bio-gadget 0.4.3 → 0.4.4

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
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-  data.tar.gz: a9fbb56f5eb610b46a138353dc3ed8f9648cd2ea
+  metadata.gz: 9bf862ca4bbf3f563456a0285f3e690a08fc2556
+  data.tar.gz: 4d4956c35b4d96374d7a73f24b37fe48dc053bfa
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+  data.tar.gz: 4851e1c1047ccc59e4862ba6e965b84f5dc609f926c497e0a9cbc1964bfd4d548961d9a545e5fbbce1906b743cb0cfd309d6c634b2fe846cd3094f6da182460a

data/README.org

@@ -16,7 +16,8 @@ Currently available commands are
 
 - dedup :: Deduplicate fastq (via STDIN)
 - demlt :: Demultiplex fastq by barcodes
-- fqxz :: automatic (re)compression of *.fq(.gz|.bz2) files
+- femrg :: Extract and merge first exons
+- fqxz :: (Re)compression of *.fq(.gz|.bz2) files
 - qvstat :: Statistics of quality values in *.qual file
 - rgt2mtx :: Convert cuffdiff read group tracking file into tab-separated matrix
 - wig5p :: Convert bam-format alignments into wig-format table

data/lib/bio-gadget.rb

@@ -1,6 +1,7 @@
 require 'bio-gadget/version'
 require 'bio-gadget/dedup'
 require 'bio-gadget/demlt'
+require 'bio-gadget/femrg'
 require 'bio-gadget/fqxz'
 require 'bio-gadget/qvstat'
 require 'bio-gadget/rgt2mtx'

data/lib/bio-gadget/femrg.rb

@@ -0,0 +1,61 @@
+module Bio
+  class Gadget < Thor
+
+    desc 'femrg [GTF...]', 'Extract and merge overlapping first exons.'
+
+    def femrg(*gtf_files)
+
+      exon1s = Hash.new
+      fp = open("| grep -h '\texon\t' #{gtf_files.nil? ? '-' : gtf_files.join(' ')} | cut -f 1,4,5,7,9")
+      fp.each { |line|
+        chr, sstart, sstop, str, attr = line.rstrip.split(/\t/)
+        exon1s[chr] = Hash.new unless exon1s.key?(chr)
+        exon1s[chr][str] = Hash.new unless exon1s[chr].key?(str)
+        id = attr.match(/transcript_id \"([^\"]+)\"/).to_a[1]
+        en = attr.match(/exon_number \"(\d+)\"/).to_a[1].to_i
+        if (!exon1s[chr][str].key?(id) ||
+            (str == "+" && en < exon1s[chr][str][id][2]) ||
+            (str == "-" && exon1s[chr][str][id][2] < en))
+          exon1s[chr][str][id] = [sstart.to_i, sstop.to_i, en]
+        end
+      }
+      fp.close
+
+      idx = 0
+      exon1s.each { |chr, exon1schr|
+        exon1schr.each { |str, exon1schrstr|
+          ids = exon1schrstr.keys.sort { |a, b|
+            exon1schrstr[a][0] <=> exon1schrstr[b][0]
+          }
+          #
+          clusters = Array.new
+          members = [id = ids.shift]
+          start, stop, en = exon1schrstr[id]
+          while ids.length > 0
+            nid = ids.shift
+            nstart, nstop, nen = exon1schrstr[nid]
+            if stop < nstart
+              clusters.push([members, start, stop])
+              members = [nid]
+              start = nstart
+              stop = nstop
+            else
+              members.push(nid)
+              start, stop = [start, stop, nstart, nstop].sort.values_at(0, 3)
+            end
+          end
+          clusters.push([members, start, stop])
+          #
+          clusters.each { |members, start, stop|
+            attr = "gene_id \"FE#{idx}\"; transcript_id \"FE#{idx}\"; "
+            puts [chr, 'bio-gadget:femrg', 'transcript', start, stop, 1000, str, '.', attr].join("\t")
+            puts [chr, 'bio-gadget:femrg', 'exon', start, stop, 1000, str, '.', "#{attr}exon_number \"1\"; member_ids \"#{members.join('|')}\""].join("\t")
+            idx += 1
+          }
+        }
+      }
+
+    end
+
+  end
+end

data/lib/bio-gadget/version.rb

@@ -3,7 +3,7 @@ require 'thor'
 module Bio
   class Gadget < Thor
 
-    VERSION = "0.4.3"
+    VERSION = "0.4.4"
 
   end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bio-gadget
 version: !ruby/object:Gem::Version
-  version: 0.4.3
+  version: 0.4.4
 platform: ruby
 authors:
 - Shintaro Katayama
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-04-14 00:00:00.000000000 Z
+date: 2013-04-30 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: thor
@@ -99,6 +99,7 @@ files:
 - lib/bio-gadget.rb
 - lib/bio-gadget/dedup.rb
 - lib/bio-gadget/demlt.rb
+- lib/bio-gadget/femrg.rb
 - lib/bio-gadget/fqxz.rb
 - lib/bio-gadget/qvstat.rb
 - lib/bio-gadget/rgt2mtx.rb