rbbt-sources 1.2.0 → 2.0.0

data/share/install/Organism/organism_helpers.rb

@@ -1,4 +1,6 @@
 require 'net/ftp'
+require 'rbbt/sources/ensembl_ftp'
+
 
 $biomart_ensembl_gene = ['Ensembl Gene ID', 'ensembl_gene_id']
 $biomart_ensembl_protein = ['Ensembl Protein ID', 'ensembl_peptide_id']
@@ -62,6 +64,10 @@ $biomart_pfam= [
   ["Pfam Domain", 'pfam'],
 ]
 
+$biomart_gene_biotype= [
+  ["Biotype", 'gene_biotype'],
+]
+
 $biomart_exons = [
   $biomart_ensembl_gene,
   ['Exon Strand','strand'],
@@ -71,6 +77,10 @@ $biomart_exons = [
 
 #{{{ Rules
 
+file 'entrez_taxids' do |t|
+  File.open(t.name, 'w') do |f| f.write $taxs * "\n" end
+end
+
 file 'scientific_name' do |t|
   File.open(t.name, 'w') do |f| f.write $scientific_name end
 end
@@ -108,7 +118,7 @@ file 'identifiers' do |t|
     end
   end
 
-  entrez_synonyms = Rbbt.share.databases.entrez.gene_info.tsv :grep => $taxs.collect{|tax| "^#{tax}"}, :key_field => 1, :fields => 4
+  entrez_synonyms = Rbbt.share.databases.entrez.gene_info.find.tsv :grep => $taxs.collect{|tax| "^#{tax}"}, :key_field => 1, :fields => [4]
   entrez_synonyms.key_field = "Entrez Gene ID"
   entrez_synonyms.fields = ["Entrez Gene Name Synonyms"]
 
@@ -174,34 +184,6 @@ file 'transcripts' => 'gene_positions' do |t|
   File.open(t.name, 'w') do |f| f.puts transcripts end
 end
 
-file 'transcript_3utr' do |t|
-  utrs = BioMart.tsv($biomart_db, $biomart_ensembl_transcript, $biomart_transcript_3utr, [], nil, :type => :flat, :namespace => $namespace)
-
-  File.open(t.name, 'w') do |f| 
-    f.puts "#: :type=:single#cast=to_i"
-    f.puts "#Ensembl Transcript ID\t3' UTR Length"
-    utrs.each do |seq,trans|
-      trans.each do |tran|
-        f.puts [tran, seq.length] * "\t" if seq =~ /^[ACTG]+$/
-      end
-    end
-  end
-end
-
-file 'transcript_5utr' do |t|
-  utrs = BioMart.tsv($biomart_db, $biomart_ensembl_transcript, $biomart_transcript_5utr, [], nil, :type => :flat, :namespace => $namespace)
-
-  File.open(t.name, 'w') do |f| 
-    f.puts "#: :type=:single#cast=to_i"
-    f.puts "#Ensembl Transcript ID\t5' UTR Length"
-    utrs.each do |seq,trans|
-      trans.each do |tran|
-        f.puts [tran, seq.length] * "\t" if seq =~ /^[ACTG]+$/
-      end
-    end
-  end
-end
-
 file 'gene_positions' do |t|
   sequences = BioMart.tsv($biomart_db, $biomart_ensembl_gene, $biomart_gene_positions, [])
 
@@ -225,25 +207,6 @@ file 'gene_sequence' do |t|
   end
 end
 
-file 'protein_sequence' => 'chromosomes' do |t|
-  #chromosomes = TSV.open(t.prerequisites.first).keys
-  #sequences = BioMart.tsv($biomart_db, $biomart_ensembl_protein, $biomart_protein_sequence, [], nil, :type => :flat, :namespace => $namespace, :chunk_filter => ['chromosome_name', chromosomes])
-  sequences = BioMart.tsv($biomart_db, $biomart_ensembl_protein, $biomart_protein_sequence, [], nil, :type => :flat, :namespace => $namespace)
-
-  File.open(t.name, 'w') do |f| 
-    f.puts "#: :type=:single"
-    f.puts "#Ensembl Protein ID\tProtein Sequence"
-    sequences.each do |seq, genes|
-      genes.each do |gene|
-        f.write gene 
-        f.write "\t" 
-        f.write seq
-        f.write "\n"
-      end
-    end
-  end
-end
-
 file 'exons' => 'gene_positions' do |t|
   exons = BioMart.tsv($biomart_db, $biomart_ensembl_exon, $biomart_exons, [], nil, :merge => false, :type => :list, :namespace => $namespace)
   exons.attach TSV.open('gene_positions'), :fields => ["Chromosome Name"]
@@ -264,18 +227,6 @@ file 'exon_phase' do |t|
 end
 
 
-#file 'transcript_phase' do |t|
-#  tsv = TSV.setup({}, :key_field => "Ensembl Transcript ID", :fields => ["Phase"], :type => :single, :cast => :to_i)
-#
-#  transcript_cds_start = BioMart.tsv($biomart_db, $biomart_ensembl_transcript, [['CDNA Start','cds_start']], [], nil, :type => :flat, :namespace => $namespace)
-#  transcript_cds_start.through do |transcript, values|
-#    phase = values.compact.reject{|p| p.empty?}.select{|p| p == "1" or p == "2"}.first
-#    tsv[transcript] = phase.to_i unless phase.nil?
-#  end
-#
-#  File.open(t.name, 'w') do |f| f.puts tsv end
-#end
-
 file 'transcript_phase' => ['exon_phase', 'transcript_exons'] do |t|
   tsv = TSV.setup({}, :key_field => "Ensembl Transcript ID", :fields => ["phase"], :type => :single, :cast => :to_i)
 
@@ -306,28 +257,10 @@ file 'transcript_phase' => ['exon_phase', 'transcript_exons'] do |t|
 end
 
 
-file 'transcript_sequence' do |t|
-  sequences = BioMart.tsv($biomart_db, $biomart_ensembl_transcript, $biomart_transcript_sequence, [], nil, :type => :flat, :namespace => $namespace)
-
-  File.open(t.name, 'w') do |f| 
-    f.puts "#: :type=:single"
-    f.puts "#Ensembl Transcript ID\tTranscript Sequence"
-    sequences.each do |seq, genes|
-      genes.each do |gene|
-        f.write gene 
-        f.write "\t" 
-        f.write seq
-        f.write "\n"
-      end
-    end
-  end
-end
-
-
 #{{{ Variations
 
 $biomart_variation_id = ["SNP ID", "refsnp_id"]
-$biomart_variation_position = [["Chromosome Name", "chr_name"], ["Chromosome Start", "chrom_start"]]
+$biomart_variation_position = [["Chromosome Name", "chr_name"], ["Chromosome Start", "chrom_start"], ["Variant Alleles", "allele"]]
 
 file 'germline_variations' do |t|
   BioMart.tsv($biomart_db_germline_variation, $biomart_variation_id, $biomart_variation_position, [], nil, :keep_empty => true, :type => :list, :filename => t.name, :namespace => $namespace)
@@ -357,7 +290,7 @@ def coding_transcripts_for_exon(exon, exon_transcripts, transcript_info)
                   []
                 end
 
-  transcripts.select{|transcript| transcript_info[transcript].first.any?}
+  transcripts.reject{|transcript| transcript_info[transcript].first.empty?}
 end
 
 def exon_offset_in_transcript(exon, transcript, exons, transcript_exons)
@@ -420,6 +353,10 @@ file 'gene_go' do |t|
   if File.basename(FileUtils.pwd) =~ /^[a-z]{3}([0-9]{4})$/i and $1.to_i <= 2009
     goterms = BioMart.tsv($biomart_db, $biomart_ensembl_gene, $biomart_go_2009, [], nil, :type => :double, :namespace => $namespace)
 
+    goterms.each do |key, values|
+      values.each do |list| list.uniq! end
+    end
+
     goterms.add_field "GO ID" do |key, values|
       values.flatten.compact.reject{|go| go.empty?}
     end
@@ -453,11 +390,48 @@ file 'gene_go_bp' => 'gene_go' do |t|
   File.open(t.name, 'w') do |f| f.puts gene_go.slice "GO ID" end
 end
 
+file 'gene_go_cc' => 'gene_go' do |t|
+  gene_go = TSV.open(t.prerequisites.first)
+   
+  gene_go.monitor = true
+  gene_go.process "GO ID" do |key, go_id, values|
+    clean = values.zip_fields.select do |id, type|
+      type == "cellular_component"
+    end
+    clean.collect{|id, type| id}
+  end
+
+
+  File.open(t.name, 'w') do |f| f.puts gene_go.slice "GO ID" end
+end
+
+file 'gene_go_mf' => 'gene_go' do |t|
+  gene_go = TSV.open(t.prerequisites.first)
+   
+  gene_go.monitor = true
+  gene_go.process "GO ID" do |key, go_id, values|
+    clean = values.zip_fields.select do |id, type|
+      type == "molecular_function"
+    end
+    clean.collect{|id, type| id}
+  end
+
+
+  File.open(t.name, 'w') do |f| f.puts gene_go.slice "GO ID" end
+end
+
+
+
+file 'gene_biotype' do |t|
+  biotype = BioMart.tsv($biomart_db, $biomart_ensembl_gene, $biomart_gene_biotype, [], nil, :type => :single, :namespace => $namespace)
+
+  File.open(t.name, 'w') do |f| f.puts biotype end
+end
 
 file 'gene_pfam' do |t|
-  goterms = BioMart.tsv($biomart_db, $biomart_ensembl_gene, $biomart_pfam, [], nil, :type => :double, :namespace => $namespace)
+  pfam = BioMart.tsv($biomart_db, $biomart_ensembl_gene, $biomart_pfam, [], nil, :type => :double, :namespace => $namespace)
 
-  File.open(t.name, 'w') do |f| f.puts goterms end
+  File.open(t.name, 'w') do |f| f.puts pfam end
 end
 
 file 'chromosomes' do |t|
@@ -471,15 +445,7 @@ rule /^chromosome_.*/ do |t|
 
   archive = File.basename(FileUtils.pwd) =~ /^([a-z]{3}[0-9]{4})$/i ? $1 : nil
 
-  release = case archive
-            when "may2009"
-              "release-54"
-            when "jun2011"
-              "release-64"
-            when nil
-              Open.read("http://www.ensembl.org/info/data/ftp/index.html", :nocache => true).match(/pub\/(\w+-\d+)\/fasta/)[1]
-            end
-
+  release = Ensembl.releases[archive]
 
   ftp = Net::FTP.new("ftp.ensembl.org")
   ftp.login
@@ -488,13 +454,16 @@ rule /^chromosome_.*/ do |t|
   ftp.chdir('dna')
   file = ftp.nlst.select{|file| file =~ /chromosome\.#{ chr }\.fa/}.first
 
-  raise "Fasta file for chromosome not found: #{ chr } - #{ archive }, #{ release }" if file.nil?
+  raise "Fasta file for chromosome not found: '#{ chr }' - #{ archive }, #{ release }" if file.nil?
 
   Log.debug("Downloading chromosome sequence: #{ file }")
-  TmpFile.with_file do |tmpfile|
-    ftp.getbinaryfile(file, tmpfile)
-    Open.write(t.name, Open.read(tmpfile, :gzip => true).sub(/^>.*\n/,'').gsub(/\s/,''))
-    ftp.close
+
+  Misc.lock t.name + '.rake' do
+    TmpFile.with_file do |tmpfile|
+      ftp.getbinaryfile(file, tmpfile)
+      Open.write(t.name, Open.read(tmpfile, :gzip => true).sub(/^>.*\n/,'').gsub(/\s/,''))
+      ftp.close
+    end
   end
 end
 
@@ -520,3 +489,298 @@ rule /[a-z]{3}[0-9]{4}\/.*/i do |t|
     BioMart.unset_archive 
   end
 end
+
+
+
+
+
+#{{{ Special riles
+require 'bio'
+
+file 'transcript_sequence' => ["exons", "transcript_exons"] do |t|
+  exon_info = TSV.open('exons', :type => :list, :fields => ["Exon Strand", "Exon Chr Start", "Exon Chr End", "Chromosome Name"], :unnamed => true)
+
+  chr_transcript_ranges ||= {}
+  transcript_strand = {}
+
+  TSV.open('transcript_exons', :unnamed => true).through do |transcript, values|
+    transcript_ranges = []
+
+    exons = Misc.zip_fields(values).sort_by{|exon,rank| rank.to_i}.collect{|exon,rank| exon}
+
+    chr = nil
+    strand = nil
+    exons.each do |exon|
+      strand, start, eend, chr = exon_info[exon]
+      start = start.to_i
+      eend = eend.to_i
+      transcript_ranges << [start, eend]
+    end
+
+    transcript_strand[transcript] = strand
+
+    chr_transcript_ranges[chr] ||= {}
+    chr_transcript_ranges[chr][transcript] ||= transcript_ranges
+  end
+
+  transcript_sequence = TSV.setup({}, :key_field => "Ensembl Transcript ID", :fields => ["Sequence"], :type => :single)
+  chr_transcript_ranges.each do |chr, transcript_ranges|
+
+    begin
+      p = Organism.root
+      p.replace File.expand_path("./chromosome_#{chr}")
+      p.sub!(/.*\/.rbbt\//,'')
+      p = Path.setup(p, 'rbbt', Organism)
+      chr_str = p.produce.read
+    rescue Exception
+      Log.debug("Chr #{ chr } failed (#{transcript_ranges.length} transcripts not covered): #{$!.message}")
+      next
+    end
+
+    transcript_ranges.each do |transcript, ranges|
+      strand = transcript_strand[transcript]
+      ranges = ranges.reverse if strand == "-1"
+
+      sequence = ranges.inject(""){|acc, range|
+        start, eend = range
+        raise "Chromosome #{ chr } is too short (#{eend - chr_str.length } bases) for transcript #{ transcript } ([#{ start }, #{ eend }])." if chr_str.length < eend
+        acc << chr_str[start-1..eend-1]
+      }
+
+      sequence = Bio::Sequence::NA.new(sequence).complement.upcase if strand == "-1"
+      transcript_sequence[transcript] = sequence
+    end
+  end
+
+  Misc.lock t.name + '.rake' do
+    Open.write(t.name, transcript_sequence.to_s)
+  end
+end
+
+file 'transcript_5utr' => ["exons", "transcript_exons", "transcripts"] do |t|
+  path = File.expand_path(t.name)
+  dirname = File.dirname(path)
+  organism = File.basename(dirname)
+
+  if organism =~ /[a-z]{3}20[0-9]{2}/
+    build = organism
+    organism = File.basename(File.dirname(dirname))
+    organism = File.join(organism, build)
+  end
+
+  translation        = Ensembl::FTP.ensembl_tsv(organism, 'translation', 'transcript_id', %w(seq_start start_exon_id seq_end end_exon_id), :type => :list, :unmamed => true)
+
+  if Ensembl::FTP.has_table?(organism, 'exon_stable_id')
+    exon2ensembl       = Ensembl::FTP.ensembl_tsv(organism, 'exon_stable_id', 'exon_id', ['stable_id'], :type => :single, :unnamed => true) 
+  else
+    exon2ensembl       = Ensembl::FTP.ensembl_tsv(organism, 'exon', 'exon_id', ['stable_id'], :type => :single, :unnamed => true) 
+  end
+
+  if Ensembl::FTP.has_table?(organism, 'exon_stable_id')
+    transcript2ensembl = Ensembl::FTP.ensembl_tsv(organism, 'transcript_stable_id', 'transcript_id', ['stable_id'], :type => :single, :unnamed => true) 
+  else
+    transcript2ensembl = Ensembl::FTP.ensembl_tsv(organism, 'transcript', 'transcript_id', ['stable_id'], :type => :single, :unnamed => true) 
+  end
+
+  transcript_protein = TSV.open("./transcripts", :key_field => "Ensembl Transcript ID", :fields => ["Ensembl Protein ID"], :type => :single,  :unmamed => true)
+  transcript_exons   = TSV.open("./transcript_exons", :unmamed => true)
+  exon_ranges        = TSV.open("./exons",:fields => ["Exon Chr Start", "Exon Chr End"], :cast => :to_i, :unmamed => true)
+
+  transcript_utr5 = TSV.setup({}, :key_field => "Ensembl Transcript ID", :fields => ["5' UTR Length"], :cast => :to_i, :type => :single)
+  transcript_utr3 = TSV.setup({}, :key_field => "Ensembl Transcript ID", :fields => ["3' UTR Length"], :cast => :to_i, :type => :single)
+
+  translation.through do |transcript_id, values|
+    start, start_exon, eend, eend_exon = values
+
+    transcript = transcript2ensembl[transcript_id]
+    protein    = transcript_protein[transcript]
+
+    start_exon = exon2ensembl[start_exon]
+    eend_exon = exon2ensembl[eend_exon]
+
+    exon_and_rank = Hash[*Misc.zip_fields(transcript_exons[transcript]).flatten]
+
+    start_exon_rank = exon_and_rank[start_exon].to_i
+    skipped_exons = exon_and_rank.select{|exon,rank| rank.to_i < start_exon_rank}.collect{|exon,rank| exon }
+    skipped_exon_bases = skipped_exons.inject(0){|acc,exon| exon_start, exon_eend = exon_ranges[exon]; acc += exon_eend - exon_start + 1}
+
+    utr5 = skipped_exon_bases + start.to_i - 1
+    transcript_utr5[transcript] = utr5
+
+    eend_exon_rank = exon_and_rank[eend_exon].to_i
+    extra_exons = exon_and_rank.select{|exon,rank| rank.to_i >= eend_exon_rank}.collect{|exon,rank| exon }
+    extra_exon_bases = extra_exons.inject(0){|acc,exon| exon_start, exon_eend = exon_ranges[exon]; acc += exon_eend - exon_start + 1}
+
+    utr3 = extra_exon_bases - eend.to_i
+    transcript_utr3[transcript] = utr3
+  end
+
+  Misc.lock t.name + '.rake' do
+    Open.write(t.name, transcript_utr5.to_s)
+    Open.write(t.name.sub('transcript_5utr', 'transcript_3utr'), transcript_utr3.to_s)
+  end
+end
+
+file 'transcript_3utr' => ["transcript_5utr"] do |t|
+end
+
+file 'protein_sequence' => ["transcripts", "transcript_5utr", "transcript_3utr", "transcript_sequence"] do |t|
+  transcript_5utr     = TSV.open(File.expand_path('./transcript_5utr'), :unnamed => true)
+  transcript_3utr     = TSV.open(File.expand_path('./transcript_3utr'), :unnamed => true)
+  transcript_sequence = TSV.open(File.expand_path('./transcript_sequence'), :unnamed => true)
+  transcript_protein  = TSV.open(File.expand_path('./transcripts'), :fields => ["Ensembl Protein ID"], :type => :single, :unnamed => true)
+
+
+  protein_sequence = TSV.setup({}, :key_field => "Ensembl Protein ID", :fields => ["Sequence"], :type => :single)
+  transcript_sequence.through do |transcript, sequence|
+    protein = transcript_protein[transcript]
+    next if protein.nil? or protein.empty?
+    utr5 = transcript_5utr[transcript]
+    utr3 = transcript_3utr[transcript]
+    psequence = Bio::Sequence::NA.new(sequence[utr5..sequence.length-utr3-1]).translate
+    protein_sequence[protein]=psequence
+  end
+
+  Misc.lock t.name + '.rake' do
+    Open.write(t.name, protein_sequence.to_s)
+  end
+end
+
+#{{{ OLD
+
+#file 'transcript_phase' do |t|
+#  tsv = TSV.setup({}, :key_field => "Ensembl Transcript ID", :fields => ["Phase"], :type => :single, :cast => :to_i)
+#
+#  transcript_cds_start = BioMart.tsv($biomart_db, $biomart_ensembl_transcript, [['CDNA Start','cds_start']], [], nil, :type => :flat, :namespace => $namespace)
+#  transcript_cds_start.through do |transcript, values|
+#    phase = values.compact.reject{|p| p.empty?}.select{|p| p == "1" or p == "2"}.first
+#    tsv[transcript] = phase.to_i unless phase.nil?
+#  end
+#
+#  File.open(t.name, 'w') do |f| f.puts tsv end
+#end
+#
+#file 'transcript_3utr' do |t|
+#  utrs = BioMart.tsv($biomart_db, $biomart_ensembl_transcript, $biomart_transcript_3utr, [], nil, :type => :flat, :namespace => $namespace)
+#
+#  File.open(t.name, 'w') do |f| 
+#    f.puts "#: :type=:single#cast=to_i"
+#    f.puts "#Ensembl Transcript ID\t3' UTR Length"
+#    utrs.each do |seq,trans|
+#      trans.each do |tran|
+#        f.puts [tran, seq.length] * "\t" if seq =~ /^[ACTG]+$/
+#      end
+#    end
+#  end
+#end
+#
+#file 'transcript_5utr' do |t|
+#  utrs = BioMart.tsv($biomart_db, $biomart_ensembl_transcript, $biomart_transcript_5utr, [], nil, :type => :flat, :namespace => $namespace)
+#
+#  File.open(t.name, 'w') do |f| 
+#    f.puts "#: :type=:single#cast=to_i"
+#    f.puts "#Ensembl Transcript ID\t5' UTR Length"
+#    utrs.each do |seq,trans|
+#      trans.each do |tran|
+#        f.puts [tran, seq.length] * "\t" if seq =~ /^[ACTG]+$/
+#      end
+#    end
+#  end
+#end
+
+
+
+#file 'transcript_sequence' do |t|
+#  sequences = BioMart.tsv($biomart_db, $biomart_ensembl_transcript, $biomart_transcript_sequence, [], nil, :type => :flat, :namespace => $namespace)
+#
+#  File.open(t.name, 'w') do |f| 
+#    f.puts "#: :type=:single"
+#    f.puts "#Ensembl Transcript ID\tTranscript Sequence"
+#    sequences.each do |seq, genes|
+#      genes.each do |gene|
+#        f.write gene 
+#        f.write "\t" 
+#        f.write seq
+#        f.write "\n"
+#      end
+#    end
+#  end
+#end
+
+#file 'transcript_phase' do |t|
+#  tsv = TSV.setup({}, :key_field => "Ensembl Transcript ID", :fields => ["Phase"], :type => :single, :cast => :to_i)
+#
+#  transcript_cds_start = BioMart.tsv($biomart_db, $biomart_ensembl_transcript, [['CDNA Start','cds_start']], [], nil, :type => :flat, :namespace => $namespace)
+#  transcript_cds_start.through do |transcript, values|
+#    phase = values.compact.reject{|p| p.empty?}.select{|p| p == "1" or p == "2"}.first
+#    tsv[transcript] = phase.to_i unless phase.nil?
+#  end
+#
+#  File.open(t.name, 'w') do |f| f.puts tsv end
+#end
+#
+#file 'transcript_3utr' do |t|
+#  utrs = BioMart.tsv($biomart_db, $biomart_ensembl_transcript, $biomart_transcript_3utr, [], nil, :type => :flat, :namespace => $namespace)
+#
+#  File.open(t.name, 'w') do |f| 
+#    f.puts "#: :type=:single#cast=to_i"
+#    f.puts "#Ensembl Transcript ID\t3' UTR Length"
+#    utrs.each do |seq,trans|
+#      trans.each do |tran|
+#        f.puts [tran, seq.length] * "\t" if seq =~ /^[ACTG]+$/
+#      end
+#    end
+#  end
+#end
+#
+#file 'transcript_5utr' do |t|
+#  utrs = BioMart.tsv($biomart_db, $biomart_ensembl_transcript, $biomart_transcript_5utr, [], nil, :type => :flat, :namespace => $namespace)
+#
+#  File.open(t.name, 'w') do |f| 
+#    f.puts "#: :type=:single#cast=to_i"
+#    f.puts "#Ensembl Transcript ID\t5' UTR Length"
+#    utrs.each do |seq,trans|
+#      trans.each do |tran|
+#        f.puts [tran, seq.length] * "\t" if seq =~ /^[ACTG]+$/
+#      end
+#    end
+#  end
+#end
+
+#file 'transcript_sequence' do |t|
+#  sequences = BioMart.tsv($biomart_db, $biomart_ensembl_transcript, $biomart_transcript_sequence, [], nil, :type => :flat, :namespace => $namespace)
+#
+#  File.open(t.name, 'w') do |f| 
+#    f.puts "#: :type=:single"
+#    f.puts "#Ensembl Transcript ID\tTranscript Sequence"
+#    sequences.each do |seq, genes|
+#      genes.each do |gene|
+#        f.write gene 
+#        f.write "\t" 
+#        f.write seq
+#        f.write "\n"
+#      end
+#    end
+#  end
+#end
+#file 'protein_sequence' => 'chromosomes' do |t|
+#  #chromosomes = TSV.open(t.prerequisites.first).keys
+#  #sequences = BioMart.tsv($biomart_db, $biomart_ensembl_protein, $biomart_protein_sequence, [], nil, :type => :flat, :namespace => $namespace, :chunk_filter => ['chromosome_name', chromosomes])
+#  sequences = BioMart.tsv($biomart_db, $biomart_ensembl_protein, $biomart_protein_sequence, [], nil, :type => :flat, :namespace => $namespace)
+#
+#  File.open(t.name, 'w') do |f| 
+#    f.puts "#: :type=:single"
+#    f.puts "#Ensembl Protein ID\tProtein Sequence"
+#    sequences.each do |seq, genes|
+#      genes.each do |gene|
+#        f.write gene 
+#        f.write "\t" 
+#        f.write seq
+#        f.write "\n"
+#      end
+#    end
+#  end
+#end
+
+
+