rbbt-study 0.2.9 → 0.2.10
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- checksums.yaml +8 -8
- data/lib/rbbt/entity/study/genotypes/knowledge_base.rb +2 -1
- metadata +2 -2
checksums.yaml
CHANGED
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@@ -1,15 +1,15 @@
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1
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---
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2
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!binary "U0hBMQ==":
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metadata.gz: !binary |-
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-
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4
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+
MjhhMDY3Y2FiN2E3YTJlZjI2NmQ2OWFlMGExOWQzYjM4YTI1ZDBmMg==
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5
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data.tar.gz: !binary |-
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6
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-
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6
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+
NDZlMzI1NjIzZDY1MDM5YzAzYWNiZjVmNTNhYTUyNTZiZmE0NmJhMg==
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7
7
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SHA512:
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metadata.gz: !binary |-
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-
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-
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11
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-
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9
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+
ZjllZGQ4NmJlN2I3NGUyZmE3MWVmNmFmNTYxYzI0MWY3NmM0MzUwYzBiMDQ4
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10
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+
NmYzMmQ3NTUxMTA5NDNjMzMzZWE4NmI1ZGMzYmU4YWZhYzZkN2I3ZjgwMmQ5
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11
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+
ZWQ2ODQ2OTA4ZWUzODg4Y2YyODE5MTBjMDRkMzdlYTI4YTBmYmY=
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data.tar.gz: !binary |-
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-
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-
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15
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-
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13
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+
OGYzYTM1ODY1NjM0NDRjMDhlMDViYmFmOWU3YTBjZGE3OTllNzQxNjRhNDNi
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14
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+
ZmQzN2VjMTk0NTcxYjc1MTYxYzAwMGY1NzMwYWY5NGU3MDNjOTUyYWRmZDBh
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15
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+
ZTZkYTQwMThjY2ZkYmI5MDA1NGQ5NThmMjIxNTA4NTM3ZmQxMTI=
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@@ -27,6 +27,7 @@ module Study
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sample_mutations = study.knowledge_base.get_database(:sample_mutations, :source => "Sample")
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all_mutations = study.all_mutations
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mutations2mutated_isoforms = Misc.process_to_hash(all_mutations){|mutations| mutations.any? ? mutations.mutated_isoforms : [] }
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+
mutations2exon_junction = Misc.process_to_hash(all_mutations){|mutations| mutations.in_exon_junction? }
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#mi2damaged = Misc.process_to_hash(MutatedIsoform.setup(mutations2mutated_isoforms.values.flatten.compact.uniq, study.organism)){|mis| mis.damaged? }
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mi2damaged = Misc.process_to_hash(MutatedIsoform.setup(mutations2mutated_isoforms.values.flatten.compact.uniq, study.organism)){|mis| [false] * mis.length }
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mi2consequence = Misc.process_to_hash(MutatedIsoform.setup(mutations2mutated_isoforms.values.flatten.compact.uniq, study.organism)){|mis| mis.consequence }
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@@ -40,7 +41,7 @@ module Study
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if mutations.any?
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GenomicMutation.setup(mutations, "Mutations in #{ sample } over #{ gene }", study.organism, study.watson)
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-
junction = mutations.
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+
junction = mutations.select{|mutation| mutations2exon_junction[mutation] }.any?
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mis = Annotated.flatten mutations2mutated_isoforms.values_at(*mutations).compact
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metadata
CHANGED
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@@ -1,14 +1,14 @@
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1
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--- !ruby/object:Gem::Specification
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name: rbbt-study
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version: !ruby/object:Gem::Version
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-
version: 0.2.
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version: 0.2.10
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platform: ruby
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authors:
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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: 2013-11-
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date: 2013-11-14 00:00:00.000000000 Z
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dependencies: []
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description: This gem add the study entity with suport for NGS, Microarray and other
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types of data
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