Module: Bio::DB::Blast

Defined in:
lib/bio/db/blast.rb

Defined Under Namespace

Classes: BlasteException

Class Method Summary collapse

Class Method Details

.align(opts = {}) ⇒ Object 



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# File 'lib/bio/db/blast.rb', line 79

def self.align(opts={})
	target=opts[:target]
	query=opts[:query]
	max_target_seqs = 15
	max_target_seqs = opts[:max_hits] * 2 if opts[:max_hits]
	cmdline = "blastn -max_target_seqs #{max_target_seqs} -query #{query} -db #{target} -outfmt '6 qseqid qstart qend qframe sseqid sstart send sframe score pident qlen slen qseq sseq'"

	status, stdout, stderr = systemu cmdline
	if status.exitstatus == 0
		alns = Array.new unless block_given?
		stdout.each_line do |e_l|
			#puts e_l
			line = to_exo(e_l)
			#puts line
			arr = line.split("\t")
			aln = Bio::DB::Exonerate::Alignment.parse_custom(line) 
			if aln
				if block_given?
					yield aln
				else
					alns << aln
				end
			end
		end
		return alns unless block_given?
	else
		raise BlasteException.new(), "Error running exonerate. Command line was '#{cmdline}'\n Blast STDERR was:\n#{stderr}"
	end
end

.to_exo(line) ⇒ Object 



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# File 'lib/bio/db/blast.rb', line 69

def self.to_exo(line)
	arr = Array.new
	arr << "RESULT:"
	arr << to_sugar(line)
	arr << line.split("\t")[9..11]
	arr << "."
	arr << to_vulgar(line)
	arr.join("\t")
end

.to_sugar(line) ⇒ Object 



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# File 'lib/bio/db/blast.rb', line 3

def self.to_sugar(line)
	fields = line.split("\t")[0..8]
	
	if  fields[3] =="-1"
		fields[3] = "-"
		fields[2] = fields[2].to_i - 1
	else
		fields[3] = "+"
		fields[1] = fields[1].to_i - 1
	end
	if fields[7] =="-1"
		fields[7] = "-"
		fields[6] = fields[6].to_i - 1
	else
		fields[7] = "+"
		fields[5] = fields[5].to_i - 1
	end
	fields.join(" ")
end

.to_vulgar(line) ⇒ Object 



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# File 'lib/bio/db/blast.rb', line 23

def self.to_vulgar(line)
	qseq, sseq = line.split("\t")[12..13]

	len = qseq.length
	l_status = ""
	l_len = 0
	str = Array.new
	statuses = ""
	for i in 0..len
		if qseq[i] == "-"
			status = "D"
		elsif sseq[i] == "-"
			status = "I"
		else
			status = "M"
		end
		statuses << status
	end
	statuses.split('').each do |e| 
		if l_status != e
			case l_status
			when "M"
				str << ["M", l_len, l_len]
			when "I"
				str << ["G", l_len, 0]
			when "D"
				str << ["G", 0, l_len]
			end
			l_len = 0
		end
		l_status = e
		l_len += 1
	end
	l_len -= 1
	case l_status
	when "M"
		str << ["M", l_len, l_len]
	when "I"
		str << ["G", l_len, 0]
	when "D"
		str << ["G", 0, l_len]
	end

	str.flatten!.join(" ")
end