Class: FastaRetriever::Retriever

Inherits:
Object
  • Object
show all
Defined in:
lib/bio-fasta_retrieve.rb

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize ⇒ Retriever

Returns a new instance of Retriever.



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# File 'lib/bio-fasta_retrieve.rb', line 23

def initialize;end

Class Method Details

.compose_fasta(sequence, organism, chr, start_coord, end_coord) ⇒ Object

End parse_xml



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# File 'lib/bio-fasta_retrieve.rb', line 47

def self.compose_fasta(sequence,organism,chr,start_coord,end_coord)
  seq=Bio::Sequence::NA.new(sequence)
  seq_res=seq.to_fasta("#{organism}_#{chr}_#{start_coord}_#{end_coord}")
  return seq_res
end

.parse_xml(xml) ⇒ Object

parse sequence from xml



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# File 'lib/bio-fasta_retrieve.rb', line 42

def self.parse_xml(xml)
  xml_res=xml.xpath("//DNA").text.tr("\n","")
  return xml_res
end

.retrieve(organism, chr, start_coord, end_coord) ⇒ Object

input organism, chromosome, start, end separated by space (i.e. hg19 chr10 1000 2000)



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# File 'lib/bio-fasta_retrieve.rb', line 27

def self.retrieve(organism,chr,start_coord,end_coord)
  address="http://genome.ucsc.edu/cgi-bin/das/#{organism}/dna?segment=#{chr}:#{start_coord},#{end_coord}"
  xml=ucsc_connect(address)
  seq=compose_fasta(xml,organism,chr,start_coord,end_coord)       
  return seq
end

.ucsc_connect(address) ⇒ Object

connects to ucsc and retrieve xml with DNA sequence



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# File 'lib/bio-fasta_retrieve.rb', line 35

def self.ucsc_connect(address)
  xml = Nokogiri::XML(open(address))
  xml_res=parse_xml(xml)
  return xml_res
end