Class: PluginAmplicons
- Defined in:
- lib/seqtrimnext/plugins/plugin_amplicons.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
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/plugin_amplicons.rb', line 135 def self.check_params(params) errors=[] comment='Blast E-value used as cut-off when searching for primers' # default_value = 1e-6 default_value = 1 params.check_param(errors,'blast_evalue_primers','Float',default_value,comment) comment='Minimum required identity (%) for a reliable primer' default_value = 95 params.check_param(errors,'blast_percent_primers','Integer',default_value,comment) comment='Minimun primer size' default_value = 15 params.check_param(errors,'min_primer_size','Integer',default_value,comment) comment='Path for primers database' # default_value = File.join($FORMATTED_DB_PATH,'adapters_ab.fasta') default_value=nil params.check_param(errors,'primers_db','DB',default_value,comment) return errors end |
Instance Method Details
#do_blasts(seqs) ⇒ Object
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# File 'lib/seqtrimnext/plugins/plugin_amplicons.rb', line 13 def do_blasts(seqs) # find MIDS with less results than max_target_seqs value blast=BatchBlast.new("-db #{@params.get_param('primers_db')}",'blastn'," -task blastn-short -perc_identity #{@params.get_param('blast_percent_primers')}") $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/plugin_amplicons.rb', line 35 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 primers into the sequence" # puts blast_query.inspect # merge hits # primers=blast_query.merged_hits! # do not merge hits, since id is important primers=blast_query.hits min_primer_size=@params.get_param('min_primer_size').to_i # puts "MERGED:" # puts primers.inspect # type = 'ActionAbAdapter' actions=[] adapter_size=0 # filter primers by size primers = primers.select{|primer| (primer.size >= min_primer_size)}.sort{|p1,p2| p1.size<=>p2.size}.reverse # puts "FILTERED:" # puts primers.inspect # reject sequences with less than two primers if primers.count < 2 seq.seq_rejected=true seq.='Primer pair not found' # @stats[:rejected_seqs]={'rejected_seqs_by_contaminants' => 1} add_stats('rejected','primers_not_found') else # has two primers, or more if seq.seq_fasta.index('N') seq.seq_rejected=true seq.='At least one N found' # @stats[:rejected_seqs]={'rejected_seqs_by_contaminants' => 1} add_stats('rejected','one_n_found') else # puts "EL DE ARRIBA" # take first two primers and order them by qbeg left_primer = primers[0..1].sort{|p1,p2| p1.q_beg<=>p2.q_beg}.first right_primer = primers[0..1].sort{|p1,p2| p1.q_beg<=>p2.q_beg}.last # puts "LEFT_PRIMER:" # puts left_primer.inspect # puts "RIGHT_PRIMER:" # puts right_primer.inspect # if (left_primer.size>= min_primer_size) && (right_primer.size>= min_primer_size) a = seq.new_action(left_primer.q_beg,left_primer.q_end,'ActionLeftPrimer') a. = left_primer.subject_id a.tag_id = left_primer.subject_id a.reversed = left_primer.reversed a.left_action = true actions.push a add_stats('primer_size',left_primer.size) add_stats('primer_id',left_primer.subject_id) a = seq.new_action(right_primer.q_beg,right_primer.q_end,'ActionRightPrimer') a. = right_primer.subject_id a.reversed = right_primer.reversed a.tag_id = right_primer.subject_id a.right_action = true actions.push a add_stats('primer_size',right_primer.size) add_stats('primer_id',right_primer.subject_id) seq.add_file_tag(2, left_primer.subject_id, :file) seq.add_file_tag(2, right_primer.subject_id, :file) # end if !actions.empty? seq.add_actions(actions) add_stats('sequences_with_primers','count') # add_stats('sequences',seq.seq_fasta) end end # end end |