class PluginVectors
Author: Almudena Bocinos Rioboo
Defines the main methods that are necessary to execute PluginVectors
Inherit: Plugin
Constants
- MAX_TARGETS_SEQS
MIN_VECTOR_SIZE=30
MAX_TO_EXTREME=(MIN_VECTOR_SIZE/2).to_i
Public Class Methods
check_params(params)
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Returns an array with the errors due to parameters are missing
# File lib/seqtrimnext/plugins/plugin_vectors.rb, line 161 def self.check_params(params) errors=[] comment='Blast E-value used as cut-off when searching for vector fragments' default_value = 1e-1 params.check_param(errors,'blast_evalue_vectors','Float',default_value,comment) comment='Minimum required identity (%) for a reliable vector fragment' default_value = 90 params.check_param(errors,'blast_percent_vectors','Integer',default_value,comment) comment='Correct sequences could contain vectors only close to the read end (not within the sequence). The following variable indicates the number of nucleotides from the 5\' or 3\' end that are allowed for considering a vector fragment located at the end. Otherwise, the vector fragment will be qualified as internal and the sequence will be rejected' default_value = 8 params.check_param(errors,'max_vector_to_end','Integer',default_value,comment) comment='If a vector fragment is qualified as internal, the fragment should be long enough to be sure that it is a true vector fragment. This is the minimum length of a vector fragment that enables sequence rejection by an internal, unexpected vector' default_value = 50 params.check_param(errors,'min_vector_seq_presence','Integer',default_value,comment) comment='Vectors database path' default_value = File.join($FORMATTED_DB_PATH,'vectors.fasta') params.check_param(errors,'vectors_db','DB',default_value,comment) comment='Rejects sequences with vectors in the middle' default_value = 'true' params.check_param(errors,'middle_vector_rejects','String',default_value,comment) # params.split_databases('vectors_db') return errors end
Public Instance Methods
all_vector_in_linker(vector_beg,vector_end,seq)
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# File lib/seqtrimnext/plugins/plugin_vectors.rb, line 21 def all_vector_in_linker(vector_beg,vector_end,seq) linkers=seq.get_actions(ActionLinker) # res=((linkers.count>=1) && (vector_beg>=linkers[0].start_pos) && (vector_end<=linkers[0].end_pos)) # puts " RES #{res} insert-start #{seq.insert_start} #{linkers.count}>=1 #{vector_beg+seq.insert_start}>=#{linkers[0].start_pos}) && #{vector_end+seq.insert_start}<=#{linkers[0].end_pos})) " return ((linkers.count>=1) && (vector_beg+seq.insert_start>=linkers[0].start_pos) && (vector_end+seq.insert_start<=linkers[0].end_pos)) end
do_blasts(seqs)
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# File lib/seqtrimnext/plugins/plugin_vectors.rb, line 28 def do_blasts(seqs) # find MIDS with less results than max_target_seqs value blast = BatchBlast.new("-db #{@params.get_param('vectors_db')}",'blastn'," -task blastn-short -evalue #{@params.get_param('blast_evalue_vectors')} -perc_identity #{@params.get_param('blast_percent_vectors')} -culling_limit 1") #get vectors $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,:xml) t1=Time.now blast_table_results = blast.do_blast(fastas,:table,false) add_plugin_stats('execution_time','blast',Time.now-t1) t1=Time.now #blast_table_results = BlastStreamxmlResult.new(blast_table_results) blast_table_results = BlastTableResult.new(blast_table_results) add_plugin_stats('execution_time','parse',Time.now-t1) # puts blast_table_results.inspect return blast_table_results end
exec_seq(seq,blast_query)
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# File lib/seqtrimnext/plugins/plugin_vectors.rb, line 61 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 $LOG.debug "[#{self.class.to_s}, seq: #{seq.seq_name}]: looking for vectors into the sequence " #blast contra contaminantes # blast = BatchBlast.new("-db #{File.join($FORMATTED_DB_PATH,'vectors.fasta')}",'blastn'," -task blastn-short -evalue #{@params.get_param('blast_evalue_vectors')} -perc_identity #{@params.get_param('blast_percent_vectors')} -culling_limit 1") #get vectors # blast_table_results = blast.do_blast(seq.seq_fasta,:xml) #rise seq to contaminants executing over blast type = "ActionVectors" # puts res # blast_table_results.inspect # blast_table_results.querys.each do |query| # adds the correspondent action to the sequence # query.hits.each do |hit| # seq.add_action(hit.q_beg,hit.q_end,type) # end # end vectors=[] vectors_ids=[] # blast_table_results.querys.each do |query| # first round to save vectors without overlap # vectors_ids.push query.hits.subject_id if (not vectors_ids.include?(query.hits.subject_id)) merge_hits(blast_query.hits,vectors,vectors_ids) # end begin vectors2=vectors # second round to save vectors without overlap vectors = [] merge_hits(vectors2,vectors) end until (vectors2.count == vectors.count) actions = [] vectors_size=0 min_vector_size=@params.get_param('min_vector_seq_presence').to_i vectors.each do |v| # adds the correspondent action to the sequence #puts "*VECTOR* #{v.subject_id[0..40].ljust(40)} #{v.q_beg.to_s.rjust(6)} #{v.q_end.to_s.rjust(6)} #{v.s_beg.to_s.rjust(6)} #{v.s_end.to_s.rjust(6)}" vector_size=v.q_end-v.q_beg+1 # puts " in PLUGIN VECTOR previous to add action #{seq.insert_start} #{seq.insert_end}" # if ((vector_size>=MIN_VECTOR_SIZE) || ((vector_size<MIN_VECTOR_SIZE) && near_to_extrem(v,seq))) if (near_to_extrem(v,seq,10) || (vector_size>=min_vector_size) ) # puts " near #{near_to_extrem(v,seq,min_vector_size)} #{vector_size}>=#{min_vector_size}" #c.q_end+seq.insert_start+max_to_end)>=seq.seq_fasta_orig.size-1) #if ab adapter is very near to the end of original sequence piro_on=@params.get_param('next_generation_sequences').to_s if (((piro_on=='true') && (!seq.range_inside_action_type?(v.q_beg,v.q_end,ActionLinker)) && (!seq.range_inside_action_type?(v.q_beg,v.q_end,ActionMultipleLinker))) || # if vectors DB not is contained inside detected linkers (piro_on=='false')) # if vector is too big, and it isn't in an extreme, then it is an unexpected vector if !near_to_extrem(v,seq,min_vector_size) type = 'ActionUnexpectedVector' if @params.get_param('middle_vector_rejects').to_s=='true' seq.seq_rejected=true seq.seq_rejected_by_message='unexpected vector' end add_stats('rejected','unexpected_vector') end a = seq.new_action(v.q_beg,v.q_end,type) a.message = v.definition # a.found_definition.push v.subject_id # save the vectors definitions, each separately a.found_definition=vectors_ids # save the vectors definitions, each separately a.reversed = v.reversed a.cut=false if (piro_on=='true') # vectors don't cut when piro is on # puts "piro on #{piro_on} vector cut #{a.cut} ________________|||||||||| " # puts " no piro" if (piro_on=='false') actions.push a # @stats[:vector_size]={vector_size => 1} add_stats('vector_size',vector_size) vectors_ids.each do |v| add_stats('vectors_ids',v) end end end end seq.add_actions(actions) # end
near_to_extrem(c,seq,min_vector_size)
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# File lib/seqtrimnext/plugins/plugin_vectors.rb, line 16 def near_to_extrem(c,seq,min_vector_size) max_to_extreme=(min_vector_size/2).to_i return ((c.q_beg-max_to_extreme<0) || (( c.q_end+max_to_extreme)>=seq.seq_fasta.size-1) ) #return if vector is very near to the extremes of insert) end