Class: SeqtrimWorker
- Inherits:
-
ScbiMapreduce::Worker
- Object
- ScbiMapreduce::Worker
- SeqtrimWorker
- Defined in:
- lib/seqtrimnext/classes/em_classes/seqtrim_worker.rb
Instance Method Summary collapse
- #add_output_data(obj) ⇒ Object
- #add_stat(stats, key, subkey, value, count = 1) ⇒ Object
- #closing_worker ⇒ Object
- #get_file(files, fn) ⇒ Object
- #get_mid_message(mid) ⇒ Object
-
#json_file(files) ⇒ Object
ACCESS TO FILES.
- #low_complexity_file(files, dir_name, file_name) ⇒ Object
- #low_sffinfo_file(files, dir_name, file_name) ⇒ Object
- #paired_file(files, dir_name, file_name) ⇒ Object
- #paired_file_ilu1(files, dir_name, file_name) ⇒ Object
- #paired_file_ilu2(files, dir_name, file_name) ⇒ Object
- #process_object(obj) ⇒ Object
- #receive_initial_config(obj) ⇒ Object
- #rejected_output_file(files) ⇒ Object
- #save_empty_insert(files, seq, stats) ⇒ Object
- #save_one_insert(files, seq, stats, inserts, qual_inserts, mid, dir_name, file_name) ⇒ Object
- #save_rejected_empty_or_single(files, seq, stats, inserts, qual_inserts, mid, dir_name, file_name) ⇒ Object
-
#save_rejected_seq(files, seq, stats) ⇒ Object
SAVE NORMAL ===============================.
- #save_two_inserts(files, seq, stats, inserts, qual_inserts, mid, dir_name, file_name) ⇒ Object
- #save_two_inserts_tuple(files, seq1, seq2, stats, inserts1, inserts2, qual_inserts1, qual_inserts2, mid, dir_name, file_name) ⇒ Object
- #sequence_file(files, dir_name, file_name) ⇒ Object
- #sffinfo_file(files, dir_name, file_name) ⇒ Object
- #starting_worker ⇒ Object
- #write_seq_to_files_normal(files, seq, stats) ⇒ Object
- #write_seq_to_files_tuple(files, seqs, stats) ⇒ Object
Instance Method Details
#add_output_data(obj) ⇒ Object
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# File 'lib/seqtrimnext/classes/em_classes/seqtrim_worker.rb', line 107 def add_output_data(obj) obj.output_text=[] if @tuple_size>1 obj.each_slice(@tuple_size) do |seqs| write_seq_to_files_tuple(obj.output_files,seqs, obj.stats) seqs.each do |seq| obj.output_text << seq.to_text end end else obj.each do |seq| write_seq_to_files_normal(obj.output_files,seq, obj.stats) obj.output_text << seq.to_text end end # @remove seqs since they are not needed anymore to write output files obj.remove_all_seqs end |
#add_stat(stats, key, subkey, value, count = 1) ⇒ Object
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# File 'lib/seqtrimnext/classes/em_classes/seqtrim_worker.rb', line 131 def add_stat(stats,key,subkey,value,count=1) stats[key]={} if !stats[key] stats[key][subkey]={} if !stats[key][subkey] stats[key][subkey][value]=0 if !stats[key][subkey][value] stats[key][subkey][value]+=count end |
#closing_worker ⇒ Object
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# File 'lib/seqtrimnext/classes/em_classes/seqtrim_worker.rb', line 102 def closing_worker end |
#get_file(files, fn) ⇒ Object
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# File 'lib/seqtrimnext/classes/em_classes/seqtrim_worker.rb', line 425 def get_file(files,fn) res=files[fn] if !res files[fn]=[] res=files[fn] end return res end |
#get_mid_message(mid) ⇒ Object
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# File 'lib/seqtrimnext/classes/em_classes/seqtrim_worker.rb', line 256 def (mid) if (mid.nil? || (mid.=='no_MID') ) # without mid mid_id = 'no_MID' = ' No MID found' else mid_id = mid.tag_id ='' if mid_id != = ' '+mid. end end return mid_id, end |
#json_file(files) ⇒ Object
ACCESS TO FILES
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# File 'lib/seqtrimnext/classes/em_classes/seqtrim_worker.rb', line 387 def json_file(files) return get_file(files,File.join(OUTPUT_PATH,'results.json')) end |
#low_complexity_file(files, dir_name, file_name) ⇒ Object
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# File 'lib/seqtrimnext/classes/em_classes/seqtrim_worker.rb', line 413 def low_complexity_file(files, dir_name, file_name) return get_file(files,File.join(OUTPUT_PATH,dir_name,'low_complexity_'+file_name+'.fastq')) end |
#low_sffinfo_file(files, dir_name, file_name) ⇒ Object
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# File 'lib/seqtrimnext/classes/em_classes/seqtrim_worker.rb', line 421 def low_sffinfo_file(files, dir_name, file_name) return get_file(files,File.join(OUTPUT_PATH,dir_name,'low_complexity_sff_info_'+file_name+'.txt')) end |
#paired_file(files, dir_name, file_name) ⇒ Object
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# File 'lib/seqtrimnext/classes/em_classes/seqtrim_worker.rb', line 400 def paired_file(files, dir_name, file_name) return get_file(files,File.join(OUTPUT_PATH,dir_name,'paired_'+file_name+'.fastq')) end |
#paired_file_ilu1(files, dir_name, file_name) ⇒ Object
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# File 'lib/seqtrimnext/classes/em_classes/seqtrim_worker.rb', line 404 def paired_file_ilu1(files, dir_name, file_name) return get_file(files,File.join(OUTPUT_PATH,dir_name,'paired_1_'+file_name+'.fastq')) end |
#paired_file_ilu2(files, dir_name, file_name) ⇒ Object
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# File 'lib/seqtrimnext/classes/em_classes/seqtrim_worker.rb', line 408 def paired_file_ilu2(files, dir_name, file_name) return get_file(files,File.join(OUTPUT_PATH,dir_name,'paired_2_'+file_name+'.fastq')) end |
#process_object(obj) ⇒ Object
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# File 'lib/seqtrimnext/classes/em_classes/seqtrim_worker.rb', line 56 def process_object(obj) running_seqs=SequenceGroup.new(obj.flatten) # execute plugins @plugin_manager.execute_plugins(running_seqs) # add output data add_output_data(running_seqs) return running_seqs end |
#receive_initial_config(obj) ⇒ Object
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# File 'lib/seqtrimnext/classes/em_classes/seqtrim_worker.rb', line 69 def receive_initial_config(obj) # Reads the parameters $WORKER_LOG.info "Params received" # @params = Params.new(params_path) @params = obj @tuple_size=@params.get_param('tuple_size') @use_qual=@params.get_param('use_qual') @use_json=@params.get_param('use_json') end |
#rejected_output_file(files) ⇒ Object
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# File 'lib/seqtrimnext/classes/em_classes/seqtrim_worker.rb', line 391 def rejected_output_file(files) return get_file(files,File.join(OUTPUT_PATH,'rejected.txt')) end |
#save_empty_insert(files, seq, stats) ⇒ Object
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# File 'lib/seqtrimnext/classes/em_classes/seqtrim_worker.rb', line 243 def save_empty_insert(files,seq, stats) seq.seq_rejected=true seq.='short insert' = 'No valid inserts found' rejected_output_file(files)<<('>'+seq.seq_name+ ' ' + ) add_stat(stats,'sequences','rejected',) add_stat(stats,'sequences','count','rejected') end |
#save_one_insert(files, seq, stats, inserts, qual_inserts, mid, dir_name, file_name) ⇒ Object
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# File 'lib/seqtrimnext/classes/em_classes/seqtrim_worker.rb', line 299 def save_one_insert(files,seq, stats,inserts,qual_inserts,mid,dir_name,file_name) mid_id,=(mid) # save fasta and qual in no MID file has_low_complexity = seq.get_actions(ActionLowComplexity) if has_low_complexity.empty? add_stat(stats,'sequences','count','output_seqs') fasta_file=sequence_file(files,dir_name,file_name) sff_file=sffinfo_file(files,dir_name,file_name) else add_stat(stats,'sequences','count','output_seqs_low_complexity') fasta_file=low_complexity_file(files,dir_name,file_name) sff_file=low_sffinfo_file(files,dir_name,file_name) end q=[] if @use_qual q=qual_inserts[0] end n=seq.seq_name c= seq_comments=seq.get_comment_line if !seq_comments.strip.empty? c=seq_comments + c end f=inserts[0] fasta_file << FastqFile.to_fastq(n,f,q,c) inserts_pos = seq.get_actions(ActionInsert) sff_file<< "#{n} #{inserts_pos[0].start_pos+1} #{inserts_pos[0].end_pos+1}" end |
#save_rejected_empty_or_single(files, seq, stats, inserts, qual_inserts, mid, dir_name, file_name) ⇒ Object
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# File 'lib/seqtrimnext/classes/em_classes/seqtrim_worker.rb', line 222 def save_rejected_empty_or_single(files,seq, stats,inserts,qual_inserts,mid,dir_name,file_name) if (seq.seq_rejected) # save to rejected sequences save_rejected_seq(files,seq, stats) elsif (inserts.empty?) #sequence with no inserts save_empty_insert(files,seq, stats) elsif (inserts.count == 1) # sequence with one insert save_one_insert(files,seq, stats,inserts,qual_inserts,mid,dir_name,file_name) end end |
#save_rejected_seq(files, seq, stats) ⇒ Object
SAVE NORMAL ===============================
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# File 'lib/seqtrimnext/classes/em_classes/seqtrim_worker.rb', line 234 def save_rejected_seq(files,seq, stats) # message = seq.seq_rejected_by_message = seq.get_comment_line rejected_output_file(files)<<('>'+seq.seq_name+ ' ' + ) add_stat(stats,'sequences','rejected',seq.) add_stat(stats,'sequences','count','rejected') end |
#save_two_inserts(files, seq, stats, inserts, qual_inserts, mid, dir_name, file_name) ⇒ Object
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# File 'lib/seqtrimnext/classes/em_classes/seqtrim_worker.rb', line 270 def save_two_inserts(files,seq, stats,inserts,qual_inserts,mid,dir_name,file_name) add_stat(stats,'sequences','count','output_seqs_paired') mid_id,=(mid) # save left read n="#{seq.seq_name}_left" c="template=#{seq.seq_name} dir=R library=#{mid_id} #{seq.get_comment_line}" f=inserts[0].reverse.tr('actgACTG','tgacTGAC') q=[] if @use_qual q=qual_inserts[0].reverse end paired_file(files,dir_name,file_name)<<FastqFile.to_fastq(n,f,q,c) # save right read n="#{seq.seq_name}_right" c="template=#{seq.seq_name} dir=F library=#{mid_id} #{seq.get_comment_line}" f=inserts[1] q=[] if @use_qual q=qual_inserts[1] end paired_file(files,dir_name,file_name)<<FastqFile.to_fastq(n,f,q,c) end |
#save_two_inserts_tuple(files, seq1, seq2, stats, inserts1, inserts2, qual_inserts1, qual_inserts2, mid, dir_name, file_name) ⇒ Object
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# File 'lib/seqtrimnext/classes/em_classes/seqtrim_worker.rb', line 190 def save_two_inserts_tuple(files,seq1,seq2, stats,inserts1,inserts2,qual_inserts1,qual_inserts2,mid,dir_name,file_name) add_stat(stats,'sequences','count','output_seqs_paired') add_stat(stats,'sequences','count','output_seqs_paired') mid_id,=(mid) # save left read n="#{seq1.seq_name}" c=seq1.get_comment_line # "template=#{seq1.seq_name} dir=R library=#{mid_id}" f=inserts1[0]#.reverse.tr('actgACTG','tgacTGAC') q=[] if @use_qual q=qual_inserts1[0] #.reverse end paired_file_ilu1(files,dir_name,file_name)<<FastqFile.to_fastq(n,f,q,c) # save right read n="#{seq2.seq_name}" c=seq2.get_comment_line # "template=#{seq2.seq_name} dir=F library=#{mid_id}" f=inserts2[0] q=[] if @use_qual q=qual_inserts2[0] end paired_file_ilu2(files,dir_name,file_name)<<FastqFile.to_fastq(n,f,q,c) end |
#sequence_file(files, dir_name, file_name) ⇒ Object
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# File 'lib/seqtrimnext/classes/em_classes/seqtrim_worker.rb', line 396 def sequence_file(files, dir_name, file_name) return get_file(files,File.join(OUTPUT_PATH,dir_name,'sequences_'+file_name+'.fastq')) end |
#sffinfo_file(files, dir_name, file_name) ⇒ Object
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# File 'lib/seqtrimnext/classes/em_classes/seqtrim_worker.rb', line 417 def sffinfo_file(files, dir_name, file_name) return get_file(files,File.join(OUTPUT_PATH,dir_name,'sff_info_'+file_name+'.txt')) end |
#starting_worker ⇒ Object
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# File 'lib/seqtrimnext/classes/em_classes/seqtrim_worker.rb', line 81 def starting_worker # $WORKER_LOG.level = Logger::ERROR #$WORKER_LOG.level = Logger::WARN $WORKER_LOG.level = Logger::INFO $WORKER_LOG.info "Loading actions" @action_manager = ActionManager.new $WORKER_LOG.info "Loading plugins" @plugin_list = @params.get_param('plugin_list') # puts in plugin_list the plugins's array $WORKER_LOG.info "PLUGIN LIST:" + @plugin_list @plugin_manager = PluginManager.new(@plugin_list,@params) # creates an instance from PluginManager. This must storage the plugins and load it rescue Exception => e puts (e.+ e.backtrace.join("\n")) end |
#write_seq_to_files_normal(files, seq, stats) ⇒ Object
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# File 'lib/seqtrimnext/classes/em_classes/seqtrim_worker.rb', line 342 def write_seq_to_files_normal(files,seq, stats) # puts stats.to_json dir_name,file_name,priority=seq.get_file_tag_path # puts File.join(dir_name,'sequences_'+file_name) # get current inserts inserts = seq.get_inserts # qualities are optional if @use_qual qual_inserts = seq.get_qual_inserts end # save json if necessary if @use_json json_file(files)<< seq.to_json end # find mids mid = seq.get_actions(ActionMid).first if (seq.seq_rejected) # save to rejected sequences save_rejected_seq(files,seq, stats) elsif (inserts.empty?) #sequence with no inserts save_empty_insert(files,seq, stats) elsif (inserts.count == 2) # sequence with two inserts = PAIRED SEQUENCES save_two_inserts(files,seq, stats,inserts,qual_inserts,mid,dir_name,file_name) elsif (inserts.count == 1) # sequence with one insert save_one_insert(files,seq, stats,inserts,qual_inserts,mid,dir_name,file_name) end end |
#write_seq_to_files_tuple(files, seqs, stats) ⇒ Object
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# File 'lib/seqtrimnext/classes/em_classes/seqtrim_worker.rb', line 140 def write_seq_to_files_tuple(files,seqs, stats) seq1=seqs[0] seq2=seqs[1] dir_name,file_name,priority=seq1.get_file_tag_path dir_name2,file_name2,priority2=seq2.get_file_tag_path # both paired sequences must go in same file, there are priorities if (dir_name!=dir_name2) || (file_name!=file_name2) if priority2>priority dir_name=dir_name2 file_name=file_name2 end end # get current inserts inserts1 = seq1.get_inserts inserts2 = seq2.get_inserts # qualities are optional if @use_qual qual_inserts1 = seq1.get_qual_inserts qual_inserts2 = seq2.get_qual_inserts end # save json if necessary if @use_json json_file(files)<< seq1.to_json json_file(files)<< seq2.to_json end # find mids mid1 = seq1.get_actions(ActionMid).first mid2 = seq2.get_actions(ActionMid).first if !inserts1.empty? && !inserts2.empty? # both have inserts # save_two_inserts(files,seq, stats,inserts,qual_inserts,mid,dir_name,file_name) save_two_inserts_tuple(files,seq1,seq2, stats,inserts1,inserts2,qual_inserts1,qual_inserts2,mid1,dir_name,file_name) else save_rejected_empty_or_single(files,seq1, stats,inserts1,qual_inserts1,mid1,dir_name,file_name) save_rejected_empty_or_single(files,seq2, stats,inserts2,qual_inserts2,mid2,dir_name,file_name) end end |