rbbt-sources 3.2.1 → 3.2.2
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/lib/rbbt/sources/signor.rb +11 -17
- data/lib/rbbt/sources/tfacts.rb +7 -0
- data/share/install/Organism/organism_helpers.rb +2 -2
- metadata +2 -2
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
|
---
|
2
2
|
SHA256:
|
3
|
-
metadata.gz:
|
4
|
-
data.tar.gz:
|
3
|
+
metadata.gz: 45945055f3bb3f73e9928b667cfa01802910d9e5ae4d9cfb3df525d9958af872
|
4
|
+
data.tar.gz: '092951fa32efdc9ccabea467ccae1f4d7729cb0b7fa24b7c064b5a8671de66d8'
|
5
5
|
SHA512:
|
6
|
-
metadata.gz:
|
7
|
-
data.tar.gz:
|
6
|
+
metadata.gz: 174dc33879a4c712a44a0574a9c772dcd06df4602f08d5ec4da98446c04297fd54104815ca5501c511d7599bf346a104bafe5744b6000b5c006117f6d21860d3
|
7
|
+
data.tar.gz: 4ff9086a6d2a83ad09823fd339bca8f4278958658faa20081f9f17f5ca7c500d569e76bf8bfd182ad742a9c8d823cd19a55d3eccd48c1e696046bfea32302366
|
data/lib/rbbt/sources/signor.rb
CHANGED
@@ -19,17 +19,7 @@ module Signor
|
|
19
19
|
end
|
20
20
|
|
21
21
|
Signor.claim Signor.data, :proc do
|
22
|
-
|
23
|
-
io_tmp = Misc.remove_quoted_new_line(sio)
|
24
|
-
io = Misc.swap_quoted_character(io_tmp, ';', '--SEMICOLON--')
|
25
|
-
|
26
|
-
tsv = TSV.open io, :header_hash => "", :sep => ";", :merge => true, :type => :double, :zipped => true, :monitor => true
|
27
|
-
tsv.each do |k,values|
|
28
|
-
clean_values = values.collect{|vs| vs.collect{|v| (v[0] == '"' and v[-1] = '"') ? v[1..-2] : v }.collect{|v| v.gsub("--SEMICOLON--", ';') } }
|
29
|
-
|
30
|
-
values.replace clean_values
|
31
|
-
end
|
32
|
-
tsv
|
22
|
+
Signor[".source/all.csv"].tsv :header_hash => '', :merge => true, :zipped => true
|
33
23
|
end
|
34
24
|
|
35
25
|
Signor.claim Signor.protein_protein, :proc do
|
@@ -69,7 +59,7 @@ module Signor
|
|
69
59
|
|
70
60
|
parser = TSV::Parser.new Signor.data
|
71
61
|
fields = parser.fields
|
72
|
-
dumper = TSV::Dumper.new :key_field => "Source (UniProt/SwissProt Accession)", :fields => ["Target (Associated Gene Name)", "Effect", "Sign", "PMID"], :type => :double, :organism => Signor.organism
|
62
|
+
dumper = TSV::Dumper.new :key_field => "Source (UniProt/SwissProt Accession)", :fields => ["Target (Associated Gene Name)", "Effect", "Sign", "PMID"], :type => :double, :merge => true, :organism => Signor.organism
|
73
63
|
dumper.init
|
74
64
|
TSV.traverse parser, :into => dumper do |k,values|
|
75
65
|
info = {}
|
@@ -82,12 +72,12 @@ module Signor
|
|
82
72
|
res = []
|
83
73
|
res.extend MultipleResult
|
84
74
|
|
85
|
-
info["TYPEB"].zip(info["IDB"]).zip(info["EFFECT"]).zip(info["MECHANISM"]).zip(info["PMID"]).each do |v|
|
86
|
-
typeb,idb,eff,mech,pmid = v.flatten
|
75
|
+
info["TYPEB"].zip(info["ENTITYB"]).zip(info["IDB"]).zip(info["EFFECT"]).zip(info["MECHANISM"]).zip(info["PMID"]).each do |v|
|
76
|
+
typeb,nameb,idb,eff,mech,pmid = v.flatten
|
87
77
|
|
88
78
|
next unless typeb == "protein"
|
89
79
|
next unless mech == "transcriptional regulation"
|
90
|
-
nameb
|
80
|
+
nameb ||= uni2name[idb]
|
91
81
|
next if nameb.nil?
|
92
82
|
sign = "Unknown"
|
93
83
|
sign = "UP" if eff.include? 'up-regulates'
|
@@ -133,6 +123,10 @@ module Signor
|
|
133
123
|
end
|
134
124
|
end
|
135
125
|
|
136
|
-
|
137
|
-
|
126
|
+
if __FILE__ == $0
|
127
|
+
Log.severity = 0
|
128
|
+
data = Signor.tf_tg.produce(true).find
|
129
|
+
Log.tsv data
|
130
|
+
#iif Signor.tf_tg.produce.find
|
131
|
+
end
|
138
132
|
|
data/lib/rbbt/sources/tfacts.rb
CHANGED
@@ -121,7 +121,7 @@ file 'identifiers' do |t|
|
|
121
121
|
names = values[name_pos]
|
122
122
|
|
123
123
|
matches = entrez.select do |e|
|
124
|
-
entrez2name.include?
|
124
|
+
entrez2name.include?(e) && (names & entrez2name[e]).any?
|
125
125
|
end
|
126
126
|
|
127
127
|
if matches.any?
|
@@ -147,7 +147,7 @@ file 'identifiers' do |t|
|
|
147
147
|
identifiers = identifiers.reorder(:key, ordered_fields)
|
148
148
|
end
|
149
149
|
|
150
|
-
entrez_synonyms = Rbbt.share.databases.entrez.gene_info.find.tsv :grep => $taxs.collect{|tax| "^#{tax}"}, :key_field => 1, :fields => [4]
|
150
|
+
entrez_synonyms = Rbbt.share.databases.entrez.gene_info.find.tsv :grep => $taxs.collect{|tax| "^#{tax}"}, :fixed_grep => false, :key_field => 1, :fields => [4]
|
151
151
|
entrez_synonyms.key_field = "Entrez Gene ID"
|
152
152
|
entrez_synonyms.fields = ["Entrez Gene Name Synonyms"]
|
153
153
|
|
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: 3.2.
|
4
|
+
version: 3.2.2
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- Miguel Vazquez
|
8
8
|
autorequire:
|
9
9
|
bindir: bin
|
10
10
|
cert_chain: []
|
11
|
-
date:
|
11
|
+
date: 2023-02-21 00:00:00.000000000 Z
|
12
12
|
dependencies:
|
13
13
|
- !ruby/object:Gem::Dependency
|
14
14
|
name: rbbt-util
|