bio-gadget 0.4.7 → 0.4.8

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 993d87f1638e12bc336223e98be4dbeeeb5a8404
-  data.tar.gz: 95cb2d5cba5cc230d960bc0c558b3f1b1b562753
+  metadata.gz: 919243e81fb8eecaf1e9af9f85914439f3aa27d5
+  data.tar.gz: 5c1a8c551f09e46857720493b9495fe499778d27
 SHA512:
-  metadata.gz: ec8586c5e171b700596500bfbf16a9467bc65c6dd2dff2c5bd0e4b34f4775e40322cc1eecb00c81745c514edf3e59fedb8f9cb57a12586dcce4d08e6b87d24dd
-  data.tar.gz: da97c93be8331cf0048dd6e99cf6d66debc9985797ec909f6c2c908a6904667df2507e2170460632a5bd58a18dde44acd465843d03e572b4c55c9773fa9223f6
+  metadata.gz: 20827e3e37d7360508c52b49d3f4ccfb0b034a647656088c56f9aedd1015794ce766a6069b3b48fd18285461488de9bec764753e141752156c354b3c91e3fe5a
+  data.tar.gz: aae01b065bf04def5d836cfc18c2b3ada4d8c8210f23d2b26796d32cffbfaebd2c0e20b5bad4a69e2cd5dc68e243c04921cdbe1587c3ae0560881c0238bbee75

data/lib/bio-gadget/peak.rb

@@ -1,3 +1,6 @@
+require 'mkfifo'
+require 'parallel'
+
 module Bio
   class Gadget < Thor
 
@@ -24,6 +27,7 @@ DESC
         fp.close
       }
 
+      chr2exon = Hash.new
       open("| grep exon #{gtf}").each { |line|
         cols = line.rstrip.split(/\t/)
         oid = cols[8].match(/oId \"([^\"]+)/).to_a[1]
@@ -33,35 +37,56 @@ DESC
         str = cols[6]
         start = cols[3].to_i
         stop = cols[4].to_i
-        peak = ''
+        chr2exon[chr] = Array.new unless chr2exon.key?(chr)
+        chr2exon[chr].push([str, oid, exn, start, stop])
+      }
+
+      fifopath = mytemppath('fifo-')
+      File.mkfifo(fifopath)
+
+      pid = Kernel.fork {
+        exec "cat #{fifopath}"
+      }
+
+      fp = open(fifopath, 'w')
+      Parallel.each(chr2exon.keys,
+                    :in_processes => Parallel.processor_count) { |chr|
         #
-        poss = Hash.new
-        nchrpos2val.each { |n, chrpos2val|
-          if chrpos2val.key?(chr)
-            pos2val = chrpos2val[chr]
-            tmppos2val = Hash.new
-            pos2val.each { |pos, val|
-              tmppos2val[pos] = val if start <= pos && pos <= stop
-            }
-            if tmppos2val.size > 0
-              tmpposs = tmppos2val.keys.sort { |a, b|
-                tmppos2val[b] == tmppos2val[a] ? (str == '+' ? (a <=> b) : (b <=> a)) : (tmppos2val[b] <=> tmppos2val[a])
+        chr2exon[chr].each { |str, oid, exn, start, stop|
+          #
+          peak = ''
+          poss = Hash.new
+          nchrpos2val.each { |n, chrpos2val|
+            if chrpos2val.key?(chr)
+              pos2val = chrpos2val[chr]
+              tmppos2val = Hash.new
+              pos2val.each { |pos, val|
+                tmppos2val[pos] = val if start <= pos && pos <= stop
               }
-              tmppos = tmpposs[0]
-              # puts "#{n} | #{chr}:#{start}-#{stop} #{str} | #{tmpposs}"
-              poss[tmppos] = poss.key?(tmppos) ? poss[tmppos]+1 : 1
+              if tmppos2val.size > 0
+                tmpposs = tmppos2val.keys.sort { |a, b|
+                  tmppos2val[b] == tmppos2val[a] ? (str == '+' ? (a <=> b) : (b <=> a)) : (tmppos2val[b] <=> tmppos2val[a])
+                }
+                tmppos = tmpposs[0]
+                # puts "#{n} | #{chr}:#{start}-#{stop} #{str} | #{tmpposs}"
+                poss[tmppos] = poss.key?(tmppos) ? poss[tmppos]+1 : 1
+              end
             end
+          }
+          if poss.size > 0
+            peaks = poss.keys.sort { |a, b|
+              poss[b] == poss[a] ? (str == '+' ? (a <=> b) : (b <=> a)) : (poss[b] <=> poss[a])
+            }
+            peak = peaks[0]
           end
+          #
+          fp.syswrite([oid, exn, peak].join("\t") + "\n")
         }
-        if poss.size > 0
-          peaks = poss.keys.sort { |a, b|
-            poss[b] == poss[a] ? (str == '+' ? (a <=> b) : (b <=> a)) : (poss[b] <=> poss[a])
-          }
-          peak = peaks[0]
-        end
         #
-        puts [oid, exn, peak].join("\t")
       }
+      fp.close
+
+      Process.waitall
 
     end
 

data/lib/bio-gadget/version.rb

@@ -3,7 +3,7 @@ require 'thor'
 module Bio
   class Gadget < Thor
 
-    VERSION = "0.4.7"
+    VERSION = "0.4.8"
 
   end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bio-gadget
 version: !ruby/object:Gem::Version
-  version: 0.4.7
+  version: 0.4.8
 platform: ruby
 authors:
 - Shintaro Katayama
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-05-30 00:00:00.000000000 Z
+date: 2013-06-09 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: thor