rbbt-sources 3.0.4 → 3.0.5

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 8db9d47e44f4e4ab79e5568922226aabf9f8f96c
-  data.tar.gz: 97e7b44d98556d925bc569aae4c4972dcf99cc95
+  metadata.gz: f7d726091f839fd461aaaec6e98dcdf9f5f846d5
+  data.tar.gz: d3a32cbf0b7a84d43ab4cb97d91a4c0ac1794fb1
 SHA512:
-  metadata.gz: 8fef91c63deabb55ce444ff322c09b9e63e30f505afd785e35f70feec8820978ef8512d327ad3baddf76fea180dce56197ae21556ce7ec1501df33e5171699fc
-  data.tar.gz: 5e53be06553d90ba8d4b952ff07698cc5da4d9e375744938665f5f3220938ebdb9d92a252b61716bcf4e8219876ed63f1b47a97a3c5b3c12d2659847b00cb622
+  metadata.gz: 40c7bced77cc6fccc91ad1be4cfe9110c5397aec28ed12508ea7ecf084b7f58bdebdd716a0d747fb74a2e28cb039bdf01161531e0c7477589c17d80aca2ad87c
+  data.tar.gz: d620dcf2f64f580eecfe32720d876f5f7eb420d88e25722cd98c23ccb330f8c640ead25b37ee006c7cd0d93f562b657da587e8d6d1b8bf8ce658ae10996e71c9

data/etc/allowed_biomart_archives

@@ -1,3 +1,5 @@
 may2009
 jun2011
 jan2013
+dec2013
+feb2014

data/share/install/Organism/organism_helpers.rb

@@ -78,17 +78,17 @@ $biomart_exons = [
 #{{{ Rules
 
 file 'entrez_taxids' do |t|
-  File.open(t.name, 'w') do |f| f.write $taxs * "\n" end
+  Misc.sensiblewrite(t.name, $taxs * "\n")
 end
 
 file 'scientific_name' do |t|
-  File.open(t.name, 'w') do |f| f.write $scientific_name end
+  Misc.sensiblewrite(t.name, $scientific_name)
 end
 
 file 'ortholog_key' do |t|
   raise "Ortholog key not defined. Set up $ortholog_key in the organism specific Rakefile; example $ortholog_key = 'human_ensembl_gene'" unless defined? $ortholog_key and not $ortholog_key.nil?
 
-  File.open(t.name, 'w') do |f| f.write $ortholog_key end
+  Misc.sensiblewrite(t.name, $ortholog_key)
 end
 
 file 'identifiers' do |t|
@@ -134,7 +134,7 @@ file 'identifiers' do |t|
     end
   end
 
-  File.open(t.name, 'w') do |f| f.puts identifiers end
+  Misc.sensiblewrite(t.name, identifiers.to_s)
 end
 
 file 'lexicon' => 'identifiers' do |t|
@@ -157,7 +157,7 @@ file 'protein_identifiers' do |t|
     end
   end
 
-  File.open(t.name, 'w') do |f| f.puts identifiers end
+  Misc.sensiblewrite(t.name, identifiers.to_s)
 end
 
 file 'transcript_probes' do |t|
@@ -168,32 +168,32 @@ file 'transcript_probes' do |t|
     end
   end
 
-  File.open(t.name, 'w') do |f| f.puts identifiers end
+  Misc.sensiblewrite(t.name, identifiers.to_s)
 end
 
 file 'gene_transcripts' do |t|
   transcripts = BioMart.tsv($biomart_db, $biomart_ensembl_gene, $biomart_gene_transcript, [], nil, :type => :flat, :namespace => $namespace)
 
-  File.open(t.name, 'w') do |f| f.puts transcripts end
+  Misc.sensiblewrite(t.name, transcripts.to_s)
 end
 
 file 'transcripts' => 'gene_positions' do |t|
   transcripts = BioMart.tsv($biomart_db, $biomart_ensembl_transcript, $biomart_transcript, [], nil, :type => :list, :namespace => $namespace)
   transcripts.attach TSV.open('gene_positions'), :fields => ["Chromosome Name"]
 
-  File.open(t.name, 'w') do |f| f.puts transcripts end
+  Misc.sensiblewrite(t.name, transcripts.to_s)
 end
 
 file 'gene_positions' do |t|
   sequences = BioMart.tsv($biomart_db, $biomart_ensembl_gene, $biomart_gene_positions, [])
 
-  File.open(t.name, 'w') do |f| f.puts sequences end
+  Misc.sensiblewrite(t.name, sequences.to_s)
 end
 
 file 'gene_sequence' do |t|
   sequences = BioMart.tsv($biomart_db, $biomart_ensembl_gene, $biomart_gene_sequence, [], nil, :type => :flat, :namespace => $namespace)
 
-  File.open(t.name, 'w') do |f| 
+  Misc.sensiblewrite(t.name) do |f|
     f.puts "#: :type=:single"
     f.puts "#Ensembl Gene ID\tGene Sequence"
     sequences.each do |seq, genes|
@@ -211,7 +211,7 @@ 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"]
 
-  File.open(t.name, 'w') do |f| f.puts exons end
+  Misc.sensiblewrite(t.name, exons.to_s)
 end
 
 file 'transcript_exons' do |t|
@@ -372,7 +372,7 @@ file 'gene_go' do |t|
   else
     goterms = BioMart.tsv($biomart_db, $biomart_ensembl_gene, $biomart_go, [], nil, :type => :double, :namespace => $namespace)
 
-    File.open(t.name, 'w') do |f| f.puts goterms end
+    Misc.sensiblewrite(t.name, goterms.to_s)
   end
 end
 
@@ -388,7 +388,7 @@ file 'gene_go_bp' => 'gene_go' do |t|
   end
 
 
-  File.open(t.name, 'w') do |f| f.puts gene_go.slice "GO ID" end
+  Misc.sensiblewrite(t.name, gene_go.slice("GO ID").to_s)
 end
 
 file 'gene_go_cc' => 'gene_go' do |t|
@@ -403,7 +403,7 @@ file 'gene_go_cc' => 'gene_go' do |t|
   end
 
 
-  File.open(t.name, 'w') do |f| f.puts gene_go.slice "GO ID" end
+  Misc.sensiblewrite(t.name, gene_go.slice("GO ID").to_s)
 end
 
 file 'gene_go_mf' => 'gene_go' do |t|
@@ -418,7 +418,7 @@ file 'gene_go_mf' => 'gene_go' do |t|
   end
 
 
-  File.open(t.name, 'w') do |f| f.puts gene_go.slice "GO ID" end
+  Misc.sensiblewrite(t.name, gene_go.slice("GO ID").to_s)
 end
 
 
@@ -426,19 +426,19 @@ 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
+  Misc.sensiblewrite(t.name, biotype.to_s)
 end
 
 file 'gene_pfam' do |t|
   pfam = BioMart.tsv($biomart_db, $biomart_ensembl_gene, $biomart_pfam, [], nil, :type => :double, :namespace => $namespace)
 
-  File.open(t.name, 'w') do |f| f.puts pfam end
+  Misc.sensiblewrite(t.name, pfam.to_s)
 end
 
 file 'chromosomes' do |t|
   goterms = BioMart.tsv($biomart_db, ['Chromosome Name', "chromosome_name"] , [] , [], nil, :type => :double, :namespace => $namespace)
 
-  File.open(t.name, 'w') do |f| f.puts goterms end
+  Misc.sensiblewrite(t.name, goterms.to_s)
 end
 
 file 'blacklist_chromosomes' => 'chromosomes' do |t|
@@ -449,12 +449,12 @@ end
 file 'blacklist_genes' => ['blacklist_chromosomes', 'gene_positions'] do |t|
   Open.read(t.prerequisites.first)
   genes = CMD.cmd("grep -f '#{t.prerequisites.first}' | cut -f 1", :in => Open.open(t.prerequisites.last)).read.split("\n").uniq
-  File.open(t.name, 'w') do |f| f.puts genes * "\n" end
+  Misc.sensiblewrite(t.name, genes * "\n")
 end
 
 file 'sanctioned_genes' => ['blacklist_genes', 'gene_positions'] do |t|
   genes = CMD.cmd("cut -f 1", :in => Open.open(t.prerequisites.last)).read.split("\n").uniq - Open.read(t.prerequisites.first).split("\n")
-  File.open(t.name, 'w') do |f| f.puts genes * "\n" end
+  Misc.sensiblewrite(t.name, genes * "\n")
 end
 
 
@@ -511,7 +511,13 @@ rule /[a-z]{3}[0-9]{4}\/.*/i do |t|
   task    = $2
   Misc.in_dir(archive) do
     BioMart.set_archive archive
-    Rake::Task[task].invoke
+    begin
+      Rake::Task[task].invoke
+    rescue
+      Log.error "Error producing archived (#{archive}) version of #{task}: #{t.name}"
+      Log.exception $!
+      raise $!
+    end
     BioMart.unset_archive 
   end
 end
@@ -520,7 +526,7 @@ end
 
 
 
-#{{{ Special riles
+#{{{ Special files
 require 'bio'
 
 file 'transcript_sequence' => ["exons", "transcript_exons"] do |t|
@@ -529,7 +535,8 @@ file 'transcript_sequence' => ["exons", "transcript_exons"] do |t|
   chr_transcript_ranges ||= {}
   transcript_strand = {}
 
-  TSV.open('transcript_exons', :unnamed => true).through do |transcript, values|
+  TSV.traverse 'transcript_exons' do |transcript,values|
+  #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}
@@ -549,18 +556,18 @@ file 'transcript_sequence' => ["exons", "transcript_exons"] do |t|
     chr_transcript_ranges[chr][transcript] ||= transcript_ranges
   end
 
-  transcript_sequence = TSV.setup({}, :key_field => "Ensembl Transcript ID", :fields => ["Sequence"], :type => :single)
+  transcript_sequence = {}
   chr_transcript_ranges.each do |chr, transcript_ranges|
 
     begin
       raise "LRG, GL, HG, and HSCHR chromosomes not supported: #{chr}" if chr =~ /^(?:LRG_|GL0|HG|HSCHR)/
-      p = Organism.root
-      p.replace File.expand_path("./chromosome_#{chr}")
+      p = File.expand_path("./chromosome_#{chr}")
+      Organism.root.annotate p
       p.sub!(%r{.*/organisms/},'share/organisms/')
-      p = Path.setup(p, 'rbbt', Organism)
       chr_str = p.produce.read
     rescue Exception
       Log.debug("Chr #{ chr } failed (#{transcript_ranges.length} transcripts not covered)")
+      Log.exception $!
       next
     end
 
@@ -578,6 +585,7 @@ file 'transcript_sequence' => ["exons", "transcript_exons"] do |t|
       transcript_sequence[transcript] = sequence
     end
   end
+  TSV.setup(transcript_sequence, :key_field => "Ensembl Transcript ID", :fields => ["Sequence"], :type => :single, :unnamed => true)
 
   Misc.sensiblewrite(t.name, transcript_sequence.to_s)
 end
@@ -623,6 +631,8 @@ file 'transcript_5utr' => ["exons", "transcript_exons", "transcripts"] do |t|
     start_exon = exon2ensembl[start_exon]
     eend_exon = exon2ensembl[eend_exon]
 
+    raise "Transcript #{ transcript } missing exons" if transcript_exons[transcript].nil?
+
     exon_and_rank = Hash[*Misc.zip_fields(transcript_exons[transcript]).flatten]
 
     start_exon_rank = exon_and_rank[start_exon].to_i

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-sources
 version: !ruby/object:Gem::Version
-  version: 3.0.4
+  version: 3.0.5
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-05-27 00:00:00.000000000 Z
+date: 2014-06-09 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rbbt-util