class PatScanError < StandardError; end;
class PatScan
- def initialize(options, file_fasta, file_pattern, file_patscan)
+ def initialize(options, tmpdir, file_pattern, cpus)
@options = options
- @file_fasta = file_fasta
+ @tmpdir = tmpdir
@file_pattern = file_pattern
- @file_patscan = file_patscan
+ @cpus = cpus
+ @files_fasta = Dir.glob(File.join(@tmpdir, "*.fna"))
pat = Pattern.new(@options)
pat.write(@file_pattern)
end
def run
+ child_count = 0
+ ch_mutex = Mutex.new
+ threads = []
+
+ @files_fasta.each do |file|
+ Thread.pass while child_count >= @cpus
+ ch_mutex.synchronize { child_count += 1 }
+
+ threads << Thread.new do
+ command = command_compile(file)
+ system(command)
+ raise PatScanError, "Command failed: #{command}" unless $?.success?
+ ch_mutex.synchronize { child_count -= 1 }
+ end
+ end
+
+ threads.each { |t| t.join }
+ end
+
+ def command_compile(file)
commands = []
commands << "nice -n 19"
commands << "scan_for_matches"
commands << @file_pattern
- commands << "< #{@file_fasta}"
- commands << "> #{@file_patscan}"
+ commands << "< #{file}"
+ commands << "> #{file}.out"
command = commands.join(" ")
- system(command)
- raise PatScanError, "Command failed: #{command}" unless $?.success?
end
def parse_results
+ files_result = Dir.glob(File.join(@tmpdir, "*.out"))
+
matches = {}
- Fasta.open(@file_patscan, mode='r') do |ios|
- ios.each_entry do |entry|
- if entry.seq_name =~ /^(\d+):\[(\d+),(\d+)\]$/
- name = $1.to_i
- start = $2.to_i - 1
- stop = $3.to_i - 1
- matches[name] = [start, stop - start + 1]
- else
- raise "Failed to parse sequence name: #{entry.seq_name}"
+ files_result.each do |file|
+ Fasta.open(file, 'r') do |ios|
+ ios.each do |entry|
+ if entry.seq_name =~ /^(\d+):\[(\d+),(\d+)\]$/
+ name = $1.to_i
+ start = $2.to_i - 1
+ stop = $3.to_i - 1
+ matches[name] = [start, stop - start + 1] unless matches.has_key? name
+ else
+ raise "Failed to parse sequence name: #{entry.seq_name}"
+ end
end
end
end
@options = options
@patterns = []
@patterns << pattern_internal
- @patterns += patterns_end if @options[:trim_end]
+ @patterns += patterns_end if @options[:partial]
end
def to_i
end
def write(file)
- File.open(file, mode='w') do |ios|
+ File.open(file, 'w') do |ios|
ios.puts self.to_i
end
end
patterns = []
adaptor = @options[:adaptor]
- raise PatternError, "trim_end_min > adaptor length: #{@options[:trim_end_min]} > #{adaptor.length - 1}" if @options[:trim_end_min] > adaptor.length - 1
+ raise PatternError, "len > adaptor length: #{@options[:len]} > #{adaptor.length - 1}" if @options[:len] > adaptor.length - 1
- (adaptor.length - 1).downto(@options[:trim_end_min]) do |i|
+ (adaptor.length - 1).downto(@options[:len]) do |i|
pattern = adaptor[0 ... i]
mis = mis_count(pattern)
ins = ins_count(pattern)
end
casts = []
-casts << {:long=>'adaptor', :short=>'a', :type=>'string', :mandatory=>true, :default=>nil, :allowed=>nil, :disallowed=>nil}
-casts << {:long=>'trim_end', :short=>'t', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
-casts << {:long=>'trim_end_min', :short=>'l', :type=>'uint', :mandatory=>false, :default=>10, :allowed=>nil, :disallowed=>'0'}
-casts << {:long=>'mismatches', :short=>'m', :type=>'uint', :mandatory=>false, :default=>10, :allowed=>nil, :disallowed=>nil}
-casts << {:long=>'insertions', :short=>'i', :type=>'uint', :mandatory=>false, :default=>5, :allowed=>nil, :disallowed=>nil}
-casts << {:long=>'deletions', :short=>'d', :type=>'uint', :mandatory=>false, :default=>5, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'adaptor', :short=>'a', :type=>'string', :mandatory=>true, :default=>nil, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'partial', :short=>'p', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'len', :short=>'l', :type=>'uint', :mandatory=>false, :default=>10, :allowed=>nil, :disallowed=>'0'}
+casts << {:long=>'mismatches', :short=>'m', :type=>'uint', :mandatory=>false, :default=>10, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'insertions', :short=>'i', :type=>'uint', :mandatory=>false, :default=>5, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'deletions', :short=>'d', :type=>'uint', :mandatory=>false, :default=>5, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'cpus', :short=>'c', :type=>'uint', :mandatory=>false, :default=>1, :allowed=>nil, :disallowed=>'0'}
+
+BASE_PER_FILE = 10_000_000
options = Biopieces.options_parse(ARGV, casts)
tmpdir = Biopieces.mktmpdir
-file_fasta = File.join(tmpdir, "data.fna")
file_records = File.join(tmpdir, "data.stream")
file_pattern = File.join(tmpdir, "pattern.txt")
-file_patscan = File.join(tmpdir, "patscan.fna")
-count = 0
+number_file = 0
+number_seq = 0
+bases = 0
Biopieces.open(options[:stream_in], file_records) do |input, output|
- Fasta.open(file_fasta, mode='w') do |out_fa|
- input.each do |record|
- output.puts record
+ file_fasta = File.join(tmpdir, "#{number_file}.fna")
+ out_fa = Fasta.open(file_fasta, 'w')
- if record.has_key? :SEQ
- record[:SEQ_NAME] = count
- out_fa.puts record
+ input.each do |record|
+ output.puts record
+
+ if record.has_key? :SEQ
+ record[:SEQ_NAME] = number_seq
+
+ seq = Seq.new_bp(record)
- count += 1;
+ out_fa.puts seq.to_fasta
+
+ number_seq += 1;
+ bases += record[:SEQ].length
+
+ if bases > BASE_PER_FILE
+ out_fa.close
+ bases = 0
+ number_file += 1
+ file_fasta = File.join(tmpdir, "#{number_file}.fna")
+ out_fa = Fasta.open(file_fasta, 'w')
end
end
end
+
+ out_fa.close if out_fa.respond_to? :close
end
-patscan = PatScan.new(options, file_fasta, file_pattern, file_patscan)
+patscan = PatScan.new(options, tmpdir, file_pattern, options[:cpus])
patscan.run
matches = patscan.parse_results
-count = 0
+number_seq = 0
Biopieces.open(file_records, options[:stream_out]) do |input, output|
input.each_record do |record|
if record.has_key? :SEQ
- if matches.has_key? count
- record[:ADAPTOR_POS] = matches[count].first
- record[:ADAPTOR_LEN] = matches[count].last
+ if matches.has_key? number_seq
+ record[:ADAPTOR_POS] = matches[number_seq].first
+ record[:ADAPTOR_LEN] = matches[number_seq].last
end
- count += 1;
+ number_seq += 1;
end
output.puts record
projects / biopieces.git / blobdiff