bio-gadget 0.2.5 → 0.2.6

data/lib/bio-gadget.rb

@@ -24,12 +24,18 @@ module Bio
       end
     end
 
-    def mytempfile(basename, tmpdir = Dir::tmpdir)
+    @@mytemppaths = Array.new
+
+    def mytemppath(basename, tmpdir = Dir::tmpdir)
       fp = Tempfile.open(basename, tmpdir)
       path = fp.path
-      fp.close #!
+      @@mytemppaths.push(path)
+      fp.close!
       path
     end
 
+    END {
+      @@mytemppaths.each { |path| File.unlink(path) if File.exist?(path) }
+    }
   end
 end

data/lib/bio-gadget/demlt.rb

@@ -33,88 +33,69 @@ module Bio
       procs = Parallel.processor_count
 
       fifo1paths = Array.new
-      procs.times { |i| fifo1paths.push(mytempfile('fifo1-')) }
+      procs.times { |i|
+        fifo1path = mytemppath('fifo1-')
+        File.mkfifo(fifo1path)
+        fifo1paths.push(fifo1path)
+      }
       pid = Kernel.fork {
         fifo1s = Array.new
-        fifo1paths.each { |fifo1path| fifo1s.push(open(fifo1path, 'w+')) }
+        fifo1paths.each { |fifo1path| fifo1s.push(open(fifo1path, 'w')) }
         total = 0
         Bio::Faster.new(:stdin).each_record(:quality => :raw) do |vals|
           fifo1 = fifo1s[total % procs]
           fifo1.puts(vals.join("\t"))
-          fifo1.flush
           total += 1
         end
-        fifo1s.each { |fifo1| fifo1.puts('*'); fifo1.close }
+        fifo1s.each { |fifo1| fifo1.close }
         Kernel.exit!
       }
 
-      fifo1paths.each { |fifo1path|
-        until File.exist?(fifo1path)
-          sleep 1
-        end
-      }
-
       fifo2paths = Array.new
       procs.times { |i|
-        fifo2path = mytempfile('fifo2-')
+        fifo2path = mytemppath('fifo2-')
+        File.mkfifo(fifo2path)
         fifo2paths.push(fifo2path)
         pid = Kernel.fork {
-          open(fifo2path, 'w+') { |fifo2|
-            fifo1 = open(fifo1paths[i], 'r+')
-            while true
-              line = fifo1.gets
-              if line.nil?
-                sleep 1
-              elsif line == "*\n"
-                break
-              else
-                seqid, seq, qvs = line.rstrip.split(/\t/)
-                tmpdists = Hash.new
-                bcs.each_index { |bcidx|
-                  tmpdists[bcidx] = Levenshtein.distance(bcs[bcidx], seq[ofs, bclen])
-                }
-                dists = tmpdists.sort { |a, b| a[1] <=> b[1] }
-                bc = dists[0][1] < 2 && dists[0][1] < dists[1][1] ? dists[0][0] : -1
-                fifo2.puts("#{bc}\t#{seqid}\t#{seq}\t#{qvs}")
-                fifo2.flush
-              end
-            end
-            fifo1.close
-            fifo2.puts('*')
+          open(fifo2path, 'w') { |fifo2|
+            open(fifo1paths[i], 'r').each { |line|
+              seqid, seq, qvs = line.rstrip.split(/\t/)
+              tmpdists = Hash.new
+              bcs.each_index { |bcidx|
+                tmpdists[bcidx] = Levenshtein.distance(bcs[bcidx], seq[ofs, bclen])
+              }
+              dists = tmpdists.sort { |a, b| a[1] <=> b[1] }
+              bc = dists[0][1] < 2 && dists[0][1] < dists[1][1] ? dists[0][0] : -1
+              fifo2.puts("#{bc}\t#{seqid}\t#{seq}\t#{qvs}")
+            }
           }
           Kernel.exit!
         }
       }
 
-      fifo2paths.each { |fifo2path|
-        until File.exist?(fifo2path)
-          sleep 1
-        end
-      }
-
       tmpwells = wells + ['other']
 
       fifo3paths = Array.new
-      tmpwells.each_index { |i| fifo3paths.push(mytempfile('fifo3-')) }
+      tmpwells.each_index { |i|
+        fifo3path = mytemppath('fifo3-')
+        File.mkfifo(fifo3path)
+        fifo3paths.push(fifo3path)
+      }
       pid = Kernel.fork {
         fifo2s = Array.new
-        fifo2paths.each { |fifo2path| fifo2s.push(open(fifo2path, 'r+')) }
+        fifo2paths.each { |fifo2path| fifo2s.push(open(fifo2path, 'r')) }
         fifo2done = Hash.new
         fifo3s = Array.new
-        fifo3paths.each { |fifo3path| fifo3s.push(open(fifo3path, 'w+')) }
+        fifo3paths.each { |fifo3path| fifo3s.push(open(fifo3path, 'w')) }
         fifo2s.cycle { |fifo2|
           unless fifo2done.key?(fifo2)
             line = fifo2.gets
             if line.nil?
-              sleep 1
-            elsif line == "*\n"
-              # puts("#{fifo2} eof.")
               fifo2done[fifo2] = ''
             else
               bcs, seqid, seq, qvs = line.rstrip.split(/\t/)
               fifo3 = fifo3s[bcs.to_i]
               fifo3.puts([seqid, seq, qvs].join("\t"))
-              fifo3.flush
             end
           end
           if fifo2done.size == fifo2s.size
@@ -122,16 +103,10 @@ module Bio
           end
         }
         fifo2s.each { |fifo2| fifo2.close }
-        fifo3s.each { |fifo3| fifo3.puts('*'); fifo3.close }
+        fifo3s.each { |fifo3| fifo3.close }
         Kernel.exit!
       }
 
-      fifo3paths.each { |fifo3path|
-        until File.exist?(fifo3path)
-          sleep 1
-        end
-      }
-
       tmpwells.each_index { |i|
         well = tmpwells[i]
         outpath = "#{options['output-dir']}/#{well}.fq.xz"
@@ -139,30 +114,14 @@ module Bio
           left = ofs+bclen
           right = ofs+bclen+len-1
           preprocess = ofs > 0 ? <<"DEDUPandFORMAT"
-| ruby -F'\\t' -anle 'f1=$F[1][0..#{right}];f2=$F[2][0..#{right}];puts([f1+f2, $F[0], f2, f1].join("\\t"))' \\
+ruby -F'\\t' -anle 'f1=$F[1][0..#{right}];f2=$F[2][0..#{right}];puts([f1+f2, $F[0], f2, f1].join("\\t"))' #{fifo3paths[i]} \\
 | sort -k 1 -r | cut -f 2- | uniq -f 2 \\
 | ruby -F'\\t' -anle 'puts(["@"+$F[0], $F[2][#{left}..-1], "+", $F[1][#{left}..-1]].join("\\n"))' \\
 DEDUPandFORMAT
           : <<"FORMAT"
-| ruby -F'\\t' -anle 'puts(["@"+$F[0], $F[1][#{left}..#{right}], "+", $F[2][#{left}..#{right}].rstrip].join("\\n"))' \\
+ruby -F'\\t' -anle 'puts(["@"+$F[0], $F[1][#{left}..#{right}], "+", $F[2][#{left}..#{right}].rstrip].join("\\n"))' #{fifo3paths[i]} \\
 FORMAT
-          preprocess += "| xz -z -c -e > #{outpath}"
-          open(preprocess, 'w') { |fp|
-            fifo3 = open(fifo3paths[i], 'r+')
-            while true
-              line = fifo3.gets
-              if line.nil?
-                sleep 1
-              elsif line == "*\n"
-                break
-              else
-                fp.puts(line)
-                fp.flush
-              end
-            end
-            fifo3.close
-          }
-          Kernel.exit!
+          exec preprocess+"| xz -z -c -e > #{outpath}"
         }
       }
 

data/lib/bio-gadget/version.rb

@@ -3,7 +3,7 @@ require 'thor'
 module Bio
   class Gadget < Thor
 
-    VERSION = "0.2.5"
+    VERSION = "0.2.6"
 
   end
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-gadget
 version: !ruby/object:Gem::Version
-  version: 0.2.5
+  version: 0.2.6
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-01-24 00:00:00.000000000 Z
+date: 2013-01-25 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: gthor