bio-ngs 0.4.7.alpha.02 → 0.4.7.alpha.03

data/VERSION

@@ -1 +1 @@
-0.4.7.alpha.02
+0.4.7.alpha.03

data/bio-ngs.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = "bio-ngs"
-  s.version = "0.4.7.alpha.02"
+  s.version = "0.4.7.alpha.03"
 
   s.required_rubygems_version = Gem::Requirement.new("> 1.3.1") if s.respond_to? :required_rubygems_version=
   s.authors = ["Francesco Strozzi", "Raoul J.P. Bonnal"]
-  s.date = "2012-05-25"
+  s.date = "2012-05-29"
   s.description = "bio-ngs provides a framework for handling NGS data with BioRuby"
   s.email = "francesco.strozzi@gmail.com"
   s.executables = ["biongs"]
@@ -31,6 +31,7 @@ Gem::Specification.new do |s|
     "ext/mkrf_conf.rb",
     "features/cufflinks_gtf_parser.feature",
     "features/cufflinks_gtf_parser_indexing.feature",
+    "features/illumina_project_rebuild.feature",
     "features/step_definitions/cufflinks_gtf.rb",
     "features/step_definitions/cufflinks_gtf_parser_indexing.rb",
     "features/support/env.rb",
@@ -115,7 +116,62 @@ Gem::Specification.new do |s|
     "spec/spec_helper.rb",
     "spec/tophat_spec.rb",
     "spec/utils_spec.rb",
+    "test/conf/projects.yaml",
     "test/conf/test_db.yml",
+    "test/data/Project_Cow/Sample_SQ_0007/SQ_0007_CGATGT_L003_R1_001.fastq.gz",
+    "test/data/Project_Cow/Sample_SQ_0007/SQ_0007_CGATGT_L003_R1_002.fastq.gz",
+    "test/data/Project_Cow/Sample_SQ_0007/SQ_0007_CGATGT_L003_R2_001.fastq.gz",
+    "test/data/Project_Cow/Sample_SQ_0007/SQ_0007_CGATGT_L003_R2_002.fastq.gz",
+    "test/data/Project_Cow/Sample_SQ_0007/filtered/SQ_0007_CGATGT_L003_R1_001.fastq.gz",
+    "test/data/Project_Cow/Sample_SQ_0007/filtered/SQ_0007_CGATGT_L003_R1_002.fastq.gz",
+    "test/data/Project_Cow/Sample_SQ_0007/filtered/SQ_0007_CGATGT_L003_R2_001.fastq.gz",
+    "test/data/Project_Cow/Sample_SQ_0007/filtered/SQ_0007_CGATGT_L003_R2_002.fastq.gz",
+    "test/data/Project_Cow/Sample_SQ_0007/trimmed/SQ_0007_CGATGT_L003_R1_TRIMMED.fastq.gz",
+    "test/data/Project_Cow/Sample_SQ_0007/trimmed/SQ_0007_CGATGT_L003_R2_TRIMMED.fastq.gz",
+    "test/data/Project_Cow/Sample_SQ_0008/SQ_0008_CGATGT_L003_R1_001.fastq.gz",
+    "test/data/Project_Cow/Sample_SQ_0008/SQ_0008_CGATGT_L003_R1_002.fastq.gz",
+    "test/data/Project_Cow/Sample_SQ_0008/SQ_0008_CGATGT_L003_R2_001.fastq.gz",
+    "test/data/Project_Cow/Sample_SQ_0008/SQ_0008_CGATGT_L003_R2_002.fastq.gz",
+    "test/data/Project_Cow/Sample_SQ_0009/SQ_0009_CGATGT_L003_R1_001.fastq.gz",
+    "test/data/Project_Cow/Sample_SQ_0009/SQ_0009_CGATGT_L003_R1_002.fastq.gz",
+    "test/data/Project_Cow/Sample_SQ_0009/SQ_0009_CGATGT_L003_R2_001.fastq.gz",
+    "test/data/Project_Cow/Sample_SQ_0009/SQ_0009_CGATGT_L003_R2_002.fastq.gz",
+    "test/data/Project_Dog/Sample_SQ_0004/SQ_0004_CGATGT_L003_R1_001.fastq.gz",
+    "test/data/Project_Dog/Sample_SQ_0004/SQ_0004_CGATGT_L003_R1_002.fastq.gz",
+    "test/data/Project_Dog/Sample_SQ_0004/SQ_0004_CGATGT_L003_R2_001.fastq.gz",
+    "test/data/Project_Dog/Sample_SQ_0004/SQ_0004_CGATGT_L003_R2_002.fastq.gz",
+    "test/data/Project_Dog/Sample_SQ_0005/SQ_0005_CGATGT_L003_R1_001.fastq.gz",
+    "test/data/Project_Dog/Sample_SQ_0005/SQ_0005_CGATGT_L003_R1_002.fastq.gz",
+    "test/data/Project_Dog/Sample_SQ_0005/SQ_0005_CGATGT_L003_R2_001.fastq.gz",
+    "test/data/Project_Dog/Sample_SQ_0005/SQ_0005_CGATGT_L003_R2_002.fastq.gz",
+    "test/data/Project_Dog/Sample_SQ_0006/SQ_0006_CGATGT_L003_R1_001.fastq.gz",
+    "test/data/Project_Dog/Sample_SQ_0006/SQ_0006_CGATGT_L003_R1_002.fastq.gz",
+    "test/data/Project_Dog/Sample_SQ_0006/SQ_0006_CGATGT_L003_R2_001.fastq.gz",
+    "test/data/Project_Dog/Sample_SQ_0006/SQ_0006_CGATGT_L003_R2_002.fastq.gz",
+    "test/data/Project_Human/Sample_SQ_0001/SQ_0001_CGATGT_L003_R1_001.fastq.gz",
+    "test/data/Project_Human/Sample_SQ_0001/SQ_0001_CGATGT_L003_R1_002.fastq.gz",
+    "test/data/Project_Human/Sample_SQ_0001/SQ_0001_CGATGT_L003_R2_001.fastq.gz",
+    "test/data/Project_Human/Sample_SQ_0001/SQ_0001_CGATGT_L003_R2_002.fastq.gz",
+    "test/data/Project_Human/Sample_SQ_0002/SQ_0002_CGATGT_L003_R1_001.fastq.gz",
+    "test/data/Project_Human/Sample_SQ_0002/SQ_0002_CGATGT_L003_R1_002.fastq.gz",
+    "test/data/Project_Human/Sample_SQ_0002/SQ_0002_CGATGT_L003_R2_001.fastq.gz",
+    "test/data/Project_Human/Sample_SQ_0002/SQ_0002_CGATGT_L003_R2_002.fastq.gz",
+    "test/data/Project_Human/Sample_SQ_0003/SQ_0003_CGATGT_L003_R1_001.fastq.gz",
+    "test/data/Project_Human/Sample_SQ_0003/SQ_0003_CGATGT_L003_R1_002.fastq.gz",
+    "test/data/Project_Human/Sample_SQ_0003/SQ_0003_CGATGT_L003_R2_001.fastq.gz",
+    "test/data/Project_Human/Sample_SQ_0003/SQ_0003_CGATGT_L003_R2_002.fastq.gz",
+    "test/data/RemoteDir/Project_Human/Sample_SQ_0001/SQ_0001_CGATGT_L010_R1_001.fastq.gz",
+    "test/data/RemoteDir/Project_Human/Sample_SQ_0001/SQ_0001_CGATGT_L010_R1_002.fastq.gz",
+    "test/data/RemoteDir/Project_Human/Sample_SQ_0001/SQ_0001_CGATGT_L010_R2_001.fastq.gz",
+    "test/data/RemoteDir/Project_Human/Sample_SQ_0001/SQ_0001_CGATGT_L010_R2_002.fastq.gz",
+    "test/data/RemoteDir/Project_Human/Sample_SQ_0002/SQ_0002_CGATGT_L003_R1_001.fastq.gz",
+    "test/data/RemoteDir/Project_Human/Sample_SQ_0002/SQ_0002_CGATGT_L003_R1_002.fastq.gz",
+    "test/data/RemoteDir/Project_Human/Sample_SQ_0002/SQ_0002_CGATGT_L003_R2_001.fastq.gz",
+    "test/data/RemoteDir/Project_Human/Sample_SQ_0002/SQ_0002_CGATGT_L003_R2_002.fastq.gz",
+    "test/data/RemoteDir/Project_Human/Sample_SQ_0003/SQ_0003_CGATGT_L003_R1_001.fastq.gz",
+    "test/data/RemoteDir/Project_Human/Sample_SQ_0003/SQ_0003_CGATGT_L003_R1_002.fastq.gz",
+    "test/data/RemoteDir/Project_Human/Sample_SQ_0003/SQ_0003_CGATGT_L003_R2_001.fastq.gz",
+    "test/data/RemoteDir/Project_Human/Sample_SQ_0003/SQ_0003_CGATGT_L003_R2_002.fastq.gz",
     "test/data/blastoutput.xml",
     "test/data/gene-GO.json",
     "test/data/goa_uniprot",

data/features/cufflinks_gtf_parser_indexing.feature

@@ -17,4 +17,9 @@ Feature: Indexing Cufflinks GTF features
   Scenario: extract multiple features from a GTF
     Given the file "transcripts.gtf" from quantification analysis
     And a range from "2" to "11"
-    Then I want to obtain a bed file for each position in the range
+    Then I want to obtain a bed file for each position in the range
+
+
+  Scenario: extract a feature from a GTF using transcript name
+    Given the file "transcripts.gtf" from quantification analysis
+    Then I want to extract feature named "ENST00000408219"

data/features/illumina_project_rebuild.feature

@@ -0,0 +1,17 @@
+Feature: build a project hierarchy from an hand made analysis
+In order to organize and automate many processes for an NGS dataset
+analyzed by hand from other bioinformaticians
+As a bioinformatician
+I want to have a querable data structure which represents most of the pre cumputed data
+
+Scenario: Explore and Build data structure
+  Given A path with many projects at the first level
+  And others at second level (inside others directories)
+  When I build the projects structure
+  Then I sould get all the projects organized in the same structure.
+
+
+# Scenario: Merge multiple data structure to find common datasets
+#   Given
+#   When
+#   Then

data/features/step_definitions/cufflinks_gtf_parser_indexing.rb

@@ -4,7 +4,14 @@ Given /^a range from "(.*?)" to "(.*?)"$/ do |start, stop|
 end
 
 Then /^I want to build its index$/ do
-  @gtf.build_idx.should == {:transcripts=>[801, 604, 425, 425, 857, 610, 610, 607, 607, 616, 622, 809, 1003, 821, 429, 412, 1023, 610, 607, 1003, 616, 607, 404, 404, 2973, 3219, 3420, 3219, 813, 1213, 1213, 1231, 613, 408, 408, 814, 1014, 626, 814, 408, 436, 610, 662, 1016, 816, 613, 2227, 616, 616, 616, 420, 643, 7588, 813, 814, 1014, 814, 614, 614, 3018, 2013, 814, 613, 865, 433, 433, 433, 643, 619, 3454, 3454, 2043, 1237, 628, 1225, 1023, 1243, 1023, 1225, 410, 410, 1662, 1238, 1004, 1023, 2642, 2237, 2439, 2033, 2439, 2236, 834, 2280, 2642, 821, 1832, 2236, 2439, 2236, 2439, 2033, 1629, 1225, 1427, 1225, 1225, 821, 1427, 412, 412, 611, 412, 412, 412, 414, 1678, 1629, 1630, 822, 620, 1225, 1267, 821, 426, 821, 626, 1831, 821, 629, 412, 418, 1831, 1629, 1670, 1427, 1694, 1427, 1831, 1630, 1831, 620, 1629, 1629, 1225, 1023, 1427, 1427, 1427, 822, 1225, 1225, 822, 620, 818, 817, 617, 4063, 3860, 3657, 3300, 1023], :exons=>[]}
+  @gtf.build_idx.should == {:transcripts=>[801, 604, 425, 425, 857, 610, 610, 607, 607, 616, 622, 809, 1003, 821, 429, 412, 1023, 610, 607, 1003, 616, 607, 404,
+    404, 2973, 3219, 3420, 3219, 813, 1213, 1213, 1231, 613, 408, 408, 814, 1014, 626, 814, 408, 436, 610, 662, 1016, 816, 613, 2227, 616, 616, 616, 420, 643, 7588,
+     813, 814, 1014, 814, 614, 614, 3018, 2013, 814, 613, 865, 433, 433, 433, 643, 619, 3454, 3454, 2043, 1237, 628, 1225, 1023, 1243, 1023, 1225, 410, 410, 1662, 
+     1238, 1004, 1023, 2642, 2237, 2439, 2033, 2439, 2236, 834, 2280, 2642, 821, 1832, 2236, 2439, 2236, 2439, 2033, 1629, 1225, 1427, 1225, 1225, 821, 1427, 412,
+      412, 611, 412, 412, 412, 414, 1678, 1629, 1630, 822, 620, 1225, 1267, 821, 426, 821, 626, 1831, 821, 629, 412, 418, 1831, 1629, 1670, 1427, 1694, 1427, 1831,
+       1630, 1831, 620, 1629, 1629, 1225, 1023, 1427, 1427, 1427, 822, 1225, 1225, 822, 620, 818, 817, 617, 4063, 3860, 3657, 3300, 1023],
+       :names=>{"ENST00000417324"=>1, "ENST00000461467"=>2, "ENST00000492842"=>3, "ENST00000335137"=>4, "ENST00000417636"=>5, "ENST00000423796"=>6, "ENST00000450696"=>7, "TCONS_00000124"=>8, "TCONS_00000125"=>9, "TCONS_00000796"=>10, "TCONS_00001368"=>11, "ENST00000446136"=>12, "TCONS_00000444"=>13, "ENST00000427857"=>14, "ENST00000408219"=>15, "ENST00000415481"=>16, "ENST00000417705"=>17, "ENST00000432961"=>18, "TCONS_00002277"=>19, "TCONS_00000073"=>20, "TCONS_00000032"=>21, "TCONS_00000134"=>22, "CUFF.8.1"=>23, "CUFF.9.1"=>24, "CUFF.10.1"=>25, "ENST00000379407"=>26, "ENST00000379410"=>27, "ENST00000379409"=>28, "ENST00000480267"=>29, "ENST00000491024"=>30, "ENST00000433179"=>31, "ENST00000341290"=>32, "ENST00000479361"=>33, "CUFF.12.1"=>34, "CUFF.13.1"=>35, "ENST00000428771"=>36, "ENST00000304952"=>37, "ENST00000481869"=>38, "ENST00000484667"=>39, "CUFF.14.5"=>40, "ENST00000423619"=>41, "TCONS_00000447"=>42, "ENST00000379389"=>43, "ENST00000427998"=>44, "ENST00000394517"=>45, "ENST00000442292"=>46, "ENST00000412397"=>47, "ENST00000456409"=>48, "ENST00000433695"=>49, "ENST00000451054"=>50, "CUFF.16.8"=>51, "ENST00000453464"=>52, "ENST00000379370"=>53, "ENST00000477585"=>54, "ENST00000469403"=>55, "ENST00000479707"=>56, "ENST00000466223"=>57, "ENST00000478677"=>58, "ENST00000492947"=>59, "ENST00000379364"=>60, "ENST00000419249"=>61, "ENST00000461111"=>62, "ENST00000418300"=>63, "ENST00000416774"=>64, "ENST00000384997"=>65, "ENST00000384875"=>66, "ENST00000362106"=>67, "ENST00000379317"=>68, "ENST00000506177"=>69, "ENST00000379290"=>70, "ENST00000379289"=>71, "ENST00000379288"=>72, "ENST00000460998"=>73, "ENST00000514695"=>74, "ENST00000486379"=>75, "ENST00000328596"=>76, "ENST00000379268"=>77, "ENST00000486728"=>78, "ENST00000379265"=>79, "CUFF.19.5"=>80, "CUFF.19.6"=>81, "ENST00000379236"=>82, "ENST00000497869"=>83, "CUFF.20.3"=>84, "ENST00000453580"=>85, "ENST00000379339"=>86, "ENST00000294576"=>87, "ENST00000448924"=>88, "ENST00000465822"=>89, "ENST00000379325"=>90, "ENST00000421241"=>91, "ENST00000487177"=>92, "ENST00000477196"=>93, "ENST00000467751"=>94, "ENST00000464905"=>95, "ENST00000379320"=>96, "ENST00000379319"=>97, "ENST00000434641"=>98, "ENST00000482816"=>99, "ENST00000457999"=>100, "ENST00000437760"=>101, "ENST00000462097"=>102, "ENST00000473600"=>103, "ENST00000475119"=>104, "ENST00000442117"=>105, "ENST00000427787"=>106, "ENST00000472741"=>107, "ENST00000480643"=>108, "CUFF.27.1"=>109, "CUFF.28.1"=>110, "CUFF.30.1"=>111, "CUFF.31.1"=>112, "CUFF.32.1"=>113, "CUFF.33.1"=>114, "CUFF.21.1"=>115, "ENST00000360001"=>116, "ENST00000465727"=>117, "ENST00000263741"=>118, "ENST00000494748"=>119, "ENST00000478938"=>120, "ENST00000403997"=>121, "ENST00000545427"=>122, "ENST00000459994"=>123, "ENST00000379198"=>124, "ENST00000462849"=>125, "ENST00000478606"=>126, "ENST00000330388"=>127, "ENST00000468365"=>128, "ENST00000486627"=>129, "CUFF.25.1"=>130, "ENST00000565563"=>131, "ENST00000450390"=>132, "ENST00000347370"=>133, "ENST00000349431"=>134, "ENST00000339385"=>135, "ENST00000348298"=>136, "ENST00000400929"=>137, "ENST00000464036"=>138, "ENST00000360466"=>139, "ENST00000400930"=>140, "ENST00000467339"=>141, "ENST00000473215"=>142, "ENST00000435198"=>143, "ENST00000509720"=>144, "ENST00000491779"=>145, "ENST00000466752"=>146, "ENST00000503294"=>147, "ENST00000477894"=>148, "ENST00000471154"=>149, "ENST00000422076"=>150, "ENST00000502382"=>151, "ENST00000461142"=>152, "ENST00000488418"=>153, "TCONS_00000799"=>154, "TCONS_00000135"=>155, "TCONS_00000136"=>156, "ENST00000379110"=>157, "ENST00000379116"=>158, "ENST00000379101"=>159, "ENST00000338555"=>160, "ENST00000470022"=>161},
+        :exons=>[]}
 end
 
 Then /^save it as "(.*?)"$/ do |gtf_index_filename|
@@ -50,4 +57,14 @@ Then /^I want to obtain a bed file for each position in the range$/ do
                  "CUFF.2-ENST00000423796.bed\n", "CUFF.2-ENST00000450696.bed\n",
                  "CUFF.2-TCONS_00000124.bed\n", "CUFF.2-TCONS_00000125.bed\n",
                  "CUFF.3-TCONS_00000796.bed\n", "XLOC_000669-TCONS_00001368.bed\n"]
-  end
+  end
+
+
+Then /^I want to extract feature named "(.*?)"$/ do |transcript_name|
+    enst00000408219 = <<DATA
+1	Cufflinks	transcript	808847	808957	1	-	.	gene_id "ENSG00000221146"; transcript_id "ENST00000408219"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000"; full_read_support "no";
+1	Cufflinks	exon	808847	808957	1	-	.	gene_id "ENSG00000221146"; transcript_id "ENST00000408219"; exon_number "1"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000";
+DATA
+
+  @gtf[transcript_name].to_s.should == enst00000408219
+end

data/lib/bio/appl/ngs/cufflinks/gtf/gtf_parser.rb

@@ -1,4 +1,4 @@
-# TODO: 
+# TODO:
 # * when select or first each trasncript create and index. Be aware to return/crete the right index for the requested filtering.
 #   issue: filtering is applied but the index is created and saved for the original source file.
 
@@ -139,10 +139,10 @@ module Bio
           fn = filename || "#{@fh.path}.gtf"
           File.open(fn, 'w') do |f|
             each_transcript do |transcript|
-                f.write transcript
+              f.write transcript
             end
           end
-          # dump_idx("#{fn}.idx") #BUGGY this saves the old index in case the user called a select 
+          # dump_idx("#{fn}.idx") #BUGGY this saves the old index in case the user called a select
         end #save
 
         def count
@@ -156,10 +156,16 @@ module Bio
         def build_idx
           idx = Hash.new {|h,k| h[k]=[]}
           idx[:transcripts]
+          idx[:names]={}
           idx[:exons]
           each_transcript do |t, f_lno|
             # t_idx=(f_lno-t.exons.size-2)
             idx[:transcripts] << t.byte_length
+            idx[:names][t.attributes[:transcript_id]] = idx[:transcripts].length
+            if t.attributes[:transcript_id]=="ENST00000408219"
+              puts t.attributes[:transcript_id]
+              puts idx[:transcripts].length
+            end
             # eidx_b = t_idx +1
             # t.exons.each_index do |ei|
             #   idx[t_idx] << eidx_b + ei
@@ -197,27 +203,35 @@ module Bio
         end
 
         # start from 1
+        # n can be a number or a name for a transcript
         def read_transcript(n=1)
           load_idx unless defined?(@idx)
-          if n==1
-            source.seek(0)
-            source.read(@idx[:transcripts][0])
-          elsif n==2
-            source.seek(@idx[:transcripts][0])
-            source.read(@idx[:transcripts][n-1])
+          if n.to_s.is_numeric?
+            n = n.to_i
+            if n==1
+              source.seek(0)
+              source.read(@idx[:transcripts][0])
+            elsif n==2
+              source.seek(@idx[:transcripts][0])
+              source.read(@idx[:transcripts][n-1])
+            else
+              source.seek(@idx[:transcripts][0..n-2].sum)
+              source.read(@idx[:transcripts][n-1])
+            end
           else
-            source.seek(@idx[:transcripts][0..n-2].sum)
-            source.read(@idx[:transcripts][n-1])
+            read_transcript(@idx[:names][n])
           end
         end
 
         def get_transcript(n=1)
-          r=read_transcript(n)
-          s=r.split("\n").first
-          e=r.split("\n")[1..-1]
-          x=Bio::Ngs::Cufflinks::Transcript.new
-          x.tra= s+"\n"
-          x.exons=e.map{|ei| ei+"\n"}
+          x=nil
+          if r=read_transcript(n)
+            s=r.split("\n").first
+            e=r.split("\n")[1..-1]
+            x=Bio::Ngs::Cufflinks::Transcript.new
+            x.tra= s+"\n"
+            x.exons=e.map{|ei| ei+"\n"}
+          end
           x
         end
 
@@ -229,6 +243,18 @@ module Bio
   end #Ngs
 end #Bio
 
+
+class String
+  # from http://railsforum.com/viewtopic.php?id=19081
+  def is_numeric?
+    Float(self)
+    true
+  rescue
+    false
+  end
+end
+
+
 # class Array
 #   def to_ranges
 #     sorted=self.sort

data/lib/bio/ngs/illumina/illumina.rb

@@ -40,8 +40,8 @@ module Bio
           projects = Projects.new("Illumina", path)
 
           Dir.chdir(path) do
-            Dir.glob(["Project_*","Undetermined_indices"]).each do |project_dir|
-              project = Project.new(project_dir.sub(/Project_/,""),project_dir)
+            Dir.glob(["**/Project_*","**/Undetermined_indices"]).each do |project_dir|
+              project = Project.new(project_dir.basename.sub(/Project_/,""),project_dir)
               projects.add(project)
               Dir.chdir(project_dir) do
                 Dir.glob("Sample*").each do |sample_dir|

data/lib/tasks/filter.thor

@@ -64,14 +64,14 @@ class Cufflinks < Thor
     end
    end
 
-   desc "tra_at_idx GTF IDX", "Extract transcripts from Cufflinks' GTF at specific location, print filename in output"
+   desc "tra_at_idx GTF IDX", "Extract transcript(s) from Cufflinks' GTF at a specific location or givin the transcript name, print filename in output"
    method_option :split, :type => :boolean,       :aliases => '-j', :desc => "split each transcript in a file"
    method_option :extract, :type => :numeric,     :aliases => '-e', :desc => "extract the n-th transcript"
    method_option :ucsc, :type => :boolean,        :aliases => '-u', :desc => "use chr as UCSC a prefix for chromosomes, otherwise uses ENSEMBL notation without chr"
    method_option :exons, :type => :boolean,       :aliases => '-x', :desc => "proved in output only exons without transcripts", :default => true
    def tra_at_idx(gtf, idx)
       data = Bio::Ngs::Cufflinks::Gtf.new gtf
-      t=data[idx.to_i]
+      t=data[idx]
       if options[:ucsc]
         t.set_ucsc_notation
       end

data/test/conf/projects.yaml

@@ -0,0 +1,58 @@
+base_dir: /mnt/iscsi/ngs
+projects:
+  Naive:
+   Samples:
+    SQ_0080:
+     location: &id001
+      type: file
+      path: 110908_H125_0119_AB01W2ABXX_Data/Project_Naive_T0/Sample_SQ_0080/filtered/TopHat_Alignment_PE_genomeV66/accepted_hits.bam
+      format: bam
+      
+
+  Th1: 2
+  Th17: 3
+  Th2: 4
+  Treg: 5
+  Tfh: 6
+
+
+
+  	   - 110908_H125_0119_AB01W2ABXX_Data/Project_Naive_T0/Sample_SQ_0080/filtered/TopHat_Alignment_PE_genomeV66/accepted_hits.bam 			  					
+	   - 110908_H125_0119_AB01W2ABXX_Data/Project_Naive_T0/Sample_SQ_0081/filtered/TopHat_Alignment_PE_genomeV66/accepted_hits.bam 	  		
+	   - 110908_H125_0119_AB01W2ABXX_Data/Project_Naive_T0/Sample_SQ_0082/filtered/TopHat_Alignment_PE_genomeV66/accepted_hits.bam 
+	   - 110714_H125_0102_Ab048uabxx_Data/Project_Naive/TopHat_Alignment_PE_genomeV66/accepted_hits.bam
+	Th1:
+        BAMS:
+        - 111013_H125_0121_AC076LACXX_Data/Project_Th1/Sample_SQ_0007/filtered/TopHat_Alignment_PE_genomeV66/accepted_hits.bam 			 		   
+		- 111013_H125_0121_AC076LACXX_Data/Project_Th1/Sample_SQ_0046/filtered/TopHat_Alignment_PE_genomeV66/accepted_hits.bam 	   
+		- 111013_H125_0121_AC076LACXX_Data/Project_Th1/Sample_SQ_0047/filtered/TopHat_Alignment_PE_genomeV66/accepted_hits.bam 
+		- 111013_H125_0121_AC076LACXX_Data/Project_Th1/Sample_SQ_0048/filtered/TopHat_Alignment_PE_genomeV66/accepted_hits.bam  
+		- 111013_H125_0121_AC076LACXX_Data/Project_Th1/Sample_SQ_0050/filtered/TopHat_Alignment_PE_genomeV66/accepted_hits.bam 
+    Th17:
+        BAMS:
+        - 111013_H125_0121_AC076LACXX_Data/Project_Th17/Sample_SQ_0011/filtered/TopHat_Alignment_PE_genomeV66_insert200/accepted_hits.bam 	 
+		- 111013_H125_0121_AC076LACXX_Data/Project_Th17/Sample_SQ_0051/filtered/TopHat_Alignment_PE_genomeV66_insert200/accepted_hits.bam 
+		- 111013_H125_0121_AC076LACXX_Data/Project_Th17/Sample_SQ_0052/filtered/TopHat_Alignment_PE_genomeV66_insert200/accepted_hits.bam 	 		
+		- 111013_H125_0121_AC076LACXX_Data/Project_Th17/Sample_SQ_0053/filtered/TopHat_Alignment_PE_genomeV66_insert200/accepted_hits.bam 	 
+		- 111013_H125_0121_AC076LACXX_Data/Project_Th17/Sample_SQ_0055/filtered/TopHat_Alignment_PE_genomeV66_insert200/accepted_hits.bam
+    Th2:
+        BAMS:
+        - 111013_H125_0121_AC076LACXX_Data/Project_Th2/Sample_SQ_0014/filtered/TopHat_Alignment_PE_genomeV66/accepted_hits.bam 
+		- 111013_H125_0121_AC076LACXX_Data/Project_Th2/Sample_SQ_0015/filtered/TopHat_Alignment_PE_genomeV66/accepted_hits.bam 	 
+		- 111013_H125_0121_AC076LACXX_Data/Project_Th2/Sample_SQ_0056/filtered/TopHat_Alignment_PE_genomeV66/accepted_hits.bam 
+		- 111013_H125_0121_AC076LACXX_Data/Project_Th2/Sample_SQ_0058/filtered/TopHat_Alignment_PE_genomeV66/accepted_hits.bam 
+		- 111013_H125_0121_AC076LACXX_Data/Project_Th2/Sample_SQ_0059/filtered/TopHat_Alignment_PE_genomeV66/accepted_hits.bam     
+    Treg:
+		BAMS:
+		- 111013_H125_0121_AC076LACXX_Data/Project_Treg/Sample_SQ_0021/filtered/TopHat_Alignment_PE_genomeV66/accepted_hits.bam 
+		- 111013_H125_0121_AC076LACXX_Data/Project_Treg/Sample_SQ_0022/filtered/TopHat_Alignment_PE_genomeV66/accepted_hits.bam 
+		- 111013_H125_0121_AC076LACXX_Data/Project_Treg/Sample_SQ_0023/filtered/TopHat_Alignment_PE_genomeV66/accepted_hits.bam 
+		- 111013_H125_0121_AC076LACXX_Data/Project_Treg/Sample_SQ_0065/filtered/TopHat_Alignment_PE_genomeV66/accepted_hits.bam  
+		- 111013_H125_0121_AC076LACXX_Data/Project_Treg/Sample_SQ_0067/filtered/TopHat_Alignment_PE_genomeV66/accepted_hits.bam 
+	Tfh
+		BAMS:
+		- 111013_H125_0121_AC076LACXX_Data/Project_Tfh_Adenoide/Sample_SQ_0074/filtered/TopHat_Alignment_PE_genomeV66/accepted_hits.bam 
+		- 111013_H125_0121_AC076LACXX_Data/Project_Tfh_Adenoide/Sample_SQ_0075/filtered/TopHat_Alignment_PE_genomeV66/accepted_hits.bam 
+		- 111013_H125_0121_AC076LACXX_Data/Project_Tfh_Adenoide/Sample_SQ_0076/filtered/TopHat_Alignment_PE_genomeV66/accepted_hits.bam 	
+		- 111013_H125_0121_AC076LACXX_Data/Project_Tfh_Adenoide/Sample_SQ_0078/filtered/TopHat_Alignment_PE_genomeV66/accepted_hits.bam 
+		- 111013_H125_0121_AC076LACXX_Data/Project_Tfh_Adenoide/Sample_SQ_0079/filtered/TopHat_Alignment_PE_genomeV66/accepted_hits.bam

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-ngs
 version: !ruby/object:Gem::Version
-  version: 0.4.7.alpha.02
+  version: 0.4.7.alpha.03
   prerelease: 6
 platform: ruby
 authors:
@@ -10,11 +10,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-05-25 00:00:00.000000000 Z
+date: 2012-05-29 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio
-  requirement: &2152729020 !ruby/object:Gem::Requirement
+  requirement: &2162360040 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -22,10 +22,10 @@ dependencies:
         version: 1.4.2
   type: :runtime
   prerelease: false
-  version_requirements: *2152729020
+  version_requirements: *2162360040
 - !ruby/object:Gem::Dependency
   name: bio-samtools
-  requirement: &2152728500 !ruby/object:Gem::Requirement
+  requirement: &2162358700 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -33,10 +33,10 @@ dependencies:
         version: 0.3.2
   type: :runtime
   prerelease: false
-  version_requirements: *2152728500
+  version_requirements: *2162358700
 - !ruby/object:Gem::Dependency
   name: thor
-  requirement: &2152727960 !ruby/object:Gem::Requirement
+  requirement: &2162357760 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - =
@@ -44,10 +44,10 @@ dependencies:
         version: 0.14.6
   type: :runtime
   prerelease: false
-  version_requirements: *2152727960
+  version_requirements: *2162357760
 - !ruby/object:Gem::Dependency
   name: rubyvis
-  requirement: &2152727380 !ruby/object:Gem::Requirement
+  requirement: &2162372800 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -55,10 +55,10 @@ dependencies:
         version: 0.5.0
   type: :runtime
   prerelease: false
-  version_requirements: *2152727380
+  version_requirements: *2162372800
 - !ruby/object:Gem::Dependency
   name: daemons
-  requirement: &2152726800 !ruby/object:Gem::Requirement
+  requirement: &2162369680 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -66,10 +66,10 @@ dependencies:
         version: 1.1.0
   type: :runtime
   prerelease: false
-  version_requirements: *2152726800
+  version_requirements: *2162369680
 - !ruby/object:Gem::Dependency
   name: ruby-ensembl-api
-  requirement: &2152726260 !ruby/object:Gem::Requirement
+  requirement: &2162367460 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -77,10 +77,10 @@ dependencies:
         version: 1.0.1
   type: :runtime
   prerelease: false
-  version_requirements: *2152726260
+  version_requirements: *2162367460
 - !ruby/object:Gem::Dependency
   name: activerecord
-  requirement: &2152725720 !ruby/object:Gem::Requirement
+  requirement: &2162365420 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -88,10 +88,10 @@ dependencies:
         version: 3.0.5
   type: :runtime
   prerelease: false
-  version_requirements: *2152725720
+  version_requirements: *2162365420
 - !ruby/object:Gem::Dependency
   name: sqlite3
-  requirement: &2152725140 !ruby/object:Gem::Requirement
+  requirement: &2162380460 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -99,10 +99,10 @@ dependencies:
         version: 1.3.3
   type: :runtime
   prerelease: false
-  version_requirements: *2152725140
+  version_requirements: *2162380460
 - !ruby/object:Gem::Dependency
   name: bio-blastxmlparser
-  requirement: &2152740860 !ruby/object:Gem::Requirement
+  requirement: &2162378780 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -110,10 +110,10 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *2152740860
+  version_requirements: *2162378780
 - !ruby/object:Gem::Dependency
   name: progressbar
-  requirement: &2152740240 !ruby/object:Gem::Requirement
+  requirement: &2162377060 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -121,10 +121,10 @@ dependencies:
         version: 0.9.0
   type: :runtime
   prerelease: false
-  version_requirements: *2152740240
+  version_requirements: *2162377060
 - !ruby/object:Gem::Dependency
   name: rake
-  requirement: &2152739680 !ruby/object:Gem::Requirement
+  requirement: &2162375820 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - =
@@ -132,10 +132,10 @@ dependencies:
         version: 0.9.2.2
   type: :runtime
   prerelease: false
-  version_requirements: *2152739680
+  version_requirements: *2162375820
 - !ruby/object:Gem::Dependency
   name: json
-  requirement: &2152739120 !ruby/object:Gem::Requirement
+  requirement: &2162374160 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -143,10 +143,10 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *2152739120
+  version_requirements: *2162374160
 - !ruby/object:Gem::Dependency
   name: parallel
-  requirement: &2152738540 !ruby/object:Gem::Requirement
+  requirement: &2162389180 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -154,10 +154,10 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *2152738540
+  version_requirements: *2162389180
 - !ruby/object:Gem::Dependency
   name: shoulda
-  requirement: &2152738020 !ruby/object:Gem::Requirement
+  requirement: &2162387820 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -165,10 +165,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2152738020
+  version_requirements: *2162387820
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &2152737500 !ruby/object:Gem::Requirement
+  requirement: &2162385760 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -176,10 +176,10 @@ dependencies:
         version: 1.1.0
   type: :development
   prerelease: false
-  version_requirements: *2152737500
+  version_requirements: *2162385760
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &2152736960 !ruby/object:Gem::Requirement
+  requirement: &2162384960 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -187,10 +187,10 @@ dependencies:
         version: 1.8.3
   type: :development
   prerelease: false
-  version_requirements: *2152736960
+  version_requirements: *2162384960
 - !ruby/object:Gem::Dependency
   name: rcov
-  requirement: &2152736400 !ruby/object:Gem::Requirement
+  requirement: &2162383380 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -198,10 +198,10 @@ dependencies:
         version: 0.9.11
   type: :development
   prerelease: false
-  version_requirements: *2152736400
+  version_requirements: *2162383380
 - !ruby/object:Gem::Dependency
   name: bio
-  requirement: &2152735800 !ruby/object:Gem::Requirement
+  requirement: &2162381840 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -209,10 +209,10 @@ dependencies:
         version: 1.4.2
   type: :development
   prerelease: false
-  version_requirements: *2152735800
+  version_requirements: *2162381840
 - !ruby/object:Gem::Dependency
   name: thor
-  requirement: &2152735180 !ruby/object:Gem::Requirement
+  requirement: &2162397200 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - =
@@ -220,10 +220,10 @@ dependencies:
         version: 0.14.6
   type: :development
   prerelease: false
-  version_requirements: *2152735180
+  version_requirements: *2162397200
 - !ruby/object:Gem::Dependency
   name: ffi
-  requirement: &2152734620 !ruby/object:Gem::Requirement
+  requirement: &2162394020 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -231,10 +231,10 @@ dependencies:
         version: 1.0.6
   type: :development
   prerelease: false
-  version_requirements: *2152734620
+  version_requirements: *2162394020
 - !ruby/object:Gem::Dependency
   name: rubyvis
-  requirement: &2152734120 !ruby/object:Gem::Requirement
+  requirement: &2162392380 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -242,10 +242,10 @@ dependencies:
         version: 0.5.0
   type: :development
   prerelease: false
-  version_requirements: *2152734120
+  version_requirements: *2162392380
 - !ruby/object:Gem::Dependency
   name: rspec
-  requirement: &2152733600 !ruby/object:Gem::Requirement
+  requirement: &2162391700 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -253,10 +253,10 @@ dependencies:
         version: 2.5.0
   type: :development
   prerelease: false
-  version_requirements: *2152733600
+  version_requirements: *2162391700
 - !ruby/object:Gem::Dependency
   name: daemons
-  requirement: &2152775800 !ruby/object:Gem::Requirement
+  requirement: &2162390160 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -264,10 +264,10 @@ dependencies:
         version: 1.1.0
   type: :development
   prerelease: false
-  version_requirements: *2152775800
+  version_requirements: *2162390160
 - !ruby/object:Gem::Dependency
   name: bio-samtools
-  requirement: &2152775280 !ruby/object:Gem::Requirement
+  requirement: &2162405360 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -275,10 +275,10 @@ dependencies:
         version: 0.3.2
   type: :development
   prerelease: false
-  version_requirements: *2152775280
+  version_requirements: *2162405360
 - !ruby/object:Gem::Dependency
   name: ruby-ensembl-api
-  requirement: &2152774760 !ruby/object:Gem::Requirement
+  requirement: &2162404740 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -286,10 +286,10 @@ dependencies:
         version: 1.0.1
   type: :development
   prerelease: false
-  version_requirements: *2152774760
+  version_requirements: *2162404740
 - !ruby/object:Gem::Dependency
   name: activerecord
-  requirement: &2152774240 !ruby/object:Gem::Requirement
+  requirement: &2162404160 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -297,10 +297,10 @@ dependencies:
         version: 3.0.5
   type: :development
   prerelease: false
-  version_requirements: *2152774240
+  version_requirements: *2162404160
 - !ruby/object:Gem::Dependency
   name: sqlite3
-  requirement: &2152773740 !ruby/object:Gem::Requirement
+  requirement: &2162403240 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -308,10 +308,10 @@ dependencies:
         version: 1.3.3
   type: :development
   prerelease: false
-  version_requirements: *2152773740
+  version_requirements: *2162403240
 - !ruby/object:Gem::Dependency
   name: bio-blastxmlparser
-  requirement: &2152773180 !ruby/object:Gem::Requirement
+  requirement: &2162401800 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -319,10 +319,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2152773180
+  version_requirements: *2162401800
 - !ruby/object:Gem::Dependency
   name: progressbar
-  requirement: &2152772640 !ruby/object:Gem::Requirement
+  requirement: &2162399920 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -330,10 +330,10 @@ dependencies:
         version: 0.9.0
   type: :development
   prerelease: false
-  version_requirements: *2152772640
+  version_requirements: *2162399920
 - !ruby/object:Gem::Dependency
   name: json
-  requirement: &2152772040 !ruby/object:Gem::Requirement
+  requirement: &2162413940 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -341,10 +341,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2152772040
+  version_requirements: *2162413940
 - !ruby/object:Gem::Dependency
   name: rake
-  requirement: &2152770800 !ruby/object:Gem::Requirement
+  requirement: &2162412560 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - =
@@ -352,10 +352,10 @@ dependencies:
         version: 0.9.2.2
   type: :development
   prerelease: false
-  version_requirements: *2152770800
+  version_requirements: *2162412560
 - !ruby/object:Gem::Dependency
   name: parallel
-  requirement: &2152769720 !ruby/object:Gem::Requirement
+  requirement: &2162411560 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -363,7 +363,7 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2152769720
+  version_requirements: *2162411560
 description: bio-ngs provides a framework for handling NGS data with BioRuby
 email: francesco.strozzi@gmail.com
 executables:
@@ -386,6 +386,7 @@ files:
 - ext/mkrf_conf.rb
 - features/cufflinks_gtf_parser.feature
 - features/cufflinks_gtf_parser_indexing.feature
+- features/illumina_project_rebuild.feature
 - features/step_definitions/cufflinks_gtf.rb
 - features/step_definitions/cufflinks_gtf_parser_indexing.rb
 - features/support/env.rb
@@ -470,7 +471,62 @@ files:
 - spec/spec_helper.rb
 - spec/tophat_spec.rb
 - spec/utils_spec.rb
+- test/conf/projects.yaml
 - test/conf/test_db.yml
+- test/data/Project_Cow/Sample_SQ_0007/SQ_0007_CGATGT_L003_R1_001.fastq.gz
+- test/data/Project_Cow/Sample_SQ_0007/SQ_0007_CGATGT_L003_R1_002.fastq.gz
+- test/data/Project_Cow/Sample_SQ_0007/SQ_0007_CGATGT_L003_R2_001.fastq.gz
+- test/data/Project_Cow/Sample_SQ_0007/SQ_0007_CGATGT_L003_R2_002.fastq.gz
+- test/data/Project_Cow/Sample_SQ_0007/filtered/SQ_0007_CGATGT_L003_R1_001.fastq.gz
+- test/data/Project_Cow/Sample_SQ_0007/filtered/SQ_0007_CGATGT_L003_R1_002.fastq.gz
+- test/data/Project_Cow/Sample_SQ_0007/filtered/SQ_0007_CGATGT_L003_R2_001.fastq.gz
+- test/data/Project_Cow/Sample_SQ_0007/filtered/SQ_0007_CGATGT_L003_R2_002.fastq.gz
+- test/data/Project_Cow/Sample_SQ_0007/trimmed/SQ_0007_CGATGT_L003_R1_TRIMMED.fastq.gz
+- test/data/Project_Cow/Sample_SQ_0007/trimmed/SQ_0007_CGATGT_L003_R2_TRIMMED.fastq.gz
+- test/data/Project_Cow/Sample_SQ_0008/SQ_0008_CGATGT_L003_R1_001.fastq.gz
+- test/data/Project_Cow/Sample_SQ_0008/SQ_0008_CGATGT_L003_R1_002.fastq.gz
+- test/data/Project_Cow/Sample_SQ_0008/SQ_0008_CGATGT_L003_R2_001.fastq.gz
+- test/data/Project_Cow/Sample_SQ_0008/SQ_0008_CGATGT_L003_R2_002.fastq.gz
+- test/data/Project_Cow/Sample_SQ_0009/SQ_0009_CGATGT_L003_R1_001.fastq.gz
+- test/data/Project_Cow/Sample_SQ_0009/SQ_0009_CGATGT_L003_R1_002.fastq.gz
+- test/data/Project_Cow/Sample_SQ_0009/SQ_0009_CGATGT_L003_R2_001.fastq.gz
+- test/data/Project_Cow/Sample_SQ_0009/SQ_0009_CGATGT_L003_R2_002.fastq.gz
+- test/data/Project_Dog/Sample_SQ_0004/SQ_0004_CGATGT_L003_R1_001.fastq.gz
+- test/data/Project_Dog/Sample_SQ_0004/SQ_0004_CGATGT_L003_R1_002.fastq.gz
+- test/data/Project_Dog/Sample_SQ_0004/SQ_0004_CGATGT_L003_R2_001.fastq.gz
+- test/data/Project_Dog/Sample_SQ_0004/SQ_0004_CGATGT_L003_R2_002.fastq.gz
+- test/data/Project_Dog/Sample_SQ_0005/SQ_0005_CGATGT_L003_R1_001.fastq.gz
+- test/data/Project_Dog/Sample_SQ_0005/SQ_0005_CGATGT_L003_R1_002.fastq.gz
+- test/data/Project_Dog/Sample_SQ_0005/SQ_0005_CGATGT_L003_R2_001.fastq.gz
+- test/data/Project_Dog/Sample_SQ_0005/SQ_0005_CGATGT_L003_R2_002.fastq.gz
+- test/data/Project_Dog/Sample_SQ_0006/SQ_0006_CGATGT_L003_R1_001.fastq.gz
+- test/data/Project_Dog/Sample_SQ_0006/SQ_0006_CGATGT_L003_R1_002.fastq.gz
+- test/data/Project_Dog/Sample_SQ_0006/SQ_0006_CGATGT_L003_R2_001.fastq.gz
+- test/data/Project_Dog/Sample_SQ_0006/SQ_0006_CGATGT_L003_R2_002.fastq.gz
+- test/data/Project_Human/Sample_SQ_0001/SQ_0001_CGATGT_L003_R1_001.fastq.gz
+- test/data/Project_Human/Sample_SQ_0001/SQ_0001_CGATGT_L003_R1_002.fastq.gz
+- test/data/Project_Human/Sample_SQ_0001/SQ_0001_CGATGT_L003_R2_001.fastq.gz
+- test/data/Project_Human/Sample_SQ_0001/SQ_0001_CGATGT_L003_R2_002.fastq.gz
+- test/data/Project_Human/Sample_SQ_0002/SQ_0002_CGATGT_L003_R1_001.fastq.gz
+- test/data/Project_Human/Sample_SQ_0002/SQ_0002_CGATGT_L003_R1_002.fastq.gz
+- test/data/Project_Human/Sample_SQ_0002/SQ_0002_CGATGT_L003_R2_001.fastq.gz
+- test/data/Project_Human/Sample_SQ_0002/SQ_0002_CGATGT_L003_R2_002.fastq.gz
+- test/data/Project_Human/Sample_SQ_0003/SQ_0003_CGATGT_L003_R1_001.fastq.gz
+- test/data/Project_Human/Sample_SQ_0003/SQ_0003_CGATGT_L003_R1_002.fastq.gz
+- test/data/Project_Human/Sample_SQ_0003/SQ_0003_CGATGT_L003_R2_001.fastq.gz
+- test/data/Project_Human/Sample_SQ_0003/SQ_0003_CGATGT_L003_R2_002.fastq.gz
+- test/data/RemoteDir/Project_Human/Sample_SQ_0001/SQ_0001_CGATGT_L010_R1_001.fastq.gz
+- test/data/RemoteDir/Project_Human/Sample_SQ_0001/SQ_0001_CGATGT_L010_R1_002.fastq.gz
+- test/data/RemoteDir/Project_Human/Sample_SQ_0001/SQ_0001_CGATGT_L010_R2_001.fastq.gz
+- test/data/RemoteDir/Project_Human/Sample_SQ_0001/SQ_0001_CGATGT_L010_R2_002.fastq.gz
+- test/data/RemoteDir/Project_Human/Sample_SQ_0002/SQ_0002_CGATGT_L003_R1_001.fastq.gz
+- test/data/RemoteDir/Project_Human/Sample_SQ_0002/SQ_0002_CGATGT_L003_R1_002.fastq.gz
+- test/data/RemoteDir/Project_Human/Sample_SQ_0002/SQ_0002_CGATGT_L003_R2_001.fastq.gz
+- test/data/RemoteDir/Project_Human/Sample_SQ_0002/SQ_0002_CGATGT_L003_R2_002.fastq.gz
+- test/data/RemoteDir/Project_Human/Sample_SQ_0003/SQ_0003_CGATGT_L003_R1_001.fastq.gz
+- test/data/RemoteDir/Project_Human/Sample_SQ_0003/SQ_0003_CGATGT_L003_R1_002.fastq.gz
+- test/data/RemoteDir/Project_Human/Sample_SQ_0003/SQ_0003_CGATGT_L003_R2_001.fastq.gz
+- test/data/RemoteDir/Project_Human/Sample_SQ_0003/SQ_0003_CGATGT_L003_R2_002.fastq.gz
 - test/data/blastoutput.xml
 - test/data/gene-GO.json
 - test/data/goa_uniprot
@@ -497,7 +553,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: -2512494530563499590
+      hash: -803718584135061941
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements: