Class: ActionPairedReads

Inherits:
SeqtrimAction show all
Defined in:
lib/seqtrimnext/actions/action_paired_reads.rb

Overview

Author: Almudena Bocinos Rioboo

Defines the main methods that are necessary to execute PluginPairedReads

Inherit: Plugin

Instance Attribute Summary

Attributes inherited from SeqtrimAction

#cut, #end_pos, #found_definition, #informative, #left_action, #message, #reversed, #right_action, #start_pos, #tag_id

Instance Method Summary collapse

Methods inherited from SeqtrimAction

#action_type, #apply_decoration, #contains?, #contains_action?, #decorate, #description, #inspect, #left_action?, #near_left?, #right_action?, #title, #to_hash, #to_human, #type

Constructor Details

#initialize(start_pos, end_pos) ⇒ ActionPairedReads

Returns a new instance of ActionPairedReads.



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# File 'lib/seqtrimnext/actions/action_paired_reads.rb', line 10

def initialize(start_pos,end_pos)
  super(start_pos,end_pos)    
  @cut =true

end

Instance Method Details

#apply_to(seq) ⇒ Object 



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# File 'lib/seqtrimnext/actions/action_paired_reads.rb', line 17

def apply_to(seq)
  $LOG.debug "Applying #{self.class}"
  
  #Storage the first and second subsequences
  subseq1 = seq.seq_fasta[0,@start_pos-1]        
  subseq2 = seq.seq_fasta[@end_pos+1,seq.seq_fasta.length-1]
  #$LOG.debug "\nSubsequence left: #{subseq1} \n Subsequence right: #{subseq2}}"

end