# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-require 'biopieces'
-require 'fasta'
-require 'seq'
-require 'pp'
+require 'maasha/biopieces'
+require 'maasha/fasta'
+require 'maasha/seq'
class Pcr
def initialize(tmpdir, infile, options)
outfile = pat_file.sub("pat", "fna")
command = "scan_for_matches"
- command << " -c"
+ # command << " -c"
command << " #{pat_file}"
command << " < #{@infile}"
command << " > #{outfile}"
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"}
-bp = Biopieces.new
-
-options = bp.parse(ARGV, casts)
-tmpdir = bp.mktmpdir
+options = Biopieces.options_parse(ARGV, casts)
+tmpdir = Biopieces.mktmpdir
infile = File.join(tmpdir, "in.fna")
-Fasta.open(infile, mode="w") do |ios|
- bp.each_record do |record|
- bp.puts record
- ios.puts record
- end
-end
+Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
+ Fasta.open(infile, mode="w") do |ios|
+ input.each_record do |record|
+ output.puts record
-outfiles = Pcr.new(tmpdir, infile, options).run
-
-outfiles.each do |outfile|
- Fasta.open(outfile, mode="r") do |ios|
- ios.each do |entry|
- record = entry.to_bp
- record[:REC_TYPE] = "PCR"
- record[:STRAND] = "+"
- 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
-
- if record[:PCR_BEG] > record[:PCR_END]
- record[:PCR_BEG], record[:PCR_END] = record[:PCR_END], record[:PCR_BEG]
- record[:STRAND] = "-"
+ if record.has_key? :SEQ
+ entry = Seq.new_bp(record)
+ ios.puts entry.to_fasta
end
+ end
+ end
- bp.puts record
+ outfiles = Pcr.new(tmpdir, infile, options).run
+
+ outfiles.each do |outfile|
+ Fasta.open(outfile, mode="r") do |ios|
+ ios.each do |entry|
+ record = entry.to_bp
+ record[:REC_TYPE] = "PCR"
+ record[:STRAND] = "+"
+ 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
+
+ if record[:PCR_BEG] > record[:PCR_END]
+ record[:PCR_BEG], record[:PCR_END] = record[:PCR_END], record[:PCR_BEG]
+ record[:STRAND] = "-"
+ end
+
+ output.puts record
+ end
end
end
end