command = "scan_for_matches"
# command << " -c"
+ command << " -o 1"
command << " #{pat_file}"
command << " < #{@infile}"
command << " > #{outfile}"
class Pattern
attr_accessor :forward, :reverse
+ # Split a primer pattern in the form of ATCG[3,2,1] into
+ # sequence and match descriptor, reverse complement the
+ # primer and append the match descriptor: CGAT[3,2,1].
+ def self.revcomp(pattern)
+ if pattern.match(/^(\w+)(\[.+\])?/)
+ primer = $1
+ descriptor = $2
+ else
+ raise "Failed splitting pattern: #{pattern}"
+ end
+
+ seq = Seq.new
+ seq.seq = primer
+ seq.type = :dna
+ seq.reverse!.complement!
+
+ descriptor ? seq.seq + descriptor : seq.seq
+ end
+
def initialize(forward, reverse, max_dist)
@forward = forward
@reverse = reverse
def save(tmpdir)
forward = @forward
reverse = @reverse
- revcomp_forward = revcomp(forward)
- revcomp_reverse = revcomp(reverse)
+ revcomp_forward = Pattern.revcomp(forward)
+ revcomp_reverse = Pattern.revcomp(reverse)
files = []
# Save a pattern to file
def save_pattern(file)
- File.open(file, mode="w") do |ios|
+ File.open(file, "w") do |ios|
ios.puts self
end
end
-
- # Split a primer pattern in the form of ATCG[3,2,1] into
- # sequence and match descriptor, reverse complement the
- # primer and append the match descriptor: CGAT[3,2,1].
- def revcomp(pattern)
- if pattern.match(/^(\w+)(\[.+\])?/)
- primer = $1
- descriptor = $2
- else
- raise "Failed splitting pattern: #{pattern}"
- end
-
- seq = Seq.new
- seq.seq = primer
- seq.type = 'dna'
- seq.revcomp
-
- descriptor ? seq.seq + descriptor : seq.seq
- end
end
casts = []
-casts << {:long=>'forward', :short=>'f', :type=>'string', :mandatory=>true, :default=>nil, :allowed=>nil, :disallowed=>nil}
-casts << {:long=>'reverse', :short=>'r', :type=>'string', :mandatory=>true, :default=>nil, :allowed=>nil, :disallowed=>nil}
-casts << {:long=>'max_dist', :short=>'m', :type=>'uint', :mandatory=>true, :default=>5000, :allowed=>nil, :disallowed=>"0"}
+casts << {:long=>'forward', :short=>'f', :type=>'string', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'forward_rc', :short=>'F', :type=>'string', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'reverse', :short=>'r', :type=>'string', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'reverse_rc', :short=>'R', :type=>'string', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'max_dist', :short=>'m', :type=>'uint', :mandatory=>true, :default=>5000, :allowed=>nil, :disallowed=>"0"}
options = Biopieces.options_parse(ARGV, casts)
tmpdir = Biopieces.mktmpdir
infile = File.join(tmpdir, "in.fna")
+if options[:forward_rc]
+ options[:forward] = Pattern.revcomp(options[:forward_rc])
+end
+
+if options[:reverse_rc]
+ options[:reverse] = Pattern.revcomp(options[:reverse_rc])
+end
+
+raise ArgumentError, "no adaptor specified" unless options[:forward] or options[:reverse]
Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
- Fasta.open(infile, mode="w") do |ios|
+ Fasta.open(infile, "w") do |ios|
input.each_record do |record|
output.puts record
- ios.puts record
+
+ if record[:SEQ]
+ entry = Seq.new_bp(record)
+ ios.puts entry.to_fasta
+ end
end
end
outfiles = Pcr.new(tmpdir, infile, options).run
outfiles.each do |outfile|
- Fasta.open(outfile, mode="r") do |ios|
+ Fasta.open(outfile, "r") do |ios|
ios.each do |entry|
record = entry.to_bp
record[:REC_TYPE] = "PCR"
record[:TYPE] = File.basename(outfile).sub(".fna", "").upcase
record[:SEQ_NAME].match(/(.+):\[(\d+),(\d+)\]$/)
record[:SEQ_NAME] = $1
- record[:PCR_BEG] = $2
- record[:PCR_END] = $3
+ record[:PCR_BEG] = $2.to_i
+ record[:PCR_END] = $3.to_i
if record[:PCR_BEG] > record[:PCR_END]
record[:PCR_BEG], record[:PCR_END] = record[:PCR_END], record[:PCR_BEG]