Class: MyWorkerEst

Inherits:
MyWorker
  • Object
show all
Defined in:
lib/full_lengther_next/my_worker_EST.rb

Instance Method Summary collapse

Methods inherited from MyWorker

#check_blast, #check_mapping, #check_ncRNA, #check_prot_db, #check_testcode, #clean_subjec_ids_name, #closing_worker, #full_lenghter2, #get_prot_sequences, #hits_statistics, #map_transcriptome, #refine_analysis_with_exonerate, #replace_hits, #rescue_sequence, #run_blast, #search_best_orf_y_fl, #select_sequences, #write_querys, #write_targets

Instance Method Details

#blast_analysis(blast, array_seqs) ⇒ Object 



40
41
42
43
44
45
46
47
48
49
50
51
52
 
# File 'lib/full_lengther_next/my_worker_EST.rb', line 40

def blast_analysis(blast, array_seqs)
	blast.querys.each_with_index do |query, i|
		if query.hits.first.nil?
			if !array_seqs[i].type == CODING #Keep if is coding
				@unmatch << array_seqs[i]
			end
		else
			seq = array_seqs[i]
			seq.hit = query.hits.first
			@match << seq
		end
	end	
end

#blastEST(array_seqs) ⇒ Object

CUSTOM FUNCTIONS



30
31
32
33
34
35
36
37
38
 
# File 'lib/full_lengther_next/my_worker_EST.rb', line 30

def blastEST(array_seqs)
	blast = run_blast(array_seqs, @blast_path, 'blastn', 1e-6, nil, false)
	if blast.nil?
		$LOG.info 'BLAST FAILED'
		Process.exit(-1)
	else
		blast_analysis(blast, array_seqs)
	end
end

#process_object(array_seqs) ⇒ Object 



19
20
21
22
23
24
 
# File 'lib/full_lengther_next/my_worker_EST.rb', line 19

def process_object (array_seqs)
	$WORKER_LOG.info "Worker LIST #{array_seqs.length}"
	array_seqs.sort!{|s1, s2| s2.t_code <=> s1.t_code} #Order by testcode
	blastEST(array_seqs)
	return [@match, @unmatch]
end

#receive_initial_config(params) ⇒ Object

WORKER FUNCTIONS



11
12
13
14
15
16
17
 
# File 'lib/full_lengther_next/my_worker_EST.rb', line 11

def receive_initial_config(params)
	# Reads the parameters
	@options = params.first
	@blast_path = params.last
	@match = [] # Any sequence matching with a EST
	@unmatch = [] # Sequences with :test_code annotation that it hasn't match with a EST
end