bio-gadget 0.4.4 → 0.4.5

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 9bf862ca4bbf3f563456a0285f3e690a08fc2556
-  data.tar.gz: 4d4956c35b4d96374d7a73f24b37fe48dc053bfa
+  metadata.gz: 99193f8b25625a2260acdce7e27c0a5af6f66b93
+  data.tar.gz: 99e00b24de7f37937725d09d52faaf74226b7099
 SHA512:
-  metadata.gz: e3565824e2b4dd2b7cd328e5ade202f350d8edf29e71377e502aaff7402a9266c62f833239d9596b3c2551375b703b5db89e4cb8887acba222b23aef6b41fe89
-  data.tar.gz: 4851e1c1047ccc59e4862ba6e965b84f5dc609f926c497e0a9cbc1964bfd4d548961d9a545e5fbbce1906b743cb0cfd309d6c634b2fe846cd3094f6da182460a
+  metadata.gz: 78156bea1d87f720078f385f1f5032970338e4884bfb64fa147853cc06b1581e5902b5ee6ce2523a9b149234b73d51e5040267cd9698e29cc020a35db90cdbd7
+  data.tar.gz: 4e2d0ab4eb9841809f4fd32ccd2439908c8099dc85f277662aa79a53212afcfe49ef6e9dc2595e883dc0ed4ec831f0b849e3573aafa804a430e17aefd0eb5e99

data/lib/bio-gadget/rgt2mtx.rb

@@ -2,10 +2,31 @@ module Bio
   class Gadget < Thor
 
     desc 'rgt2mtx [RGT]', <<DESC
-Convert cuffdiff read group tracking file into tab-separated matrix. If no given name of tracking file, it reads from standard input.
+Convert cuffdiff read group tracking file (*.read_group_tracking) into tab-separated matrix. If no given name of tracking file, it reads from standard input.
 DESC
+    option 'gtf', :aliases => '-g', :type => :string, :desc => 'GTF to revert old transcript_id (oId) renamed by cuffcompare. Moreover, "RNA_SPIKE_*" chromosome names will be inserted for the transcripts aligned on the forward strand of spike-in sequences.'
+    option 'sample', :aliases => '-s', :type => :string, :desc => 'Mapping from condition/replicate to sample ID for the column names of output matrix. Tab-separated text with three columns of condition, replicate and the sample ID.'
     def rgt2mtx(rgt="/dev/stdin")
 
+      tid2oid = Hash.new
+      unless options['gtf'].nil?
+        open(options['gtf']).each { |line|
+          cols = line.rstrip.split(/\t/)
+          tid = cols[8].match(/transcript_id \"([^\"]+)/).to_a[1]
+          oid = cols[8].match(/oId \"([^\"]+)/).to_a[1]
+          oid = "#{cols[0]}.#{oid}" if cols[0] =~ /^RNA_SPIKE_/
+          tid2oid[tid] = oid
+        }
+      end
+
+      cr2sid = Hash.new
+      unless options['sample'].nil?
+        open(options['sample']).each { |line|
+          c, r, sid = line.rstrip.split(/\t/)
+          cr2sid["#{c}|#{r}"] = sid
+        }
+      end
+
       id = nil
       header = true
       raws = Hash.new
@@ -14,10 +35,16 @@ DESC
         id = cols[0] if id.nil?
         if id != cols[0]
           if header
-            puts (['tracking_id'] + raws.keys.sort).join("\t")
+            if options['sample'].nil?
+              puts ([''] + raws.keys.sort).join("\t")
+            else
+              tmp = ['']
+              raws.keys.sort.each { |cr| tmp.push(cr2sid[cr]) }
+              puts tmp.join("\t")
+            end
             header = false
           end
-          tmp = [id]
+          tmp = [tid2oid.key?(id) ? tid2oid[id] : id]
           raws.keys.sort.each { |k| tmp.push(raws[k]) }
           puts tmp.join("\t")
           id = cols[0]

data/lib/bio-gadget/version.rb

@@ -3,7 +3,7 @@ require 'thor'
 module Bio
   class Gadget < Thor
 
-    VERSION = "0.4.4"
+    VERSION = "0.4.5"
 
   end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bio-gadget
 version: !ruby/object:Gem::Version
-  version: 0.4.4
+  version: 0.4.5
 platform: ruby
 authors:
 - Shintaro Katayama
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-04-30 00:00:00.000000000 Z
+date: 2013-05-03 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: thor