Class: MyWorkerManager

Inherits:
ScbiMapreduce::WorkManager
  • Object
show all
Defined in:
lib/full_lengther_next/classes/my_worker_manager.rb

Class Method Summary collapse

Instance Method Summary collapse

Class Method Details

.end_work_manager ⇒ Object

close files



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# File 'lib/full_lengther_next/classes/my_worker_manager.rb', line 52

def self.end_work_manager
	# @@fasta_file.close
	
	@@annotation_file.close
	@@alignment_file.close
	@@prot_file.close
	@@nts_file.close
	@@tcode_file.close
	@@nc_rna_file.close
	
	if (!@@options[:chimera].nil?)
		@@chimera_file.close
	end
	
	# @@error_fasta_file.close
	# @@error_file.close
	
	summary_stats
end

.init_work_manager(options, chunk_size = 100) ⇒ Object

open files and prepare global data



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# File 'lib/full_lengther_next/classes/my_worker_manager.rb', line 11

def self.init_work_manager(options,chunk_size=100)

	input_file=options[:fasta]
	
	if !File.exists?('fln_results')
		Dir.mkdir('fln_results')
	end
	
	file_head = "Query_id\tfasta_length\tSubject_id\tdb_name\tStatus\tt_code\te_value\tp_ident\tprotein_length\ts_length\tWarning_msgs\tframe\tORF_start\tORF_end\ts_start\ts_end\tDescription\tProtein_sequence"
	
	@@fasta_file = FastaQualFile.new(input_file,'')
	@@chunk_size=chunk_size
	@@options = options

	@@annotation_file = File.open("fln_results/dbannotated.txt", 'w')
	@@annotation_file.puts file_head

	@@alignment_file = File.open("fln_results/alignments.txt", 'w')
	@@prot_file = File.open("fln_results/proteins.fasta", 'w')
	@@nts_file = File.open("fln_results/nt_seq.txt", 'w')
	@@tcode_file=File.open("fln_results/new_coding.txt", 'w')
	@@tcode_file.puts file_head

	@@nc_rna_file = File.open("fln_results/nc_rnas.txt", 'w')
	@@nc_rna_file.puts file_head

	if (!options[:chimera].nil?)
		@@chimera_file = File.open("fln_results/chimeric_sequences.txt", 'w')
		@@chimera_file.puts file_head
	else
		if File.exists?("fln_results/chimeric_sequences.txt")
			File.delete("fln_results/chimeric_sequences.txt")
		end
	end

	# @@error_fasta_file = File.open("fln_results/error_seqs.fasta", 'w')
	# @@error_file = File.open("fln_results/errors_info.txt", 'w')

end

Instance Method Details

#error_received(worker_error, obj) ⇒ Object 



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# File 'lib/full_lengther_next/classes/my_worker_manager.rb', line 72

def error_received(worker_error, obj)
puts "Error while processing object #{obj.inspect}\n" + worker_error.original_exception.message + ":\n" +worker_error.original_exception.backtrace.join("\n")
end

#next_work ⇒ Object

this method is called every time a worker needs a new work Return the work data or nil if no more data is available



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# File 'lib/full_lengther_next/classes/my_worker_manager.rb', line 87

def next_work
	
   # seqs=[]
	# if (@@count % 2==0)
	# 	$LOG.info("Processed #{@@count}")
	# end
				
	# prepare work
   # @@chunk_size.times do
	n,f,q = @@fasta_file.next_seq
	
	if !n.nil?
			return Sequence.new(n,f,q)
		else
			return nil
	end
   
   # end
	
	# return work
	# if !seqs.empty?
	#       return seqs
	#     else
	#       return nil
	#     end
	
end

#too_many_errors_received ⇒ Object 



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# File 'lib/full_lengther_next/classes/my_worker_manager.rb', line 76

def too_many_errors_received
$LOG.error "Too many errors: #{@@error_count} errors on #{@@count} executed sequences, exiting before finishing"
end

#work_received(obj) ⇒ Object

this method is ejecuted each time an obj is finished



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# File 'lib/full_lengther_next/classes/my_worker_manager.rb', line 116

def work_received(obj)

		obj.each do |seq|
			# puts seq.seq_name
			
			write_seq(seq)
			
		end
end

#worker_initial_config ⇒ Object

send initial config



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# File 'lib/full_lengther_next/classes/my_worker_manager.rb', line 81

def worker_initial_config
	return @@options
end

#write_seq(seq) ⇒ Object 



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# File 'lib/full_lengther_next/classes/my_worker_manager.rb', line 127

def write_seq(seq)
	begin
# --------------------------------------------------------     Chimeric Seqs
		if (!@@options[:chimera].nil?)
			if (q=seq.get_annotations(:chimera).first)
				@@chimera_file.puts q[:message]
# --------------------------------------------------     Complete Seqs
			elsif (e=seq.get_annotations(:complete).first)

				@@annotation_file.puts e[:message]
			
				if (a=seq.get_annotations(:alignment).first)
					@@alignment_file.puts a[:message]
				end
			
				if (p=seq.get_annotations(:protein).first)
					@@prot_file.puts p[:message]
				end
			
				if (n=seq.get_annotations(:nucleotide).first)
					@@nts_file.puts n[:message]
				end
# ---------------------------------------------------    Non Complete Seqs
			elsif (e=seq.get_annotations(:tmp_annotation).first)

				@@annotation_file.puts e[:message][0]
			
				if (a=seq.get_annotations(:alignment).first)
					if !a[:message].empty?
						@@alignment_file.puts a[:message]
					end
				end
			
				if (p=seq.get_annotations(:protein).first)
					if !p[:message].empty?
						@@prot_file.puts p[:message]
					end
				end
			
				if (n=seq.get_annotations(:nucleotide).first)
					@@nts_file.puts n[:message]
				end
# -------------------------------------------------     nc RNA
			elsif (nc=seq.get_annotations(:ncrna).first)
				@@nc_rna_file.puts nc[:message]
# -------------------------------------------------     Test Code
			elsif (t=seq.get_annotations(:tcode).first)
  				@@tcode_file.puts t[:message]
			end
# ---------------------------------------------------------------------------------
# --------------------------------------------------------    without Chimeric Seqs Mode
		else
# -------------------------------------------------     Complete Seqs
			if (e=seq.get_annotations(:complete).first)

				@@annotation_file.puts e[:message]
			
				if (a=seq.get_annotations(:alignment).first)
					@@alignment_file.puts a[:message]
				end
			
				if (p=seq.get_annotations(:protein).first)
					@@prot_file.puts p[:message]
				end
			
				if (n=seq.get_annotations(:nucleotide).first)
					@@nts_file.puts n[:message]
				end
# -------------------------------------------------     Non Complete Seqs
			elsif (e=seq.get_annotations(:tmp_annotation).first)

				@@annotation_file.puts e[:message][0]
			
				if (a=seq.get_annotations(:alignment).first)
					if !a[:message].empty?
						@@alignment_file.puts a[:message]
					end
				end
			
				if (p=seq.get_annotations(:protein).first)
					if !p[:message].empty?
						@@prot_file.puts p[:message]
					end
				end
			
				if (n=seq.get_annotations(:nucleotide).first)
					@@nts_file.puts n[:message]
				end
# -------------------------------------------------     nc RNA
			elsif (nc=seq.get_annotations(:ncrna).first)
				@@nc_rna_file.puts nc[:message]
# -------------------------------------------------     Test Code
			elsif (t=seq.get_annotations(:tcode).first) 
  				@@tcode_file.puts t[:message]
			end
		end
# -------------------------------------------------     errors
		# if e=seq.get_annotations(:error).first
		# 	if !e[:message].empty?
		# 		@@error_fasta_file.puts ">#{seq.seq_name}\n#{seq.seq_fasta}"
		# 		@@error_file.puts e[:message]
		# 	end
		# end

	rescue
		puts "Error printing #{seq.seq_name}"
	end
	
end