Class: Piro

Inherits:
FastaQualReader
  • Object
show all
Defined in:
lib/seqtrimnext/classes/piro.rb

Overview

Author

Almudena Bocinos Rioboo

Extract stats like mean of sequence’s length

Inherit

FastaReader

Instance Method Summary collapse

Constructor Details

#initialize(path_fasta, path_qual) ⇒ Piro

attr_accessor :na



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# File 'lib/seqtrimnext/classes/piro.rb', line 20

def initialize(path_fasta,path_qual)
  @path_fasta=path_fasta
  super(path_fasta,path_qual)
  MakeBlastDb.execute('../sequences/gemini.fasta')
  
  
end

Instance Method Details

#on_end_process ⇒ Object 



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# File 'lib/seqtrimnext/classes/piro.rb', line 67

def on_end_process()
  


  
 
 
end

#on_process_sequence(name_seq, fasta_seq, qual_seq) ⇒ Object 



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# File 'lib/seqtrimnext/classes/piro.rb', line 28

def on_process_sequence(name_seq,fasta_seq,qual_seq)
  puts "in piro, in on process sequence, #{name_seq}"
  
 
  blast = BatchBlast.new('-db '+ @path_fasta ,'blastn',' -task blastn -evalue 1e-10 -perc_identity 95')  #get contaminants
  #blast = BatchBlast.new('DB/vectors.fasta','blastn',' -task blastn ')  #get vectors

   $LOG.debug "-------OK----"

  # puts seq.seq_fasta
   res = blast.do_blast(fasta_seq)             #rise seq to contaminants  executing over blast
  # 
  #     blast_table_results = BlastTableResult.new(res,nil)
  
  # vectors=[]
  #     blast_table_results.querys.each do |query|     # first round to save contaminants without overlap
  #       merge_hits(query.hits,vectors)
  #     end
  # 
  #     begin 
  #       vectors2=vectors                            # second round to save contaminants without overlap
  #       vectors = []
  #       merge_hits(vectors2,vectors)
  #     end until (vectors2.count == vectors.count) 
  # 
  # 
  #     vectors.each do |c|                           # adds the correspondent action to the sequence
  #       #if @seq_specie!=seq_specie-contaminant
  # 
  #       if (@params.get_param('genus')!=c.subject_id.split('_')[1])
  #          # puts "DIFFERENT SPECIE #{specie} ,#{hit.subject_id.split('_')[1].to_s}"
  #          a = seq.add_action(c.q_beg,c.q_end,type)
  #          a.message = c.subject_id
  #       end
  #     end
  
  
end