transrate 1.0.0.alpha.1 → 1.0.0.alpha.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 329f398d7dc832c5e56dfe90b6483fb00321bfce
-  data.tar.gz: 52acb0232a8f42cb3604c2981899f0d931a1195b
+  metadata.gz: 42c9c17a154a468377a5175f9937eb849c97e796
+  data.tar.gz: ddf0feca917a5d832ddf10143622ef121cd0cb73
 SHA512:
-  metadata.gz: 35f079c3474e02aa98a896cf6bbe4cd3d87ef7b7e95c91d13abea585eeb54b598ffe9539f7fc7b8c87a40ec78df92a8e1ba9fd23ac46e4da9c8f616919ab004e
-  data.tar.gz: fca938cc86122088ecb0308273d8552e1ebb26dd47e52e8154015aa27e68814016cedda45553f4bf76fcc9b164bcaaaf1cad1787c4f8296f316e6833b235e6bc
+  metadata.gz: 995833e4d14e1ceddebfd4c6f8f4c6a53fe1267a0ed53017844161803d575e7a3eaf17761315211b750fdf81c297179d17a975e737f1d2d17ca79e1a590f945e
+  data.tar.gz: 97f1ec6b36ec186e67c2c8b0550c6e90ac6ac4e59364a9c95c12b6c3ed516543a7143306ad641b8176c5da3148e0e762ddc03a42fc1c1236891832f5af73ba44

data/lib/transrate/contig.rb

@@ -27,9 +27,9 @@ module Transrate
       @reference_coverage = 0
       @has_crb = false
       @in_bridges = 0
+      @p_good = 0
       @p_seq_true = 0
       @low_uniqueness_bases = 0
-      @p_good = -1
       @uncovered_bases = length
       @p_uncovered_bases = 1
       @p_unique = 0
@@ -56,22 +56,15 @@ module Transrate
     end
 
     def read_metrics
-      read = @p_good>=0 ? {
+      {
         :in_bridges => in_bridges,
-        :p_good => @p_good,
+        :p_good => p_good,
         :p_bases_covered => p_bases_covered,
         :p_seq_true => p_seq_true,
         :score => score,
         :p_unique => p_unique,
-        :p_not_segmented => p_not_segmented
-      } : {
-        :in_bridges => "NA",
-        :p_good => "NA",
-        :p_bases_covered => "NA",
-        :p_seq_true => "NA",
-        :score => "NA",
-        :p_unique => p_unique,
-        :p_not_segmented => p_not_segmented
+        :p_not_segmented => p_not_segmented,
+        :expression => coverage
       }
     end
 

data/lib/transrate/read_metrics.rb

@@ -57,7 +57,7 @@ module Transrate
       # classify bam file into valid and invalid alignments
       sorted_bam = "#{File.basename(bamfile, '.bam')}.merged.sorted.bam"
       readsorted_bam = "#{File.basename(bamfile, '.bam')}.valid.sorted.bam"
-      unless File.exist? sorted_bam
+      unless File.exist? readsorted_bam
         valid_bam, invalid_bam = split_bam bamfile
         readsorted_bam = Samtools.readsort_bam(valid_bam, threads)
         File.delete valid_bam

data/lib/transrate/snap.rb

@@ -102,7 +102,6 @@ module Transrate
     def build_index file, threads
       @index_name = File.basename(file, File.extname(file))
       unless Dir.exists?(@index_name)
-        overflow = 500
         cmd = "#{@snap} index #{file} #{@index_name}"
         cmd << " -s 23"
         cmd << " -t#{threads}"

data/lib/transrate/version.rb

@@ -11,7 +11,7 @@ module Transrate
     MAJOR = 1
     MINOR = 0
     PATCH = 0
-    BUILD = 'alpha.1'
+    BUILD = 'alpha.2'
 
     STRING = [MAJOR, MINOR, PATCH, BUILD].compact.join('.')
   end

data/test/test_bin.rb

@@ -16,6 +16,7 @@ class TestTransrateBin < Test::Unit::TestCase
       "assembly.2_into_Os.protein.2.1.blast",
       "sorghum_transcript.nhr", "sorghum_transcript.nin", "sorghum_transcript.nsq",
       "Os.protein.2_into_sorghum_transcript.2.blast",
+      "Os.protein.2_into_assembly.2.2.blast",
       "assembly.2.nhr",  "assembly.2.nin",  "assembly.2.nsq",
       "Os.protein.2.phr",  "Os.protein.2.pin",  "Os.protein.2.psq",
       "transrate_assemblies.csv", "params.xprs",

data/transrate.gemspec

@@ -19,7 +19,7 @@ Gem::Specification.new do |gem|
 
   gem.add_dependency 'yell', '~> 2.0', '>= 2.0.4'
   gem.add_dependency 'trollop', '~> 2.0'
-  gem.add_dependency 'bindeps', '~> 0.1', '>= 0.1.0'
+  gem.add_dependency 'bindeps', '~> 0.1', '>= 0.1.2'
   gem.add_dependency 'bio', '~> 1.4', '>= 1.4.3'
   gem.add_dependency 'crb-blast', '~> 0.4', '>= 0.4.2'
   gem.add_dependency 'ruby-prof', '~> 0.15', '>= 0.15.1'

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: transrate
 version: !ruby/object:Gem::Version
-  version: 1.0.0.alpha.1
+  version: 1.0.0.alpha.2
 platform: ruby
 authors:
 - Richard Smith-Unna
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-10-15 00:00:00.000000000 Z
+date: 2014-10-17 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: yell
@@ -54,7 +54,7 @@ dependencies:
         version: '0.1'
     - - ">="
       - !ruby/object:Gem::Version
-        version: 0.1.0
+        version: 0.1.2
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
@@ -64,7 +64,7 @@ dependencies:
         version: '0.1'
     - - ">="
       - !ruby/object:Gem::Version
-        version: 0.1.0
+        version: 0.1.2
 - !ruby/object:Gem::Dependency
   name: bio
   requirement: !ruby/object:Gem::Requirement