rbbt-sources 3.0.10 → 3.0.11
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 +4 -4
- data/etc/organisms +1 -0
- data/lib/rbbt/sources/organism.rb +24 -3
- metadata +3 -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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SHA1:
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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: 50fb25a49bcb8eb484852db15e30ae3fc66c933e
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4
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+
data.tar.gz: 58ae0bb2aff4eb3f1776fb5a5b403aa14f7803c4
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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: 8bb383dac78af82b81515f29f9e8672bda18bc607b3caa0aba54a1a0b93e90669e903cc12bc2f0d7a2ef63c31827d6c88e71b863ac98f13631fd4459a800e566
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7
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+
data.tar.gz: 506c293e96504a23e2f1f6f4ef036e1ba17a4d428e2fab814a82ba65be0c1724940a1e03fa45f245476564019504f12edde2fe7638eb1f37cd70b32a3cdabf6b
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data/etc/organisms
ADDED
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@@ -0,0 +1 @@
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1
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+
Hsa
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@@ -6,10 +6,24 @@ module Organism
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6
6
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self.pkgdir = "rbbt"
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7
7
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self.subdir = "share/organisms"
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8
8
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9
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-
def self.
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9
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+
def self.organism_codes(organism = nil)
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10
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if organism
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11
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Rbbt.etc.allowed_biomart_archives.list.collect{|build| [organism, build] * "/" }
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12
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else
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13
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Rbbt.etc.organisms.list.collect{|organism|
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14
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organism =~ /\// ? organism : Rbbt.etc.allowed_biomart_archives.list.collect{|build| [organism, build] * "/" }
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15
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}.flatten.compact.uniq
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16
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end
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17
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end
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18
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+
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19
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+
def self.installed_organisms
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10
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Rbbt.share.install.Organism.find.glob('???').collect{|f| File.basename(f)}
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11
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end
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12
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23
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+
def self.installable_organisms
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24
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self.installed_organisms
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25
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end
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26
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+
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13
27
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def self.allowed_biomart_archives
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14
28
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Rbbt.etc.allowed_biomart_archives.exists? ?
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15
29
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Rbbt.etc.allowed_biomart_archives.list :
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@@ -29,12 +43,19 @@ module Organism
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29
43
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raise "Only organism 'Hsa' (Homo sapiens) supported" unless organism =~ /^Hsa/
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31
45
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32
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-
return '
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46
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+
return 'hg20' unless organism =~ /\//
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33
47
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date = organism.split("/")[1]
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34
48
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35
49
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release = Ensembl.releases[date]
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36
50
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37
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-
release.sub(/.*-/,'').to_i
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51
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+
release_number = release.sub(/.*-/,'').to_i
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52
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if release_number <= 54
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53
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'hg18'
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54
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elsif release_number <= 70
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55
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'hg19'
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56
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else
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57
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'hg20'
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58
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end
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38
59
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end
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39
60
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40
61
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def self.liftOver(positions, source, target)
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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
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name: rbbt-sources
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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: 3.0.11
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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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11
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-
date: 2014-07-
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11
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+
date: 2014-07-20 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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@@ -88,6 +88,7 @@ extra_rdoc_files: []
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88
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files:
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- etc/allowed_biomart_archives
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- etc/biomart/missing_in_archive
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91
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- etc/organisms
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91
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- lib/rbbt/sources/COSTART.rb
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92
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- lib/rbbt/sources/CTCAE.rb
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93
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- lib/rbbt/sources/HPRD.rb
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