rbbt-sources 3.0.18 → 3.0.19
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- checksums.yaml +4 -4
- data/lib/rbbt/sources/kegg.rb +38 -38
- metadata +2 -2
checksums.yaml
CHANGED
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@@ -1,7 +1,7 @@
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---
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SHA1:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 09103120ab258ebec5b5229f3af3b8f81b08a09d
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data.tar.gz: 859133185352820244010f79dcbff16fb74c8472
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 973ad5daac0276bf77ca2d8379415ffb8933dbee131a40795c07316b4f78af6e1776a24c4036b52248f435864264a339d7f3205516094f2d332e5e8a2032f59e
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7
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data.tar.gz: 2ff6ccd29f102f4c256a4aa84e151210e6fb51586dc97e1f19ed08b9ab7b0e9afcbc61ed39543b9d0a1be68edcce2627ab92ebc4afc1537f124a6cd4f7306499
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data/lib/rbbt/sources/kegg.rb
CHANGED
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@@ -79,44 +79,44 @@ if defined? Entity
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79
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if defined? Gene and Entity === Gene
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module Gene
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def to_kegg
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end
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def from_kegg
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end
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def self.gene_kegg_pathway_index
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end
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property :to => :array2single do |new_format|
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end
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82
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add_identifiers KEGG.identifiers
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#def to_kegg
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85
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# return self if format == "KEGG Gene ID"
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86
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# if Array === self
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87
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# Gene.setup(KEGG.index2kegg.values_at(*to("Ensembl Gene ID")), "KEGG Gene ID", organism).tap{|o| o.extend AnnotatedArray if AnnotatedArray === self }
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88
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# else
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# Gene.setup(KEGG.index2kegg[to("Ensembl Gene ID")], "KEGG Gene ID", organism).tap{|o| o.extend AnnotatedArray if AnnotatedArray === self }
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# end
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#end
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#def from_kegg
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# return self unless format == "KEGG Gene ID"
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# if Array === self
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# Gene.setup(KEGG.index2ens.values_at(*self), "Ensembl Gene ID", organism).tap{|o| o.extend AnnotatedArray if AnnotatedArray === self }
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# else
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# Gene.setup(KEGG.index2ens[self], "Ensembl Gene ID", organism).tap{|o| o.extend AnnotatedArray if AnnotatedArray === self }
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# end
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#end
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#def self.gene_kegg_pathway_index
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# @@gene_kegg_pathway_index ||=
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# KEGG.gene_pathway.tsv(:persist => true, :key_field => "KEGG Gene ID", :fields => ["KEGG Pathway ID"], :type => :flat, :merge => true)
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#end
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#property :to => :array2single do |new_format|
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# case
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# when format == new_format
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# self
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# when format == "KEGG Gene ID"
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# ensembl = from_kegg.clean_annotations
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# Gene.setup(Translation.job(:tsv_translate, "", :organism => organism, :genes => ensembl, :format => new_format).exec.chunked_values_at(ensembl), new_format, organism).tap{|o| o.extend AnnotatedArray if AnnotatedArray === self }
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# when new_format == "KEGG Gene ID"
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# to_kegg
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# else
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# Gene.setup(Translation.job(:tsv_translate, "", :organism => organism, :genes => self, :format => new_format).exec.chunked_values_at(self), new_format, organism).tap{|o| o.extend AnnotatedArray if AnnotatedArray === self }
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# end
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#end
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property :kegg_pathways => :array2single do
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@kegg_pathways ||= Gene.gene_kegg_pathway_index.values_at(*self.to_kegg).
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metadata
CHANGED
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@@ -1,14 +1,14 @@
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1
1
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--- !ruby/object:Gem::Specification
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2
2
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name: rbbt-sources
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3
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version: !ruby/object:Gem::Version
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4
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version: 3.0.
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4
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version: 3.0.19
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5
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platform: ruby
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6
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authors:
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7
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- Miguel Vazquez
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autorequire:
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bindir: bin
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cert_chain: []
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date: 2014-
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date: 2014-10-17 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: rbbt-util
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