rbbt-sources 3.1.49 → 3.1.50
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- checksums.yaml +4 -4
- data/lib/rbbt/sources/organism.rb +3 -3
- data/share/install/Organism/Rno/Rakefile +1 -0
- metadata +2 -2
checksums.yaml
CHANGED
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@@ -1,7 +1,7 @@
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1
1
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---
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2
2
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SHA256:
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3
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-
metadata.gz:
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4
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-
data.tar.gz:
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3
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+
metadata.gz: 76650eb77129f5a072416944c24e3155e507ffe75f79372c505d62b919899e48
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4
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+
data.tar.gz: 70bf96eb1fa599f121cf65f40388aae545c4a6bb03ca006bc24f4ec83c78175d
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5
5
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SHA512:
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|
6
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-
metadata.gz:
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|
7
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-
data.tar.gz:
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6
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+
metadata.gz: dc1fc3dd34681ee50feaff3a447b98abf484eb5ed2775804e6aa2268e14dede03e16970ed7c5bfe5c5015b081514cb3309f178cbca973434848f83368ba27778
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|
7
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+
data.tar.gz: 1ce0587059951ee335cf08f3cf22ceb24c0b0deaaf9798689be141a53871934e1e679efbf2faf578fb10bf3088386539204cecc121a68becddedcdb0aad988c5
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@@ -149,12 +149,12 @@ module Organism
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149
149
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new_positions = {}
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150
150
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151
151
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TmpFile.with_file(positions_bed) do |source_bed|
|
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152
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-
TmpFile.with_file
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|
153
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-
TmpFile.with_file
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152
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+
TmpFile.with_file do |unmapped_file|
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|
153
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+
TmpFile.with_file do |map_file|
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154
154
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155
155
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156
156
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Open.write(map_file, Open.read(map_url))
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157
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-
new_mutations = TmpFile.with_file
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157
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+
new_mutations = TmpFile.with_file do |target_bed|
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|
158
158
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FileUtils.chmod(755, Rbbt.software.opt.bin.liftOver.produce.find)
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|
159
159
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CMD.cmd("#{Rbbt.software.opt.bin.liftOver.find} '#{source_bed}' '#{map_file}' '#{target_bed}' '#{unmapped_file}'").read
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|
160
160
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Open.read(target_bed) do |line|
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@@ -20,6 +20,7 @@ $biomart_lexicon = [
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20
20
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21
21
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$biomart_identifiers = [
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22
22
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['Entrez Gene ID', "entrezgene"],
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23
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+
['Ensembl Protein ID', "ensembl_peptide_id" ],
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23
24
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['Associated Gene Name' , "rgd_symbol"],
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24
25
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['Protein ID' , "protein_id"] ,
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25
26
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['UniProt/SwissProt ID' , "uniprot_swissprot"] ,
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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
3
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version: !ruby/object:Gem::Version
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4
|
-
version: 3.1.
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4
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+
version: 3.1.50
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5
5
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platform: ruby
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|
6
6
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authors:
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|
7
7
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- Miguel Vazquez
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|
8
8
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autorequire:
|
|
9
9
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bindir: bin
|
|
10
10
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cert_chain: []
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|
11
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-
date: 2020-
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|
11
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+
date: 2020-11-02 00:00:00.000000000 Z
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|
12
12
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dependencies:
|
|
13
13
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- !ruby/object:Gem::Dependency
|
|
14
14
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name: rbbt-util
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