rbbt-sources 3.1.18 → 3.1.19
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- checksums.yaml +4 -4
- data/lib/rbbt/sources/GTRD.rb +23 -0
- data/lib/rbbt/sources/corum.rb +2 -2
- data/lib/rbbt/sources/kegg.rb +1 -2
- metadata +4 -3
checksums.yaml
CHANGED
@@ -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: 2e37f4f4156576088ee39f1836f07941e4a26619
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4
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+
data.tar.gz: 6f223756910829b3fc37348c93b7d7b73caa3e9f
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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: 8daf49212a7f547fb6c098b578c698daa5999b5d299b1f0435bb6b4437070ec8105488a4180c6b7726ab0f16498b32476bfdcc0e0af95e6ae910967aa6e044a0
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7
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+
data.tar.gz: 4661d5dd8c2d02ef2426d21fe42569b5eb536666929c1a66b0a171baf7f6db6756366b7683d4eec2eb1ec966410cd7f602e9ef8bd7a6a39ae55fdbf087dd31e2
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@@ -0,0 +1,23 @@
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1
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+
require 'rbbt-util'
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2
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+
require 'rbbt/resource'
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3
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+
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4
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+
module GTRD
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5
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+
extend Resource
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6
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+
self.subdir = 'share/databases/GTRD'
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7
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+
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8
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+
def self.organism(org="Hsa")
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9
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+
Organism.default_code(org)
|
10
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+
end
|
11
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+
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12
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+
#self.search_paths = {}
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13
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+
#self.search_paths[:default] = :lib
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14
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+
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15
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+
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16
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+
GTRD.claim GTRD.tfClass, :proc do
|
17
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+
url = "http://gtrd.biouml.org/downloads/current/tfClass2ensembl.txt.gz"
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18
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+
CMD.cmd("grep Homo | cut -f 2", :in => Open.read(url)).read
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19
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+
end
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20
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+
end
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21
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+
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22
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+
iif GTRD.tfClass.produce.find if __FILE__ == $0
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23
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+
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data/lib/rbbt/sources/corum.rb
CHANGED
@@ -11,7 +11,7 @@ module CORUM
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11
11
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end
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12
12
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13
13
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CORUM.claim CORUM.complex_names, :proc do
|
14
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-
url = "http://mips.helmholtz-muenchen.de/corum/download/allComplexes.txt"
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14
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+
url = "http://mips.helmholtz-muenchen.de/corum/download/allComplexes.txt.zip"
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15
15
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tsv = TSV.open(url, :header_hash => "", :sep2 => ';', :fix => Proc.new{|l| "CORUM:" + l.gsub('"','')})
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16
16
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tsv.namespace = organism
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17
17
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tsv.fields = tsv.fields.collect{|f| f.gsub('"','')}
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@@ -22,7 +22,7 @@ module CORUM
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22
22
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end
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23
23
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24
24
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CORUM.claim CORUM.complexes, :proc do
|
25
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-
url = "http://mips.helmholtz-muenchen.de/corum/download/allComplexes.txt"
|
25
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+
url = "http://mips.helmholtz-muenchen.de/corum/download/allComplexes.txt.zip"
|
26
26
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tsv = TSV.open(url, :header_hash => "", :sep2 => ';', :fix => Proc.new{|l| "CORUM:" + l.gsub('"','')})
|
27
27
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tsv.namespace = organism
|
28
28
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tsv.fields = tsv.fields.collect{|f| f.gsub('"','')}.collect{|f|
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data/lib/rbbt/sources/kegg.rb
CHANGED
metadata
CHANGED
@@ -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
|
3
3
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version: !ruby/object:Gem::Version
|
4
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-
version: 3.1.
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4
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+
version: 3.1.19
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5
5
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platform: ruby
|
6
6
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authors:
|
7
7
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- Miguel Vazquez
|
8
8
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autorequire:
|
9
9
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bindir: bin
|
10
10
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cert_chain: []
|
11
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-
date: 2017-
|
11
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+
date: 2017-09-27 00:00:00.000000000 Z
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12
12
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dependencies:
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13
13
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- !ruby/object:Gem::Dependency
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14
14
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name: rbbt-util
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@@ -92,6 +92,7 @@ files:
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92
92
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- lib/rbbt/sources/CASCADE.rb
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93
93
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- lib/rbbt/sources/COSTART.rb
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94
94
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- lib/rbbt/sources/CTCAE.rb
|
95
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+
- lib/rbbt/sources/GTRD.rb
|
95
96
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- lib/rbbt/sources/HPRD.rb
|
96
97
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- lib/rbbt/sources/MCLP.rb
|
97
98
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- lib/rbbt/sources/MSigDB.rb
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@@ -181,7 +182,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
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|
181
182
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version: '0'
|
182
183
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requirements: []
|
183
184
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rubyforge_project:
|
184
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-
rubygems_version: 2.6.
|
185
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+
rubygems_version: 2.6.13
|
185
186
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signing_key:
|
186
187
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specification_version: 4
|
187
188
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summary: Data sources for the Ruby Bioinformatics Toolkit (rbbt)
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