Class: PluginLinker

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

Overview

Author: Almudena Bocinos Rioboo

Defines the main methods that are necessary to execute PluginLinker

Inherit: Plugin

Constant Summary collapse

MAX_LINKER_ERRORS = 
2

Instance Attribute Summary

Attributes inherited from Plugin

#stats

Class Method Summary collapse

Instance Method Summary collapse

Methods inherited from Plugin

#add_plugin_stats, #add_stats, #add_text_stats, auto_setup, #can_execute?, check_param, #execute, 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



207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
 
# File 'lib/seqtrimnext/plugins/plugin_linker.rb', line 207

def self.check_params(params)
  errors=[]  
  
  comment='Blast E-value used as cut-off when searching for linkers in paired-ends'
default_value = 1e-10
params.check_param(errors,'blast_evalue_linkers','Float',default_value,comment)

comment='Minimum required identity (%) for a reliable linker'
default_value = 95
params.check_param(errors,'blast_percent_linkers','Integer',default_value,comment)

  comment='Path for 454 linkers database'
default_value = File.join($FORMATTED_DB_PATH,'linkers.fasta')
params.check_param(errors,'linkers_db','DB',default_value,comment)

  
  return errors
end

Instance Method Details

#do_blasts(seqs) ⇒ Object 



73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
 
# File 'lib/seqtrimnext/plugins/plugin_linker.rb', line 73

def do_blasts(seqs)
   # find MIDS  with less results than max_target_seqs value 
   blast = BatchBlast.new("-db #{@params.get_param('linkers_db')}",'blastn'," -task blastn-short  -evalue #{@params.get_param('blast_evalue_linkers')} -perc_identity #{@params.get_param('blast_percent_linkers')}")  #get linkers          

   $LOG.debug('BLAST:'+blast.get_blast_cmd)

   fastas=[]

   seqs.each do |seq|
    fastas.push ">"+seq.seq_name
    fastas.push seq.seq_fasta
   end

   # fastas=fastas.join("\n")

   blast_table_results = blast.do_blast(fastas)

   # puts blast_table_results.inspect

   return blast_table_results
end

#exec_seq(seq, blast_query) ⇒ Object 



96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
 
# File 'lib/seqtrimnext/plugins/plugin_linker.rb', line 96

def exec_seq(seq,blast_query)
  if blast_query.query_id != seq.seq_name
    raise "Blast and seq names does not match, blast:#{blast_query.query_id} sn:#{seq.seq_name}"
  end
   $LOG.debug "[#{self.class.to_s}, seq: #{seq.seq_name}]: looking for linker into the sequence"
   
   # key_beg,key_end=search_key(seq,0,3)   if false       
   # blast = BatchBlast.new("-subject #{File.join($FORMATTED_DB_PATH,'linkers.fasta')}",'blastn'," -task blastn  -evalue #{@params.get_param('blast_evalue_linkers')} -perc_identity #{@params.get_param('blast_percent_linkers')}")  #get linkers
   # blast = BatchBlast.new("-db #{File.join($FORMATTED_DB_PATH,'linkers.fasta')}",'blastn'," -task blastn-short  -evalue #{@params.get_param('blast_evalue_linkers')} -perc_identity #{@params.get_param('blast_percent_linkers')}")  #get linkers          
   # 
   # blast_table_results = blast.do_blast(seq.seq_fasta)             #rise seq to linkers  executing over blast 
  

   #blast_table_results = BlastTableResult.new(res) 
   actions=[]  
   linker_size=0
        
   if (!blast_query.hits.empty?) #linker found
   
	linkers = merge_hits_with_same_qbeg_and_qend(blast_query.hits)

	if linkers.count ==1
	
       linker=linkers.first
       
       linker_size=linker.q_end-linker.q_beg+1
     
     if (linker.gaps+linker.mismatches>MAX_LINKER_ERRORS) # number of ERRORS and GAPs is higher than MAX_LINKER_ERRORS, 
         seq.seq_rejected=true
         seq.seq_rejected_by_message='linker with mismatches'
         # @stats[:rejected_seqs]={'rejected_seqs_by_errors' => 1}
         add_stats('rejected','by_linker_errors')
	 		   add_stats('linker_errors',linker.gaps+linker.mismatches)
     else     
       #Create an ActionLinker
        a = seq.new_action(linker.q_beg,linker.q_end,'ActionLinker') # adds the ActionLinker to the sequence 
        a.message = linker.subject_id 
        a.tag_id = linker.subject_id
        actions.push a  
        
          # seq.add_file_tag(0, 'paired', :file)
        
        add_stats('linker_id',linker.subject_id)
        add_stats('linker_id','total')
        
     end
     
	else # multiple linkers found
	  q_begs=[]
	  q_ends=[]

	  linker_count=linkers.count
	  
		linkers.each do |linker|
			#puts "*MULTILINKER* #{linker.subject_id[0..40].ljust(40)} #{linker.q_beg.to_s.rjust(6)} #{linker.q_end.to_s.rjust(6)} #{linker.s_beg.to_s.rjust(6)} #{linker.s_end.to_s.rjust(6)}"
			q_begs.push linker.q_beg
			q_ends.push linker.q_end

		end
     		
   		first_linker = linkers.first
   		last_linker = linkers.last
     	
 		  a = seq.new_action(q_begs.min,q_ends.max,'ActionMultipleLinker') # adds the ActionLinker to the sequence
      a.message = "#{linker_count} x #{first_linker.subject_id}"
      a.tag_id = first_linker.subject_id
      
      #determine with part (left or right) has the best quality
      left_quals = seq.seq_qual[0,q_begs.min]
	  sum_left=sum_quals(left_quals)
      
      right_quals = seq.seq_qual[q_ends.max+1..seq.seq_qual.length]
      sum_right=sum_quals(right_quals)
      
      if sum_left>=sum_right
       a.right_action=true
     else
     		a.left_action=true
     	end
      
      #puts "SUM QUAL LEFT:#{sum_left} count:#{left_quals.length}"
      #puts "SUM QUAL RIGHT:#{sum_right} count:#{right_quals.length}"
      
      
      actions.push a
      
      add_stats('multiple_linker_id',first_linker.subject_id)
      add_stats('multiple_linker_id','total')
      add_stats('multiple_linker_count',linker_count)
      
#				puts "=== > seq_qual: #{seq.seq_qual.count}"
#        seq.get_qual_inserts.each do |qi|
#        		puts "==> #{qi.join(' ')}"
#        end

			end
			
		else # no linker found
 		add_stats('without_linker',linker_size)
  end
   
   
  if !actions.empty?
  #Add actions
  seq.add_actions(actions)
 end

end

#merge_hits_with_same_qbeg_and_qend(hits) ⇒ Object 



61
62
63
64
65
66
67
68
69
70
71
 
# File 'lib/seqtrimnext/plugins/plugin_linker.rb', line 61

def merge_hits_with_same_qbeg_and_qend(hits)
 	res =[]

		hits.each do |hit|
		if !res.find{|h| (h.q_beg==hit.q_beg) && (h.q_end==hit.q_end)}
			res.push hit
		end
		end  

		return res
end

#sum_quals(a) ⇒ Object

It’s created an ActionInsert or ActionShortInsert after the ActionLinker

def add_action_after_linker(p_q_end,size_insert,actions,seq) 

size_min_insert = @params.get_param('size_min_insert').to_i     

if ((p_q_end<seq.seq_fasta.size-1) && (size_insert>=size_min_insert) )  #if linker's positions are right 
  #It's created an ActionInsert after the ActionLinker
  a = seq.new_action(p_q_end+1,seq.seq_fasta.size-1,"ActionInsert") # adds the ActionInsert to the sequence before adding the actionMid

  actions.push a

elsif (p_q_end<seq.seq_fasta.size-1)   #if linker's positions are right and insert's size is short 
  #It's created an ActionInsert after the ActionLinker
  a = seq.new_action(p_q_end+1,seq.seq_fasta.size-1,"ActionShortInsert") # adds the ActionInsert to the sequence before adding the actionMid

  actions.push a 
end

end



53
54
55
56
57
58
59
 
# File 'lib/seqtrimnext/plugins/plugin_linker.rb', line 53

def sum_quals(a)
 	res = 0
 	
 	a.map{|e| res+=e}
 	
return res
end