Class: Bio::Ngs::Homology

Inherits:
Object
  • Object
show all
Defined in:
lib/bio/ngs/homology.rb

Class Method Summary collapse

Class Method Details

.blast2text(file_in, file_out) ⇒ Object 



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# File 'lib/bio/ngs/homology.rb', line 44

def self.blast2text(file_in,file_out)
  out = File.open(file_out,"w")
  out.write("Query ID\tTarget ID\tTarget Description\tE-value\tIdentity\tPositive\n")
  Bio::Blast::XmlIterator.new(file_in).to_enum.each do |iter|
    iter.each do |hit|
      identity = 0.0
      positive = 0.0
      evalue = []
      length = 0
      hit.each do |hsp|
        identity += hsp.identity.to_f
        positive += hsp.positive.to_f
        evalue << hsp.evalue
        length += hsp.align_len
      end
      identity =  (identity / length)*100
      positive = (positive / length)*100
      evalue = evalue.inject{ |sum, el| sum + el }.to_f / evalue.size
      out.write([iter.query_def,hit.hit_id,hit.hit_def,evalue,identity,positive].join("\t")+"\n")
    end
  end
  out.close 
end

.blast_import(file, yaml_file = nil) ⇒ Object

Method to import a Blast XML output file into a BlastOuput table created according to ActiveRecord model Params: XML Blast file, YAML file for db connection, optional ActiveRecord models file



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# File 'lib/bio/ngs/homology.rb', line 16

def self.blast_import(file,yaml_file=nil)
  db = Bio::Ngs::Db.new :homology,yaml_file
  inserts = []
  Bio::Blast::XmlIterator.new(file).to_enum.each do |iter|
    iter.each do |hit|
      identity = 0.0
      positive = 0.0
      evalue = []
      length = 0
      hit.each do |hsp|
        identity += hsp.identity.to_f
        positive += hsp.positive.to_f
        evalue << hsp.evalue
        length += hsp.align_len
      end
      identity =  (identity / length)*100
      positive = (positive / length)*100
      evalue = evalue.inject{ |sum, el| sum + el }.to_f / evalue.size
      inserts << [iter.query_def,hit.hit_id.split('|')[1],hit.hit_def,evalue,identity,positive]
      if inserts.size == 1000
        db.insert_many(:blast_outputs,"INSERT INTO blast_outputs(query_id,target_id,target_description,evalue,identity,positive) VALUES(?,?,?,?,?,?)",inserts)
        inserts = []
      end  
    end
  end
  db.insert_many(:blast_outputs,"INSERT INTO blast_outputs(query_id,target_id,target_description,evalue,identity,positive) VALUES(?,?,?,?,?,?)",inserts) if inserts.size > 0
end

.go_annotation_to_json(file_out, library = nil, yaml_file = nil) ⇒ Object

Method to export the associations among genes and GO and store them into a JSON file that can be imported into the Ontology db Params: file to write JSON data



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# File 'lib/bio/ngs/homology.rb', line 88

def self.go_annotation_to_json(file_out,library=nil,yaml_file=nil)
  db = Bio::Ngs::Db.new :homology, yaml_file
  ontologies = []
  BlastOutput.find(:all).each do |result|
    ontology = Bio::Ngs::Ontology.new result.query_id
    ontology.go = result.go_annotations.map {|goa| goa.go_id}
    ontology.library = library
    ontologies << ontology
  end
  File.open(file_out,"w") {|f| f.write ontologies.to_json}
end

.goa_import(file, yaml_file = nil) ⇒ Object

Method to import a GO Annotation file into GoAnnotation table created according to ActiveRecord model Params: GOA file, YAML file for db connection (optional)



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# File 'lib/bio/ngs/homology.rb', line 71

def self.goa_import(file,yaml_file=nil)
  db = Bio::Ngs::Db.new :homology, yaml_file
  inserts = []
  File.open(file).each do |line|
    next if line.start_with? "!"
    line.chomp!
    inserts << line.split("\t")[0..14]
    if inserts.size == 1000
      db.insert_many(:go_annotations,"INSERT INTO go_annotations(db,entry_id,symbol,qualifier,go_id,db_ref,evidence,additional_identifier,aspect,name,synonym,molecule_type,taxon_id,date,assigned_by) VALUES(?,?,?,?,?,?,?,?,?,?,?,?,?,?,?)",inserts)
      inserts = []
    end
  end
  db.insert_many(:go_annotations,"INSERT INTO go_annotations(db,entry_id,symbol,qualifier,go_id,db_ref,evidence,additional_identifier,aspect,name,synonym,molecule_type,taxon_id,date,assigned_by) VALUES(?,?,?,?,?,?,?,?,?,?,?,?,?,?,?)",inserts) if inserts.size > 0
end