd=getMutationData&genetic_profile_id=#{study}_mutations&gene_list=#{self.get_xref('urn:miriam:hgnc.symbol').id}") do |f|
				f.each_line do |line|
					dat = line.chomp.split(/\t/)
					
					if dat[5] == 'Missense_Mutation'
						
						occurrents[study][dat[7].split(/(\d+)/)[1]] = [] if !occurrents[study].has_key?(dat[7].split(/(\d+)/)[1])
						occurrents[study][dat[7].split(/(\d+)/)[1]].push(dat[2])
						
					end
					
				end
				
				
			end
		end
		
		self.occurrents.clear if self.occurrents
		
		occurrents.each_pair do |cancertype, v|
			v.each_pair do |position, occur|
				self.occurrents << Occurrent.new({cancertype: cancertype, position: position, occur: occur.uniq.sort, casenumber: totalcase[cancertype]})
			end
		end
		
		self.save!
		
	end
	
end

#dl_seq! ⇒ Object

Download sequence from web service please use by caution. NCBI will block scamming sequest



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# File 'lib/exodb/datamodel/reference.rb', line 71

def dl_seq!
	
	case self.chrrefseq
	when /\Aurn:miriam:refseq:/
		self.sequence = Bio::FastaFormat.new(Bio::NCBI::REST.efetch(self.chrrefseq.split(':', 4), {"db"=>"nucleotide", "rettype"=>"fasta", "retmode"=>"text", "seq_start"=>self.start, "seq_stop"=>self.end})).seq
	end
	
	self.save!
	
end

#dl_symbol! ⇒ Object

Download gene symbol from HGNC service



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# File 'lib/exodb/datamodel/reference.rb', line 84

def dl_symbol!
	
	baseuri = "http://rest.genenames.org/search"
	
	
	query = ""
	
	if self.get_xref('urn:miriam:refseq')
		query = "#{baseuri}/refseq_accession/#{self.chrrefseq.id.split('.')[0]}"
	elsif self.get_xref('urn:miriam:ncbigene')
		query = ""
	end
	
	if !query.empty?
		response = JSON.parse(open(query, 'Accept' => 'application/json').read)['response']
		if !response['docs'].empty?
			
			response['docs'].each do |e|
				self.add_to_set(:xrefs, "urn:miriam:hgnc:#{e["hgnc_id"]}")
				self.add_to_set(:xrefs, "urn:miriam:hgnc.symbol:#{e["symbol"]}")
			end
			
			self.save!
			
		end
		
	end
	
end

#has_sequence? ⇒ Boolean

Check if Generef has sequence

Returns:

  • (Boolean) —

    Return true if there is a sequence



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# File 'lib/exodb/datamodel/reference.rb', line 205

def has_sequence?()
	return self[:sequence] ? true : false
end

#has_splices? ⇒ Boolean

Check that this gene has any splice variant

Returns:

  • (Boolean) —

    true if has any splices



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# File 'lib/exodb/datamodel/reference.rb', line 198

def has_splices?
	return self.isoforms.exists?
end

#longest_splice ⇒ Object

return longest splice of this gene



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# File 'lib/exodb/datamodel/reference.rb', line 180

def longest_splice()
	length = 0
	longest = nil
	self.isoforms.each do |e|
		
		if e.prot_len > length
			length = e.prot_len
			longest = e
		end
		
	end
	
	return longest
end

#symbol ⇒ String

Get gene symbol

Returns:

  • (String) —

    Return gene symbol or any id from xrefs or ‘nosymbol’



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# File 'lib/exodb/datamodel/reference.rb', line 219

def symbol
	
	if self.get_xref('urn:miriam:hgnc.symbol')
		return self.get_xref('urn:miriam:hgnc.symbol').id
	elsif self.xrefs && !self.xrefs.empty?
		return self.xrefs.sort[0].id
	else
		return 'nosymbol'
	end
	
end

#to_seq ⇒ Bio::Sequence

return sequence as Bio::Sequence object

Returns:

  • (Bio::Sequence) —

    the contents reversed lexically



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# File 'lib/exodb/datamodel/reference.rb', line 175

def to_seq
	return self.sequence ? Bio::Sequence.auto(self.sequence) : Bio::Sequence.auto("")
end