Class: BlastQuery

Inherits:
Object
  • Object
show all
Defined in:
lib/scbi_blast/blast_query.rb

Overview

Object to encapsulate a Blast Query

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(query_id) ⇒ BlastQuery

initializes a new Query object



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# File 'lib/scbi_blast/blast_query.rb', line 30

def initialize(query_id)
  @query_id = query_id
  @query_def = query_id
  @full_query_length = 0
  @hits = []
  # inspect
end

Instance Attribute Details

#full_query_length ⇒ Object

Returns the value of attribute full_query_length.



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# File 'lib/scbi_blast/blast_query.rb', line 27

def full_query_length
  @full_query_length
end

#hits ⇒ Object

Returns the value of attribute hits.



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# File 'lib/scbi_blast/blast_query.rb', line 26

def hits
  @hits
end

#query_def ⇒ Object

Returns the value of attribute query_def.



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# File 'lib/scbi_blast/blast_query.rb', line 27

def query_def
  @query_def
end

#query_id ⇒ Object

Returns the value of attribute query_id.



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# File 'lib/scbi_blast/blast_query.rb', line 27

def query_id
  @query_id
end

Instance Method Details

#add_hit(h) ⇒ Object

add a hit to query



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# File 'lib/scbi_blast/blast_query.rb', line 39

def add_hit(h)
  @hits.push h
end

#compare?(query) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/scbi_blast/blast_query.rb', line 78

def compare?(query)
  res=true
  

  # same hits
  res &&=( @hits.count==query.hits.count)
  
  # if !res 
  #    puts "Queries not equal:"
  #    puts inspect
  #    puts "="*20
  #    puts query.inspect
  #  end
  
  if res
    @hits.each_with_index do |h,i|
      res &&= h.compare?(query.hits[i])
    end
  end
  
  # if !res 
  #    puts "Queries hits not equal:"
  #    puts inspect
  #    puts "="*20
  #    puts query.inspect
  #  end
  
  res &&=( @query_id==query.query_id)
  res &&=( @query_def==query.query_def)
  res &&=( @full_query_length==query.full_query_length)
  
  
  return res
end

#inspect ⇒ Object

inspect query values with all hits



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# File 'lib/scbi_blast/blast_query.rb', line 44

def inspect
  res = "\n * Query  #{@query_id}, #{@query_def}, #{@full_query_length} :"
  res += "subject_id ident align_len mismatches gaps q_beg q_end s_beg s_end e_val bit_score reversed\n\n"
  @hits.each{ |h| res+= "=="+h.inspect+"\n" }

  return res
end

#merged_hits!(overlap_threshold = 0, merged_ids = nil) ⇒ Object

merge overlapping hits



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# File 'lib/scbi_blast/blast_query.rb', line 63

def merged_hits!(overlap_threshold=0, merged_ids=nil)
  res = []

  merge_hits(@hits,res,merged_ids)

  begin
    res2=res # iterate until no more overlaps
    res = []
    merge_hits(res2,res,merged_ids)
  end until (res2.count == res.count)


  return res
end

#size ⇒ Object

get num of hits



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# File 'lib/scbi_blast/blast_query.rb', line 53

def size
  return @hits.size
end

#sort(comand) ⇒ Object

sort hits by command



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# File 'lib/scbi_blast/blast_query.rb', line 58

def sort(comand)
  return @hits.sort(comand)
end