Class: PluginKey

Inherits:
Plugin show all
Defined in:
lib/seqtrimnext/plugins/plugin_key.rb

Overview

Author: Almudena Bocinos Rioboo

Defines the main methods that are necessary to execute PluginKey

Inherit: Plugin

Instance Attribute Summary

Attributes inherited from Plugin

#stats

Class Method Summary collapse

Instance Method Summary collapse

Methods inherited from Plugin

#add_stats, #add_text_stats, auto_setup, check_param, get_graph_filename, get_graph_title, graph_ignored?, ignored_graphs, #initialize, #merge_hits, #overlapX?, plot_setup, valid_graphs

Constructor Details

This class inherits a constructor from Plugin

Class Method Details

.check_params(params) ⇒ Object

Returns an array with the errors due to parameters are missing



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# File 'lib/seqtrimnext/plugins/plugin_key.rb', line 56

def self.check_params(params)
  errors=[]
  
  # self.check_param(errors,params,'blast_evalue_mids','Float')
  # self.check_param(errors,params,'blast_percent_mids','Integer')
  comment='sequences containing with diferent keys (barcodes) are saved to separate folders'
 default_value='false'
 params.check_param(errors,'use_independent_folder_for_each_key','String',default_value,comment)
  
  
  return errors
end

Instance Method Details

#exec_seq(seq) ⇒ Object 



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# File 'lib/seqtrimnext/plugins/plugin_key.rb', line 23

def exec_seq(seq)
  $LOG.info "[#{self.class.to_s}, seq: #{seq.seq_name}]: marking key into the sequence" 
  # blast_table_results.inspect        
  
  actions=[]
  
  key_size=0
  # mid_size=0
  key_beg,key_end=[0,3]
  key_size=4
  key=seq.seq_fasta[0..3].upcase
  
  a = seq.new_action(key_beg,key_end,'ActionKey') # adds the actionKey to the sequence
  actions.push a       
  
  #Add actions  
  seq.add_actions(actions)
  
  
  if @group_by_key
    
    seq.add_file_tag(0,'key_' + key, :dir)
    add_stats('key_tag',key)
  end
  
  add_stats('key_size',key_size)
  # add_stats('mid_size',mid_size)
        

  
end

#execute(seqs) ⇒ Object

Begins the pluginKey’s execution to warn where is a key in the sequence “seq”



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# File 'lib/seqtrimnext/plugins/plugin_key.rb', line 14

def execute(seqs)
  @group_by_key=(@params.get_param('use_independent_folder_for_each_key')=='true')
  
  seqs.each do |s|
      exec_seq(s)
  end
end