X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bp_bin%2Fpcr_seq;h=dec3ea0e4f1b4c01c6841a9499a5c47394248ec5;hb=ad1772aebdbd833813826c1e414d92e1da82c9a8;hp=ff930cca29e6201b18f273eb57fdb7d285859b3d;hpb=1aaa3e635bdbfed13485bb1e87b0c6e9b137bb87;p=biopieces.git

diff --git a/bp_bin/pcr_seq b/bp_bin/pcr_seq
index ff930cc..dec3ea0 100755
--- a/bp_bin/pcr_seq
+++ b/bp_bin/pcr_seq
@@ -29,10 +29,9 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-require 'biopieces'
-require 'fasta'
-require 'seq'
-require 'pp'
+require 'maasha/biopieces'
+require 'maasha/fasta'
+require 'maasha/seq'
 
 class Pcr
   def initialize(tmpdir, infile, options)
@@ -51,7 +50,7 @@ class Pcr
       outfile = pat_file.sub("pat", "fna")
 
       command =  "scan_for_matches"
-      command << " -c"
+      # command << " -c"
       command << " #{pat_file}"
       command << " < #{@infile}"
       command << " > #{outfile}"
@@ -157,39 +156,39 @@ casts << {:long=>'forward',  :short=>'f', :type=>'string', :mandatory=>true, :de
 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
+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
+      ios.puts record
+    end
   end
-end
 
-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] = "-"
+  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
-
-      bp.puts record
     end
   end
 end