Module: Transcript

Extended by:
Entity
Defined in:
lib/rbbt/entity/transcript.rb

Constant Summary

Constants included from Entity

Entity::UNPERSISTED_PREFIX

Class Method Summary collapse

Methods included from Entity

extended

Class Method Details

.enst2ense(organism, transcript) ⇒ Object 



38
39
40
41
42
43
44
45
46
47
 
# File 'lib/rbbt/entity/transcript.rb', line 38

def self.enst2ense(organism, transcript)
  @@enst2ense ||= {}
  @@enst2ense[organism] ||= Organism.transcript_exons(organism).tsv(:persist => true, :fields => "Ensembl Exon ID", :unnamed => true)
  res = if Array === transcript
          @@enst2ense[organism].chunked_values_at transcript
        else
          @@enst2ense[organism][transcript]
        end
  res
end

.enst2ensg(organism, transcript) ⇒ Object 



11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
 
# File 'lib/rbbt/entity/transcript.rb', line 11

def self.enst2ensg(organism, transcript)
  @@enst2ensg ||= {}
  @@enst2ensg[organism] ||= Organism.gene_transcripts(organism).tsv(:type => :single, :key_field => "Ensembl Transcript ID", :fields => ["Ensembl Gene ID"], :persist => true, :unnamed => true)
  res = if Array === transcript
          @@enst2ensg[organism].values_at *transcript
        else
          @@enst2ensg[organism][transcript]
        end

  if defined? Gene
    Gene.fast_setup(res, {:format => "Ensembl Gene ID", :organism => organism})
  end

  res
end

.enst2ensp(organism, transcript) ⇒ Object 



27
28
29
30
31
32
33
34
35
36
 
# File 'lib/rbbt/entity/transcript.rb', line 27

def self.enst2ensp(organism, transcript)
  @@enst2ensp ||= {}
  @@enst2ensp[organism] ||= Organism.transcripts(organism).tsv(:type => :single, :key_field => "Ensembl Transcript ID", :fields => ["Ensembl Protein ID"], :persist => true, :unnamed => true)
  res = if Array === transcript
          @@enst2ensp[organism].values_at *transcript
        else
          @@enst2ensp[organism][transcript]
        end
  Protein.setup(res, "Ensembl Protein ID", organism)
end