rbbt-sources 3.1.40 → 3.1.41
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- checksums.yaml +4 -4
- data/etc/allowed_biomart_archives +1 -0
- data/etc/biomart/missing_in_archive +2 -0
- data/lib/rbbt/sources/signor.rb +1 -4
- data/lib/rbbt/sources/uniprot.rb +3 -3
- metadata +3 -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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SHA256:
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3
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-
metadata.gz:
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4
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-
data.tar.gz:
|
3
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+
metadata.gz: e0a35626b221e15867cb54ca9e8bbeb007762b5a99afed75d57d6b473385c287
|
4
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+
data.tar.gz: 59d067abbfdcd686f39b3604282a280ca9bf4a0e8f3284698202dae8d9d50d55
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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:
|
6
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+
metadata.gz: 1c9c6a2dc5184319e94af671762227bba331b49784cf3e4ac0550b6c023c7b072920d75175b0547c2d8cb4034dbca53dda9514238773cf98f103cc6be978c4ec
|
7
|
+
data.tar.gz: df52691bf65b891a906217f5e2647577bc74940bbd3fa1752115f624a313472a70a43fb96b786e30a4612bc71badb7b3e68c539e0024fe0f0958ee5f33d910af
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data/lib/rbbt/sources/signor.rb
CHANGED
@@ -102,7 +102,6 @@ module Signor
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102
102
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end
|
103
103
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|
104
104
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Signor.claim Signor.phospho_sites, :proc do
|
105
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-
uni2name = UniProt.identifiers.Hsa.index :target => "Associated Gene Name", :fields => ["UniProt/SwissProt Accession"], :persist => true
|
106
105
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|
107
106
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dumper = TSV::Dumper.new :key_field => "Phosphosite", :fields => ["Effect"], :type => :flat, :organism => Signor.organism
|
108
107
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dumper.init
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@@ -119,10 +118,8 @@ module Signor
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119
118
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else
|
120
119
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next
|
121
120
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end
|
122
|
-
name = uni2name[target]
|
123
|
-
next if name.nil?
|
124
121
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next if residue.nil? or residue.empty?
|
125
|
-
site = [
|
122
|
+
site = [target, residue] * ":"
|
126
123
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positive = effect.include? "up-regulates"
|
127
124
|
|
128
125
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activates = kinase && positive || (!kinase && !positive)
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data/lib/rbbt/sources/uniprot.rb
CHANGED
@@ -66,7 +66,7 @@ module UniProt
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66
66
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67
67
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|
68
68
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UniProt.claim UniProt.annotated_variants, :proc do
|
69
|
-
url = "
|
69
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+
url = "https://www.uniprot.org/docs/humsavar.txt"
|
70
70
|
tsv = TSV.open(CMD.cmd('tail -n +31 | head -n -4|grep "[[:alpha:]]"', :in => Open.open(url), :pipe => true),
|
71
71
|
:fix => Proc.new{|line| parts = line.split(/\s+/); (parts[1..5] + [(parts[6..-1] || []) * " "]) * "\t"},
|
72
72
|
:type => :double,
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@@ -89,8 +89,8 @@ module UniProt
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|
89
89
|
tsv.to_s
|
90
90
|
end
|
91
91
|
|
92
|
-
UNIPROT_TEXT="
|
93
|
-
UNIPROT_FASTA="
|
92
|
+
UNIPROT_TEXT="https://www.uniprot.org/uniprot/[PROTEIN].txt"
|
93
|
+
UNIPROT_FASTA="https://www.uniprot.org/uniprot/[PROTEIN].fasta"
|
94
94
|
|
95
95
|
def self.get_uniprot_entry(uniprotids)
|
96
96
|
_array = Array === uniprotids
|
metadata
CHANGED
@@ -1,14 +1,14 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: rbbt-sources
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 3.1.
|
4
|
+
version: 3.1.41
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- Miguel Vazquez
|
8
8
|
autorequire:
|
9
9
|
bindir: bin
|
10
10
|
cert_chain: []
|
11
|
-
date: 2019-
|
11
|
+
date: 2019-11-15 00:00:00.000000000 Z
|
12
12
|
dependencies:
|
13
13
|
- !ruby/object:Gem::Dependency
|
14
14
|
name: rbbt-util
|
@@ -190,7 +190,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
|
|
190
190
|
- !ruby/object:Gem::Version
|
191
191
|
version: '0'
|
192
192
|
requirements: []
|
193
|
-
rubygems_version: 3.0.
|
193
|
+
rubygems_version: 3.0.6
|
194
194
|
signing_key:
|
195
195
|
specification_version: 4
|
196
196
|
summary: Data sources for the Ruby Bioinformatics Toolkit (rbbt)
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