rbbt-sources 3.0.17 → 3.0.18
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- checksums.yaml +4 -4
- data/lib/rbbt/sources/PSI_MI.rb +3 -1
- data/lib/rbbt/sources/pina.rb +31 -5
- 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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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: 2bffa0f27abdce0727b9aa6a95a2538c275cac02
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4
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+
data.tar.gz: 014e18755856b61315c6e1566f3fb2a7b4470892
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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: b78601699a107f0a8565efa66068ee2b85185d4c55868cb813186fc0969140f11763666bf6e14b73f9e4c797d4a21b1dcee5a253a41d15275627e802be3a2da9
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7
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+
data.tar.gz: 181eab2593ad778f945632522802b5992b9f28718a6ec91f1fd56cc1112cf52261f572d195878919846ee4e661f69c56117473281a2ac275584e87d280cc6bf0
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data/lib/rbbt/sources/PSI_MI.rb
CHANGED
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@@ -12,6 +12,8 @@ module PSI_MI
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12
12
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tsv = TSV.setup({}, :type => :list, :key_field => "PSI-MI Term", :fields => ["Name", "Description"])
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13
13
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Open.open(URL).read.split("[Term]").each do |chunk|
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14
14
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id = chunk.scan(/id: ([^\n]*)/)[0]
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15
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+
next if id.nil?
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16
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+
id = id.first
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15
17
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name = chunk.scan(/name: ([^\n]*)/)[0]
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16
18
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description = chunk.scan(/def: "([^\n]*)"/)[0]
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17
19
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tsv[id] = [name, description]
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@@ -29,7 +31,7 @@ if defined? Entity
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29
31
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module PSI_MITerm
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30
32
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extend Entity
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31
33
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32
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-
self.format = "PSI-MI Term"
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34
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+
self.format = "PSI-MI Term", "Method"
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33
35
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34
36
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property :name => :array2single do
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35
37
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@@index ||= PSI_MI.identifiers.tsv(:persist => true, :fields => ["Name"], :type => :single)
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data/lib/rbbt/sources/pina.rb
CHANGED
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@@ -1,11 +1,38 @@
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1
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-
require 'rbbt'
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2
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-
require 'rbbt/resource'
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1
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+
require 'rbbt-util'
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3
2
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4
3
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module Pina
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|
5
4
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extend Resource
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|
6
5
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self.subdir = "share/databases/pina"
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7
6
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8
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-
Pina.claim Pina.
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7
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+
Pina.claim Pina.protein_protein, :proc do
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|
8
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+
require 'rbbt/sources/organism'
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|
9
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+
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10
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+
url = "http://cbg.garvan.unsw.edu.au/pina/download/Homo%20sapiens-20121210.txt"
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|
11
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+
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12
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+
dumper = TSV::Dumper.new :type => :list, :type => :double,
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|
13
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+
:key_field => 'UniProt/SwissProt Accession', :namespace => Organism.default_code("Hsa"),
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14
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+
:fields => ['Interactor UniProt/SwissProt Accession', 'Method', 'Publication']
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|
15
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+
|
|
16
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+
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|
17
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+
dumper.init
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|
18
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+
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19
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+
TSV.traverse Open.open(url), :type => :array, :into => dumper do |line|
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20
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+
next if line =~ /Publication/
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|
21
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+
|
|
22
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+
parts = line.split("\t")
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|
23
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+
uni1, uni2 = parts.values_at(0,1).collect{|v| v.partition(":").last}
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24
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+
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25
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+
mi = parts[6].split("|").collect{|v| v.sub(/\(.*/,'').strip }
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26
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+
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27
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+
pubmed = parts[8].split("|").collect{|v| v.partition(":").last}
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28
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+
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29
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+
mi, pubmed = Misc.zip_fields(mi.zip(pubmed).uniq)
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|
30
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+
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31
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+
[uni1, [[uni2], [mi * ";;"], [pubmed * ";;"]]]
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|
32
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+
end
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33
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+
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34
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+
Misc.collapse_stream(Misc.sort_stream(dumper.stream))
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|
35
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+
end
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9
36
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end
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10
37
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11
38
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if defined? Entity and defined? Gene and Entity === Gene
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@@ -15,7 +42,7 @@ if defined? Entity and defined? Gene and Entity === Gene
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15
42
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module Gene
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16
43
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property :pina_interactors => :array2single do
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17
44
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ens2uniprot = Organism.identifiers(organism).tsv :key_field => "Ensembl Gene ID", :fields => ["UniProt/SwissProt Accession"], :type => :flat, :persist => true, :unnamed => true
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18
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-
pina = Pina.protein_protein.tsv(:persist => true, :fields => ["Interactor UniProt/SwissProt Accession", "Method", "
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45
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+
pina = Pina.protein_protein.tsv(:persist => true, :fields => ["Interactor UniProt/SwissProt Accession", "Method", "Publication"], :type => :double, :merge => true, :unnamed => true)
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19
46
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20
47
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int = self.ensembl.collect do |ens|
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21
48
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uniprot = ens2uniprot[ens]
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@@ -31,4 +58,3 @@ if defined? Entity and defined? Gene and Entity === Gene
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31
58
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end
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32
59
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end
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33
60
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end
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34
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-
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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
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-
version: 3.0.
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|
4
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+
version: 3.0.18
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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:
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|
9
9
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bindir: bin
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10
10
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cert_chain: []
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|
11
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-
date: 2014-09-
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|
11
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+
date: 2014-09-29 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
|
|
14
14
|
name: rbbt-util
|