Class: PluginAdaptersOld
- Defined in:
- lib/seqtrimnext/plugins_old/plugin_adapters_old.rb
Overview
Author: Almudena Bocinos Rioboo
Defines the main methods that are necessary to execute PluginAdapters
Inherit: Plugin
Instance Attribute Summary
Attributes inherited from Plugin
Class Method Summary collapse
-
.check_params(params) ⇒ Object
Returns an array with the errors due to parameters are missing.
Instance Method Summary collapse
- #cut_by_right(adapter, seq) ⇒ Object
- #do_blasts(seqs) ⇒ Object
- #exec_seq(seq, blast_query) ⇒ Object
- #get_type_adapter(p_start, p_end, seq) ⇒ Object
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
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# File 'lib/seqtrimnext/plugins_old/plugin_adapters_old.rb', line 137 def self.check_params(params) errors=[] comment='Blast E-value used as cut-off when searching for adapters or primers' default_value = 1e-6 params.check_param(errors,'blast_evalue_adapters','Float',default_value,comment) comment='Minimum required identity (%) for a reliable adapter' default_value = 95 params.check_param(errors,'blast_percent_adapters','Integer',default_value,comment) comment='Path for adapter database' default_value = File.join($FORMATTED_DB_PATH,'adapters.fasta') params.check_param(errors,'adapters_db','DB',default_value,comment) return errors end |
Instance Method Details
#cut_by_right(adapter, seq) ⇒ Object
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# File 'lib/seqtrimnext/plugins_old/plugin_adapters_old.rb', line 36 def cut_by_right(adapter,seq) left_size = adapter.q_beg-seq.insert_start+1 right_size = seq.insert_end-adapter.q_end+1 left_size=0 if (left_size<0) right_size=0 if (right_size<0) return (left_size>(right_size/2).to_i) end |
#do_blasts(seqs) ⇒ Object
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# File 'lib/seqtrimnext/plugins_old/plugin_adapters_old.rb', line 47 def do_blasts(seqs) # find MIDS with less results than max_target_seqs value blast=BatchBlast.new("-db #{@params.get_param('adapters_db')}",'blastn'," -task blastn-short -evalue #{@params.get_param('blast_evalue_adapters')} -perc_identity #{@params.get_param('blast_percent_adapters')}") $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
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# File 'lib/seqtrimnext/plugins_old/plugin_adapters_old.rb', line 69 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 $LOG.debug "[#{self.class.to_s}, seq: #{seq.seq_name}]: looking for adapters into the sequence" # blast=BatchBlast.new("-db #{File.join($FORMATTED_DB_PATH,'adapters.fasta')}",'blastn'," -task blastn-short -evalue #{@params.get_param('blast_evalue_adapters')} -perc_identity #{@params.get_param('blast_percent_adapters')}") # blast with only one sequence, no with many sequences from a database #--------------------------------------------------------------------- # blast_table_results = blast.do_blast(seq.seq_fasta) #rise seq to adapterss executing over blast #blast_table_results = BlastTableResult.new(res) # blast_table_results.inspect adapters=[] # blast_table_results.querys.each do |query| # first round to save adapters without overlap merge_hits(blast_query,adapters) # end begin adapters2=adapters # second round to save adapters without overlap adapters = [] merge_hits(adapters2,adapters) end until (adapters2.count == adapters.count) actions=[] adapter_size=0 # @stats['adapter_size']={} adapters.each do |ad| # adds the correspondent action to the sequence type = get_type_adapter(ad.q_beg,ad.q_end,seq) a = seq.new_action(ad.q_beg,ad.q_end,type) # puts " state left_action #{a.left_action} right_action #{a.right_action}" adapter_size=ad.q_end-ad.q_beg+1 if cut_by_right(ad,seq) # puts "action right end1 #{seq.insert_end}" a.right_action=true #mark rigth action to get the left insert else # puts " cut1 by left #{seq.insert_start} ad #{ad.q_beg+seq.insert_start} #{ad.q_end+seq.insert_start}" a.left_action = true #mark left action to get the right insert end a. = ad.subject_id a.reversed = ad.reversed actions.push a # @stats[:adapter_size]={adapter_size => 1} add_stats('adapter_size',adapter_size) end seq.add_actions(actions) # end |
#get_type_adapter(p_start, p_end, seq) ⇒ Object
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# File 'lib/seqtrimnext/plugins_old/plugin_adapters_old.rb', line 12 def get_type_adapter(p_start,p_end,seq) #if q_beg is nearer the left, add adapter action by the left, #if q_end esta is nearer the right , add adapter action by the right #NOTE: If the adapter is very near from left and rigth, #then the sequence isn't valid, because almost sequence is adapter. v1= p_end.to_i v2= p_start.to_i # puts " startadapter #{v2} endadapter #{v1} insert_start #{seq.insert_start} insert_end #{seq.insert_end}" # puts " #{v2+seq.insert_start} <? #{seq.seq_fasta.length - v1 - 1 + seq.seq_fasta_orig.length - seq.insert_end-1}" if (v2+seq.insert_start < (seq.seq_fasta.length - v1 - 1+ seq.seq_fasta_orig.length - seq.insert_end-1)) #IF THE NEAREST ONE IS THE LEFT type = "ActionLeftAdapter" else type = "ActionRightAdapter" end return type end |