X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bp_bin%2Fblast_seq_pair;h=73c74154a7340809fbe0784726dc83791f1dc071;hb=2f0fd91b461033529a4a72e161bd133252a22eb6;hp=1963eafc4b128d94579d6d02e86cddf14964962c;hpb=5a9b7c80e4e4428e404575ed3c0290cde15a7402;p=biopieces.git

diff --git a/bp_bin/blast_seq_pair b/bp_bin/blast_seq_pair
index 1963eaf..73c7415 100755
--- a/bp_bin/blast_seq_pair
+++ b/bp_bin/blast_seq_pair
@@ -61,6 +61,7 @@ class Blast
     commands << "-j #{@infile2}"
     commands << "-o #{@outfile}"
     commands << "-p #{@program}"
+    commands << "-W #{options[:word_size]}" if options[:word_size]
     commands << "-D 1" # tabular output
     commands << "-e #{options[:e_val]}"
     commands << (options[:megablast] ? "-m T" : "-m F")
@@ -79,7 +80,7 @@ class Blast
   def each
     record = {}
 
-    File.open(@outfile, mode="r") do |ios|
+    File.open(@outfile, 'r') do |ios|
       ios.each_line do |line|
         if line !~ /^#/
           fields = line.chomp.split("\t")
@@ -121,14 +122,14 @@ class Blast
   def program_choose(type1, type2)
     program = ""
 
-    if type1 == 'protein'
-      if type2 == 'protein'
+    if type1 == :protein
+      if type2 == :protein
         program = 'blastp'
       else
         program = 'tblastn'
       end
     else
-      if type2 == 'protein'
+      if type2 == :protein
         program = 'blastx'
       else
         program = 'blastn'
@@ -147,6 +148,7 @@ casts << {:long=>'e_val',     :short=>'e', :type=>'float',  :mandatory=>false, :
 casts << {:long=>'filter',    :short=>'f', :type=>'string', :mandatory=>false, :default=>'no', :allowed=>'yes,no',    :disallowed=>nil}
 casts << {:long=>'megablast', :short=>'m', :type=>'flag',   :mandatory=>false, :default=>nil,  :allowed=>nil,         :disallowed=>nil}
 casts << {:long=>'no_gaps',   :short=>'G', :type=>'flag',   :mandatory=>false, :default=>nil,  :allowed=>nil,         :disallowed=>nil}
+casts << {:long=>'word_size', :short=>'w', :type=>'uint',   :mandatory=>false, :default=>nil,  :allowed=>nil,         :disallowed=>nil}
 
 options = Biopieces.options_parse(ARGV, casts)
 
@@ -155,8 +157,8 @@ infile1 = File.join(tmpdir, "in1.fna")
 infile2 = File.join(tmpdir, "in2.fna")
 outfile = File.join(tmpdir, "blast.out")
 
-got1    = false
-got2    = false
+got1    = nil
+got2    = nil
 type1   = ""
 type2   = ""
 
@@ -167,36 +169,37 @@ Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
     if record[:SEQ_NAME] and record[:SEQ]
       seq = Seq.new_bp(record)
 
-      unless got1
-        Fasta.open(infile1, mode="w") do |fasta_io|
+      if got1.nil?
+        Fasta.open(infile1, "w") do |fasta_io|
           fasta_io.puts seq.to_fasta
         end
 
         got1  = true
         type1 = Seq.new(nil, record[:SEQ][0 ... 100]).type_guess
-        next
-      end
-
-      unless got2
-        Fasta.open(infile2, mode="w") do |fasta_io|
+      elsif got2.nil?
+        Fasta.open(infile2, "w") do |fasta_io|
           fasta_io.puts seq.to_fasta
         end
 
         got2  = true
         type2 = Seq.new(nil, record[:SEQ][0 ... 100]).type_guess
       end
-    end
-  end
 
-  if got1 and got2
-    blast = Blast.new(infile1, infile2, outfile)
-    blast.program_set(type1, type2, options[:program])
-    blast.run(options)
+      if got1 and got2
+        blast = Blast.new(infile1, infile2, outfile)
+        blast.program_set(type1, type2, options[:program])
+        blast.run(options)
 
-    blast.each do |record|
-      output.puts record
+        blast.each do |new_record|
+          output.puts new_record
+        end
+
+        got1 = nil
+        got2 = nil
+      end
     end
   end
+
 end