bio-ngs 0.4.6.alpha.01 → 0.4.6.alpha.02

data/lib/tasks/rna.thor

@@ -25,6 +25,13 @@ class Rna < Thor
     wrapper.run :arguments=>[bam], :separator => "="
   end
 
+  desc "quantdenovo GTF_guide OUTPUTDIR BAM ", "Genes and transcripts quantification discovering de novo transcripts"
+  Bio::Ngs::Cufflinks::QuantificationDenovo.new.thor_task(self, :quantdenovo) do |wrapper, task, gtf_guide, outputdir, bam|
+    wrapper.params = task.options
+    wrapper.params = {"num-threads" => 6, "output-dir" => outputdir, "GTF-guide" => gtf_guide }
+    wrapper.run :arguments=>[bam], :separator => "="
+  end
+
   #GTFS_QUANTIFICATION is a comma separated list of gtf file names
   desc "compare GTF_REF OUTPUTDIR GTFS_QUANTIFICATION", "GTFS_QUANTIFICATIONS, use a comma separated list of gtf"
   Bio::Ngs::Cufflinks::Compare.new.thor_task(self, :compare) do |wrapper, task, gtf_ref, outputdir, gtfs_quantification|
@@ -42,6 +49,25 @@ class Rna < Thor
     wrapper.run :arguments=>[gtfs_quantification.split(',')]
     # Dir.chdir("../")
   end
+
+
+  desc "merge GTF_REF FASTA_REF ASSEMBLY_GTF_LIST", "GTFS_QUANTIFICATIONS, use a comma separated list of gtf"
+  Bio::Ngs::Cufflinks::Merge.new.thor_task(self, :merge) do |wrapper, task, gtf_ref, fasta_ref, assembly_gtf_list|
+    # unless Dir.exists?(outputdir)
+    #   Dir.mkdir(outputdir)
+    # end
+    # Dir.chdir(outputdir)
+    # #I assume GTS_QUANTIFICATION is a comma separated list of single gtf files
+    # gtf_tracking_filename = "#{outputdir}.gtf_tracking"
+    # File.open(gtf_tracking_filename, 'w') do |file|
+    #   file.puts gtfs_quantification.gsub(/,/,"\n")
+    # end #file
+    wrapper.params = task.options
+    wrapper.params = {"ref-gtf"=>gtf_ref, "ref-sequence"=>fasta_ref}
+    wrapper.run :arguments=>[assembly_gtf_list], :separator => "="
+    # Dir.chdir("../")
+  end
+
   
   desc "mapquant DIST INDEX OUTPUTDIR FASTQS", "map and quantify"
   method_option :paired, :type => :boolean, :default => false, :desc => 'Are reads paired? If you chose

data/lib/wrapper.rb

@@ -43,6 +43,15 @@ module Bio
         @options = options
         @params = {}
         @pipe_ahead = []
+        @path = options.delete(:path) || "."
+      end
+
+      def path
+        @path
+      end
+
+      def path=(path)
+        @path=path
       end
 
       # Parameters are accepted ONLY if the key is present as
@@ -215,6 +224,15 @@ module Bio
       end
 
       module ClassMethods
+
+        # Propagate class variable in the superclass to the inherited class,
+        # so options defined in a previous wrap can be recicled.
+        def inherited(subclass)
+          self.instance_variables.each do |var|
+            subclass.instance_variable_set(var, self.instance_variable_get(var))
+          end
+        end
+
         #TODO: do I need to set a default program name using class name or not ?
         #       or do we need to specify somewhere a defaitl path and looking for a real binary ?
 
@@ -242,6 +260,16 @@ module Bio
           @options = (@options || {}).merge(name.to_s=>opt)
         end
 
+        # Remove an option from the class
+        def delete_option(name)
+          @options.delete(name)
+        end
+
+        # An alias reuse the properties of a specific method and giving them another name
+        # def add_alias(source, dest)
+        #   @options = (@options || {}).merge(name.to_s=>@options[dest.to_s]) unless @options[dest]
+        # end
+
         alias set_program program=
         alias set_sub_program sub_program=
 

data/spec/bio/ngs/fs_spec.rb

@@ -0,0 +1,70 @@
+@TestDirectory = File.expand_path(File.join(File.dirname(__FILE__) + '/../../'))
+
+require File.expand_path(File.join(@TestDirectory, 'spec_helper'))
+
+describe "File System utilities for BioNGS" do 
+
+ before(:each) do
+    @data_dir = File.join(File.expand_path(File.join(File.dirname(__FILE__) + '/../../')), 'fixture')
+  end
+
+
+describe Bio::Ngs::FS, ".cat" do
+  it "concatenates the content of multiple files in just one file" do
+  	fn_one=File.join(@data_dir, 'test.fastq.gz')
+  	fn_two=File.join(@data_dir, 'test-filtered-reference.fastq.gz')
+  	fn_merged=File.join(@data_dir, 'test-merged.fastq.gz')
+  	fn_merged_reference=File.join(@data_dir, 'test-merged-reference.fastq.gz')
+    Bio::Ngs::FS.cat([fn_one, fn_two], fn_merged)
+
+    fmerged_reference=File.open(fn_merged_reference,"rb:binary").read
+    fmerged=File.open(fn_merged, "rb:binary").read
+    fmerged.to_s.should == fmerged_reference.to_s
+  end
+end
+
+
+describe Bio::Ngs::FS, ".files" do
+  context "when input is a string" do
+    context "representing an existing file" do
+        it "gives back an array with the file name" do
+          Bio::Ngs::FS.files(File.join(@data_dir, "test-filtered-reference.fastq.gz")).should =~ [File.join(@data_dir, "test-filtered-reference.fastq.gz")]
+        end
+    end    
+    context "representing a non existing file" do
+        it "gives back nil" do
+          Bio::Ngs::FS.files(File.join(@data_dir, "fake.file")).should be_nil
+        end
+    end    
+    context "representing a regular expression and there is not subdirectory in the path" do
+        it "gives back an array of file names" do
+          Bio::Ngs::FS.files(File.join(@data_dir, "*reference*")).should =~ [File.join(@data_dir, "test-filtered-reference.fastq.gz"), File.join(@data_dir, "test-merged-reference.fastq.gz")]
+        end
+    end    
+    context "representing a regular expression and there are subdirectories in the path" do
+        it "gives back an array of file names without single subdirectories names" do
+          Bio::Ngs::FS.files(File.join(@data_dir,"../", "*spec*")).should =~ %w(converter_qseq_spec.rb cufflinks_spec.rb 
+                                                                                quality_spec.rb sff_extract_spec.rb spec_helper.rb 
+                                                                                tophat_spec.rb utils_spec.rb).map{|item| File.expand_path(File.join(@data_dir,"../", item))  }
+        end
+    end    
+    context "representing a regular expression and there are subdirectories in the path to be traversed" do
+        it "gives back an array of file names without single subdirectories names" do
+          Bio::Ngs::FS.files(File.join(@data_dir,"../", "**/*.fastq")).should =~ %w(s_1_1_1108_qseq.fastq test.fastq).map{|item| File.expand_path(File.join(@data_dir, item))}
+        end
+    end    
+    context "representing the local directory lib" do
+        it "gives back an array of file names in it" do
+          Bio::Ngs::FS.files("lib").should =~ %w(bio-ngs.rb development_tasks.rb enumerable.rb wrapper.rb).map{|item| File.expand_path(File.join(@data_dir,"../../lib/", item))}
+        end
+    end
+    context "representing the local directory lib with a specific suffix" do
+        it "gives back an array of file names in lib with suffix spec.rb" do
+          Bio::Ngs::FS.files("spec/fixture", ".fastq").should =~ %w(test.fastq s_1_1_1108_qseq.fastq).map{|item| File.expand_path(File.join(@data_dir, item))}
+        end
+    end    
+  end 
+end #.files
+
+
+end #File System utilities for BioNGS

data/spec/bio/ngs/illumina/fastq_spec.rb

@@ -0,0 +1,52 @@
+# fastq_spec.rb
+#require 'bio/ngs/illumina/fastq'
+@TestDirectory = File.expand_path(File.join(File.dirname(__FILE__) + '/../../../'))
+
+require File.expand_path(File.join(@TestDirectory, 'spec_helper'))
+
+
+describe "Illumina Fastq compressed with Gzip" do 
+
+ before(:each) do
+    @data_dir = File.join(File.expand_path(File.join(File.dirname(__FILE__) + '/../../../')), 'fixture')
+  end
+
+
+describe Bio::Ngs::Illumina::FastqGz, "::gets_uncompressed" do
+  it "returns reads from Illumina fastq compressed archive" do
+  	ftest=File.join(@data_dir, 'test.fastq.gz')
+    n_reads = Bio::Ngs::Illumina::FastqGz.gets_uncompressed(ftest) do |read_header, reader_seq, read_splitter, read_qual|
+      read_header
+    end
+     n_reads.should be 10
+  end
+end
+
+describe Bio::Ngs::Illumina::FastqGz, "::gets_filtered" do
+  it "returns the filterd reads from Illumina" do
+  	reads_header = ""
+  	ftest=File.join(@data_dir, 'test.fastq.gz')
+    n_reads = Bio::Ngs::Illumina::FastqGz.gets_filtered(ftest) do |read_header, reader_seq, read_splitter, read_qual|
+      reads_header+=read_header
+    end
+    reads_header.should eq "@H125:125:D0C0DACXX:5:1307:20682:66201 1:N:0:ATCACG\n@H125:125:D0C0DACXX:5:1307:20749:66215 1:N:0:ATCACG\n@H125:125:D0C0DACXX:5:1307:20707:66224 1:N:0:ATCACG\n@H125:125:D0C0DACXX:5:1307:20846:66039 1:N:0:ATCACG\n@H125:125:D0C0DACXX:5:1307:20878:66172 1:N:0:ATCACG\n@H125:125:D0C0DACXX:5:1307:20854:66177 1:N:0:ATCACG\n@H125:125:D0C0DACXX:5:1307:20830:66194 1:N:0:ATCACG\n@H125:125:D0C0DACXX:5:1307:20773:66233 1:N:0:ATCACG\n@H125:125:D0C0DACXX:5:1307:21088:66002 1:N:0:ATCACG\n"
+    n_reads.should be 9
+  end
+end
+
+describe Bio::Ngs::Illumina::FastqGz, "::gets_compressed" do
+  it "returns compressed reads by Gzip" do
+  	reads=[]
+  	ftest=File.join(@data_dir, 'test.fastq.gz')
+  	ftest_filtered=File.join(@data_dir, 'test-filtered.fastq.gz')
+    Bio::Ngs::Illumina::FastqGz.gets_compressed(ftest_filtered) do |compress|
+    	Bio::Ngs::Illumina::FastqGz.gets_filtered(ftest) do |read_header, reader_seq, read_splitter, read_qual|
+          compress.write(read_header + reader_seq + read_splitter + read_qual)
+    	end
+    end #compress
+    #TODO: test
+  end
+end
+
+
+end #"Illumina Fastq compressed with Gzip"

data/spec/bio/ngs/illumina/illumina_spec.rb

@@ -0,0 +1,21 @@
+# illumina_spec.rb
+@TestDirectory = File.expand_path(File.join(File.dirname(__FILE__) + '/../../../'))
+
+require File.expand_path(File.join(@TestDirectory, 'spec_helper'))
+
+
+describe "Illumina" do 
+
+ before(:each) do
+    @data_dir = File.join(File.expand_path(File.join(File.dirname(__FILE__) + '/../../../../')), 'test', 'data')
+  end
+
+
+describe Bio::Ngs::Illumina, ".build" do
+  it "returns an array of projects" do
+  	projects = Bio::Ngs::Illumina.build(@data_dir)
+    projects.should be nil
+  end
+end
+
+end #"Illumina Fastq compressed with Gzip"

data/spec/filter_spec.rb

@@ -0,0 +1,25 @@
+require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
+require 'thor/base'
+
+describe Filter do 
+  describe "#by_list" do
+  	it 'finds rows with first column equal to TCONS_00000005 or TCONS_00000010' do
+      table = File.expand_path(File.dirname(__FILE__) + '/fixture/table_filter_source.tsv')
+      list = File.expand_path(File.dirname(__FILE__) + '/fixture/table_filter_list_first_column.txt')
+      filter = Filter.new
+
+      data = capture(:stdout){filter.invoke(:by_list, [table, list], :skip_table_header => true, :skip_list_header => false, :zero_index_system=>true)}
+      data.should == "TCONS_00000005  =       uc001aaq.1      XLOC_000003     QUERTY,JIM       -       chr1:321083-321114      31      -       0       0       0       OK      0       0       0       OK      0       0       0       OK\nTCONS_00000010  =       uc010nxu.1      XLOC_000006     OR4F16  -       chr1:367658-368595      937     -       0       0       0       OK      0       0       0       OK      9.00455 0       27.0137 OK\n"
+  	end
+
+  	it 'finds rows with 5th column equal to JIM or WATSON or SAMD11' do
+      table = File.expand_path(File.dirname(__FILE__) + '/fixture/table_filter_source.tsv')
+      list = File.expand_path(File.dirname(__FILE__) + '/fixture/table_filter_list.txt')
+      filter = Filter.new
+
+      data = capture(:stdout){filter.invoke(:by_list, [table, list], :skip_table_header => true, :skip_list_header => false, :zero_index_system=>true, :tablekey=>4, :in_column_delimiter=>',')}
+      data.should == "TCONS_00000005  =       uc001aaq.1      XLOC_000003     QUERTY,JIM       -       chr1:321083-321114      31      -       0       0       0       OK      0       0       0       OK      0       0       0       OK\nTCONS_00000014  =       uc001abb.2      XLOC_000010     CRICK,WATSON       -       chr1:568843-568912      69      -       0       0       0       OK      0       0       0       OK      0       0       0       OK\nTCONS_00000023  =       uc001abv.1      XLOC_000015     SAMD11  TSS7    chr1:860529-894679      490     -       1.40488 0       10.5489 OK      3.5127  0       12.9469 OK      372.514 0       4986.76 OK\nTCONS_00000024  =       uc001abw.1      XLOC_000015     SAMD11  TSS8    chr1:860529-894679      2554    -       2.92757 0.0526766       5.80247 OK      2.54641 0       5.1809  OK      64.8329 0       645.748 OK\nTCONS_00000025  =       uc001abx.1      XLOC_000015     SAMD11  TSS9    chr1:860529-894679      2121    -       7.77732 2.80074 12.7539 OK      45.2404 11.7902 78.6907 OK      176.15  0       750.086 OK\n"
+  	end
+
+  end
+end

data/spec/fixture/table_filter_list.txt

@@ -0,0 +1,3 @@
+JIM
+WATSON
+SAMD11

data/spec/fixture/table_filter_list_first_column.txt

@@ -0,0 +1,2 @@
+TCONS_00000005
+TCONS_00000010

data/spec/fixture/table_filter_source.tsv

@@ -0,0 +1,44 @@
+tracking_id     class_code      nearest_ref_id  gene_id gene_short_name tss_id  locus   length  coverage        hESC_FPKM       hESC_conf_lo    hESC_conf_hi    hESC_status     Fibroblasts_FPKM        Fibroblasts_conf_lo     Fib
+roblasts_conf_hi     Fibroblasts_status      iPS_FPKM        iPS_conf_lo     iPS_conf_hi     iPS_status
+TCONS_00000001  =       uc001aaa.3      XLOC_000001     -       TSS1    chr1:11873-29961        1652    -       0       0       0       OK      11.9107 3.85498 19.9665 OK      9.5637  0       23.6841 LOWDATA
+TCONS_00000002  =       uc010nxq.1      XLOC_000001     -       TSS1    chr1:11873-29961        1488    -       0.723836        0       3.01108 OK      0       0       8.55378 OK      32.9344 17.9313 47.9376 OK
+TCONS_00000003  =       uc010nxr.1      XLOC_000001     -       TSS1    chr1:11873-29961        1595    -       0       0       0       OK      4.49036 0       12.71   LOWDATA 11.5691 0       25.9784 LOWDATA
+TCONS_00000004  =       uc001aal.1      XLOC_000002     OR4F5   -       chr1:69090-70008        918     -       0       0       0       OK      0       0       0       OK      0       0       0       OK
+TCONS_00000005  =       uc001aaq.1      XLOC_000003     QUERTY,JIM       -       chr1:321083-321114      31      -       0       0       0       OK      0       0       0       OK      0       0       0       OK
+TCONS_00000006  =       uc001aar.1      XLOC_000004     -       -       chr1:321145-321223      78      -       1.2e+06 162569  2.23743e+06     OK      22616.4 0       158315  OK      0       0       0       OK
+TCONS_00000007  =       uc009vjk.2      XLOC_000005     -       TSS2    chr1:322036-328580      2750    -       595.704 503.466 687.941 OK      26.4917 1.43941 51.544  OK      511.421 215.823 807.019 OK
+TCONS_00000008  =       uc001aau.2      XLOC_000005     -       TSS3    chr1:322036-328580      4369    -       543.316 466.279 620.352 OK      3.44334 0       9.11684 OK      160.528 1.55069 319.506 OK
+TCONS_00000009  =       uc001aav.3      XLOC_000005     -       TSS3    chr1:322036-328580      4272    -       0.0145297       0       0.759868        OK      11.2294 0.0930141       22.3658 OK      272.359 82.1678 462.551 OK
+TCONS_00000010  =       uc010nxu.1      XLOC_000006     OR4F16  -       chr1:367658-368595      937     -       0       0       0       OK      0       0       0       OK      9.00455 0       27.0137 OK
+TCONS_00000011  =       uc001aax.1      XLOC_000007     -       TSS4    chr1:420205-421839      802     -       0       0       0       OK      0       0       0       OK      0       0       0       OK
+TCONS_00000012  =       uc001aaz.2      XLOC_000008     -       -       chr1:566461-568045      1584    -       0       0       0       OK      0       0       0       OK      0       0       0       OK
+TCONS_00000013  =       uc001aba.1      XLOC_000009     -       -       chr1:568148-568842      694     -       0       0       0       OK      0       0       0       OK      0       0       0       OK
+TCONS_00000014  =       uc001abb.2      XLOC_000010     CRICK,WATSON       -       chr1:568843-568912      69      -       0       0       0       OK      0       0       0       OK      0       0       0       OK
+TCONS_00000015  =       uc001abc.2      XLOC_000011     -       -       chr1:569326-570349      1023    -       0       0       0       OK      0       0       0       OK      0       0       0       OK
+TCONS_00000016  =       uc009vjn.1      XLOC_000012     -       TSS5    chr1:763063-789740      510     -       0       0       0       OK      34.9207 0       96.2612 OK      17.4388 0       77.2131 OK
+TCONS_00000017  =       uc001abp.1      XLOC_000012     -       TSS5    chr1:763063-789740      854     -       0       0       0       OK      0       0       42.2696 OK      0       0       0       OK
+TCONS_00000018  =       uc001abq.1      XLOC_000012     -       TSS5    chr1:763063-789740      701     -       133.009 85.2827 180.735 OK      13.2916 0       61.5645 LOWDATA 0       0       0       OK
+TCONS_00000019  =       uc009vjo.1      XLOC_000012     -       TSS5    chr1:763063-789740      517     -       0       0       0       OK      36.6304 0       97.0895 OK      114.161 0       230.929 OK
+TCONS_00000020  =       uc001abr.1      XLOC_000012     -       TSS5    chr1:763063-789740      1543    -       163.639 123.583 203.694 OK      196.063 166.543 225.583 OK      206.249 62.4043 350.094 OK
+TCONS_00000021  =       uc001abs.2      XLOC_000013     -       -       chr1:791897-794579      2682    -       46.0811 34.122  58.0403 OK      70.4959 22.1574 118.834 OK      21.8276 2.67005 40.9851 OK
+TCONS_00000022  =       uc001abu.1      XLOC_000014     -       TSS6    chr1:846814-850328      3043    -       45.1192 33.5358 56.7025 OK      0.515295        0       1.48694 OK      21.3767 3.02453 39.7289 OK
+TCONS_00000023  =       uc001abv.1      XLOC_000015     SAMD11  TSS7    chr1:860529-894679      490     -       1.40488 0       10.5489 OK      3.5127  0       12.9469 OK      372.514 0       4986.76 OK
+TCONS_00000024  =       uc001abw.1      XLOC_000015     SAMD11  TSS8    chr1:860529-894679      2554    -       2.92757 0.0526766       5.80247 OK      2.54641 0       5.1809  OK      64.8329 0       645.748 OK
+TCONS_00000025  =       uc001abx.1      XLOC_000015     SAMD11  TSS9    chr1:860529-894679      2121    -       7.77732 2.80074 12.7539 OK      45.2404 11.7902 78.6907 OK      176.15  0       750.086 OK
+TCONS_00000026  =       uc001aca.1      XLOC_000016     KLHL17  TSS10   chr1:895966-901095      2560    -       298.022 237.764 358.279 OK      122.511 40.1187 204.904 OK      168.624 44.5393 292.709 OK
+TCONS_00000027  =       uc001acb.1      XLOC_000016     KLHL17  TSS11   chr1:895966-901095      955     -       278.216 184.728 371.703 OK      52.7344 0       302.971 OK      150.602 0       392.283 OK
+TCONS_00000028  =       uc001acc.1      XLOC_000016     KLHL17  TSS12   chr1:895966-901095      2003    -       353.647 280.621 426.674 OK      87.9438 20.0799 155.808 OK      70.8841 0       183.538 OK
+TCONS_00000029  =       uc010nyb.1      XLOC_000016     KLHL17  TSS13   chr1:895966-901095      1149    -       301.147 217.831 384.464 OK      54.9418 0       239.78  OK      81.363  0       282.265 OK
+TCONS_00000030  =       uc001acd.2      XLOC_000017     PLEKHN1 TSS14   chr1:901876-910482      2398    -       20.9859 6.94352 35.0283 OK      4.71542 0       22.2944 OK      15.2268 1.51879 28.9348 OK
+TCONS_00000031  =       uc001ace.2      XLOC_000017     PLEKHN1 TSS14   chr1:901876-910482      2554    -       16.0979 3.29643 28.8994 OK      29.6547 2.71604 56.5934 OK      0.000219517     0       5.22308 OK
+TCONS_00000032  =       uc001acf.2      XLOC_000017     PLEKHN1 TSS14   chr1:901876-910482      2293    -       0       0       0       OK      16.1706 0       35.9766 OK      0       0       0       OK
+TCONS_00000033  =       uc001acj.3      XLOC_000018     ISG15   TSS15   chr1:948846-949915      662     -       1610.23 1305.56 1914.9  OK      3203.25 1608.81 4797.68 OK      1484.47 595.792 2373.14 OK
+TCONS_00000034  =       uc001ack.1      XLOC_000019     AGRN    TSS16   chr1:955502-991492      7319    -       3024.77 1584.21 4465.34 OK      2468.9  1169.65 3768.16 OK      422.846 233.227 612.465 OK
+TCONS_00000035  =       uc009vjs.1      XLOC_000020     -       TSS17   chr1:995082-1001833     673     -       1.54186 0       7.69648 OK      2.84929 0       8.58809 OK      6.59269 0       33.843  OK
+TCONS_00000036  =       uc001acl.1      XLOC_000020     -       TSS17   chr1:995082-1001833     971     -       49.4519 29.6823 69.2214 OK      46.8237 5.06013 88.5873 OK      53.6594 10.0201 97.2987 OK
+TCONS_00000037  =       uc001acv.2      XLOC_000021     -       TSS18   chr1:1072396-1079432    1616    -       2.67097 0       6.3719  OK      0       0       0       OK      0       0       0       OK
+TCONS_00000038  =       uc001acw.2      XLOC_000022     -       -       chr1:1102483-1102578    95      -       0       0       0       OK      0       0       0       OK      0       0       0       OK
+TCONS_00000039  =       uc010nye.1      XLOC_000023     -       -       chr1:1103242-1103332    90      -       0       0       0       OK      0       0       0       OK      0       0       0       OK
+TCONS_00000040  =       uc010nyf.1      XLOC_000024     -       -       chr1:1104384-1104467    83      -       0       0       0       OK      0       0       0       OK      0       0       0       OK
+TCONS_00000041  =       uc001acy.2      XLOC_000025     TTLL10  TSS19   chr1:1108435-1133313    2259    -       15.4348 7.53054 23.3391 OK      0       0       0       OK      0       0       0       OK
+TCONS_00000042  =       uc010nyg.1      XLOC_000025     TTLL10  TSS19   chr1:1108435-1133313    2278    -       0.0037386       0       1.45822 OK      0       0       0       OK      0       0       0       OK

data/spec/meta_spec.rb

@@ -0,0 +1,117 @@
+require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
+require 'thor/base'
+require 'meta'
+
+describe do
+  context Meta::Data do
+
+    mf = Meta::Data.new('filename.rb', {type:'generic', user:'duck', group:'workers'})
+
+    it 'has name' do
+      mf.name.should == 'filename.rb'
+    end #name
+
+    it 'has tags' do
+      mf.metadata.should == {type:'generic', user:'duck', group:'workers', :name => "filename.rb"}
+    end #name
+
+  end #File
+
+
+
+  describe Meta::Pool do
+    before(:each) do
+      @mf = Meta::Data.new('filename.rb', {type:'generic', user:'duck', group:'workers'})
+      @mp = Meta::Pool.new(:my_pool)
+    end
+
+    describe "instance variables" do
+    it 'has name' do
+      @mp.name.should == :my_pool
+    end
+
+    it 'has a pool' do
+      @mp.pool.should_not be nil
+    end
+  end
+
+  describe "#add" do
+    it 'adds a file to the pool' do
+      @mp.add @mf
+      @mp.pool.first[1].should == Meta::Data.new("filename.rb", {:type=>"generic", :user=>"duck", :group=>"workers"})
+    end
+  end
+
+  describe '#get_by_name' do
+    it do
+      @mp.add @mf
+      @mp.get_by_name('filename.rb').should == Meta::Data.new("filename.rb", {:type=>"generic", :user=>"duck", :group=>"workers"})
+    end
+  end
+
+  describe '#get_by_tag' do
+    it do
+      @mp.add @mf      
+      @mp.add Meta::Data.new('filename_spec.rb', {type:'spec', user:'donald', group:'workers'})
+      @mp.get(:type).pool.should ==  @mp.pool
+      #[ Meta::Data.new('filename.rb', {type:'generic', user:'duck', group:'workers'}), Meta::Data.new('filename_spec.rb', {type:'spec', user:'donald', group:'workers'})]
+    end
+  end
+
+  describe '#get_by_tag_and_value' do
+    it do
+      @mp.add @mf      
+      @mp.add Meta::Data.new('filename_spec.rb', {type:'spec', user:'donald', group:'workers'})
+      @mp.get_by_tag_and_value(:group, "workers").pool.should == @mp.pool
+      #[ Meta::Data.new('filename.rb', {type:'generic', user:'duck', group:'workers'}), Meta::Data.new('filename_spec.rb', {type:'spec', user:'donald', group:'workers'})]      
+    end
+  end
+
+
+  describe "#get" do
+    before(:each) do
+      @mp.add @mf
+    end
+    it 'looks for name' do
+      @mp.add Meta::Data.new('filename_spec.rb', {type:'spec', user:'donald', group:'workers'})
+      @mp.get('filename.rb').should == Meta::Data.new('filename.rb', {type:'generic', user:'duck', group:'workers'})
+    end
+    it 'looks for tag' do
+      @mp.add Meta::Data.new('filename_spec.rb', {type:'spec', user:'donald', group:'workers', size:10})
+      @mp.get(:size).first.should == Meta::Data.new('filename_spec.rb', {type:'spec', user:'donald', group:'workers', size:10})
+    end
+    it 'looks for value' do
+      @mp.add Meta::Data.new('filename_spec.rb', {type:'spec', user:'donald', group:'workers'})
+      @mp.get("workers").pool.should == @mp.pool
+      #[ Meta::Data.new('filename.rb', {type:'generic', user:'duck', group:'workers'}),
+      #Meta::Data.new('filename_spec.rb', {type:'spec', user:'donald', group:'workers'})]
+    end
+  end
+
+
+  describe "#get_by_value" do
+    before(:each) do
+      @mp.add @mf
+    end
+    it 'gets only one file' do
+      mft = Meta::Data.new('filename_spec.rb', {type:'spec', user:'donald', group:'workers'})
+      @mp.add mft
+      @mp.get_by_value("donald").first.should == mft
+    end
+
+    it 'gets multiple files' do
+      mft = Meta::Data.new('filename_spec.rb', {type:'spec', user:'donald', group:'workers'})
+      @mp.add mft
+      @mp.get_by_value("workers").pool.should == @mp.pool #[ Meta::Data.new('filename.rb', {type:'generic', user:'duck', group:'workers'}), Meta::Data.new('filename_spec.rb', {type:'spec', user:'donald', group:'workers'})]
+    end
+
+  end
+
+  # it 'gets a file by one of its tag name and value' do
+  #   should fail
+  #   #mp.add Meta::File.new('filename_spec.rb', {type:'spec', user:'donald', group:'workers'})
+  #   #mp.get('filename.rb').should == Meta::File.new("filename.rb", {:type=>"generic", :user=>"duck", :group=>"workers"})
+  # end
+
+end #Pool
+end  #Meta

data/spec/spec_helper.rb

@@ -25,7 +25,7 @@ ARGV.clear
 Thor::Base.shell = Thor::Shell::Basic
 
 # Load fixtures
-%w(bwa history project quality rna sff_extract).each do |task|
+%w(bwa history project quality rna sff_extract filter).each do |task|
   load File.join(File.dirname(__FILE__), "..", "lib", "tasks", "#{task}.thor" )
 end