rbbt-study 0.2.9 → 0.2.10
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +8 -8
- data/lib/rbbt/entity/study/genotypes/knowledge_base.rb +2 -1
- metadata +2 -2
checksums.yaml
CHANGED
|
@@ -1,15 +1,15 @@
|
|
|
1
1
|
---
|
|
2
2
|
!binary "U0hBMQ==":
|
|
3
3
|
metadata.gz: !binary |-
|
|
4
|
-
|
|
4
|
+
MjhhMDY3Y2FiN2E3YTJlZjI2NmQ2OWFlMGExOWQzYjM4YTI1ZDBmMg==
|
|
5
5
|
data.tar.gz: !binary |-
|
|
6
|
-
|
|
6
|
+
NDZlMzI1NjIzZDY1MDM5YzAzYWNiZjVmNTNhYTUyNTZiZmE0NmJhMg==
|
|
7
7
|
SHA512:
|
|
8
8
|
metadata.gz: !binary |-
|
|
9
|
-
|
|
10
|
-
|
|
11
|
-
|
|
9
|
+
ZjllZGQ4NmJlN2I3NGUyZmE3MWVmNmFmNTYxYzI0MWY3NmM0MzUwYzBiMDQ4
|
|
10
|
+
NmYzMmQ3NTUxMTA5NDNjMzMzZWE4NmI1ZGMzYmU4YWZhYzZkN2I3ZjgwMmQ5
|
|
11
|
+
ZWQ2ODQ2OTA4ZWUzODg4Y2YyODE5MTBjMDRkMzdlYTI4YTBmYmY=
|
|
12
12
|
data.tar.gz: !binary |-
|
|
13
|
-
|
|
14
|
-
|
|
15
|
-
|
|
13
|
+
OGYzYTM1ODY1NjM0NDRjMDhlMDViYmFmOWU3YTBjZGE3OTllNzQxNjRhNDNi
|
|
14
|
+
ZmQzN2VjMTk0NTcxYjc1MTYxYzAwMGY1NzMwYWY5NGU3MDNjOTUyYWRmZDBh
|
|
15
|
+
ZTZkYTQwMThjY2ZkYmI5MDA1NGQ5NThmMjIxNTA4NTM3ZmQxMTI=
|
|
@@ -27,6 +27,7 @@ module Study
|
|
|
27
27
|
sample_mutations = study.knowledge_base.get_database(:sample_mutations, :source => "Sample")
|
|
28
28
|
all_mutations = study.all_mutations
|
|
29
29
|
mutations2mutated_isoforms = Misc.process_to_hash(all_mutations){|mutations| mutations.any? ? mutations.mutated_isoforms : [] }
|
|
30
|
+
mutations2exon_junction = Misc.process_to_hash(all_mutations){|mutations| mutations.in_exon_junction? }
|
|
30
31
|
#mi2damaged = Misc.process_to_hash(MutatedIsoform.setup(mutations2mutated_isoforms.values.flatten.compact.uniq, study.organism)){|mis| mis.damaged? }
|
|
31
32
|
mi2damaged = Misc.process_to_hash(MutatedIsoform.setup(mutations2mutated_isoforms.values.flatten.compact.uniq, study.organism)){|mis| [false] * mis.length }
|
|
32
33
|
mi2consequence = Misc.process_to_hash(MutatedIsoform.setup(mutations2mutated_isoforms.values.flatten.compact.uniq, study.organism)){|mis| mis.consequence }
|
|
@@ -40,7 +41,7 @@ module Study
|
|
|
40
41
|
|
|
41
42
|
if mutations.any?
|
|
42
43
|
GenomicMutation.setup(mutations, "Mutations in #{ sample } over #{ gene }", study.organism, study.watson)
|
|
43
|
-
junction = mutations.
|
|
44
|
+
junction = mutations.select{|mutation| mutations2exon_junction[mutation] }.any?
|
|
44
45
|
|
|
45
46
|
mis = Annotated.flatten mutations2mutated_isoforms.values_at(*mutations).compact
|
|
46
47
|
|
metadata
CHANGED
|
@@ -1,14 +1,14 @@
|
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
|
2
2
|
name: rbbt-study
|
|
3
3
|
version: !ruby/object:Gem::Version
|
|
4
|
-
version: 0.2.
|
|
4
|
+
version: 0.2.10
|
|
5
5
|
platform: ruby
|
|
6
6
|
authors:
|
|
7
7
|
- Miguel Vazquez
|
|
8
8
|
autorequire:
|
|
9
9
|
bindir: bin
|
|
10
10
|
cert_chain: []
|
|
11
|
-
date: 2013-11-
|
|
11
|
+
date: 2013-11-14 00:00:00.000000000 Z
|
|
12
12
|
dependencies: []
|
|
13
13
|
description: This gem add the study entity with suport for NGS, Microarray and other
|
|
14
14
|
types of data
|