rbbt-sources 3.1.39 → 3.1.40
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- checksums.yaml +4 -4
- data/lib/rbbt/sources/CASCADE.rb +9 -3
- metadata +2 -2
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
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---
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2
2
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SHA256:
|
3
|
-
metadata.gz:
|
4
|
-
data.tar.gz:
|
3
|
+
metadata.gz: 58f9941a36498e575420dbe3fd97c726269e168d4565fa0e587d002706c6f6d6
|
4
|
+
data.tar.gz: 0c684724f4a5d9a4290c4e74f22f3d84dca18c31ec270eed8075649ea8cf6032
|
5
5
|
SHA512:
|
6
|
-
metadata.gz:
|
7
|
-
data.tar.gz:
|
6
|
+
metadata.gz: e31b8a35bf7cc518cb825003ff6d521c4d94cca64f2adb4f8da7fb634bd9882e135875e1df8ed8d1cacb458e7f1dc9916c1d18281437569c37021ed18d6d38ec
|
7
|
+
data.tar.gz: f942919c06a57079b74414829c0bfcc9c46be2cfc2c8213ed7293d20c00fedad1ec4cc94e4d9b581746f7c0e7430793562e81df5d6a18797aa87e099434a4c27
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data/lib/rbbt/sources/CASCADE.rb
CHANGED
@@ -39,16 +39,23 @@ module CASCADE
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|
39
39
|
associations = {}
|
40
40
|
|
41
41
|
interactions.through do |source, values|
|
42
|
-
|
42
|
+
Misc.zip_fields(values.values_at("ENTITYB", "TYPEA", "IDA","DATABASEA", "TYPEB", "IDB", "DATABASEB", "EFFECT")).each do |target,typea,ida,databasea,typeb,idb,databaseb,effect|
|
43
43
|
next if typea == 'gene'
|
44
|
+
typea.strip!
|
45
|
+
typeb.strip!
|
46
|
+
|
47
|
+
typea = 'output' if typea == 'phenotype'
|
48
|
+
typeb = 'output' if typeb == 'phenotype'
|
44
49
|
|
45
50
|
if typeb == 'gene'
|
46
51
|
target.sub!('_g','')
|
47
52
|
type = '-t'
|
48
53
|
elsif typeb == 'output' or typea == 'output'
|
49
54
|
type = '-ap'
|
50
|
-
|
55
|
+
elsif typeb == 'protein' or typeb == 'protein family' or typeb == 'protein complex' or typeb == 'second messenger'
|
51
56
|
type = '-a'
|
57
|
+
else
|
58
|
+
raise "Unknown type #{typeb} #{source} #{target}"
|
52
59
|
end
|
53
60
|
|
54
61
|
proteins << source unless source.include? '_f' or source.include? '_c'
|
@@ -93,7 +100,6 @@ module CASCADE
|
|
93
100
|
end
|
94
101
|
end
|
95
102
|
|
96
|
-
|
97
103
|
associations.each do |p,i|
|
98
104
|
source, target = p
|
99
105
|
type, symbol = i
|
metadata
CHANGED
@@ -1,14 +1,14 @@
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|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: rbbt-sources
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 3.1.
|
4
|
+
version: 3.1.40
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- Miguel Vazquez
|
8
8
|
autorequire:
|
9
9
|
bindir: bin
|
10
10
|
cert_chain: []
|
11
|
-
date: 2019-07-
|
11
|
+
date: 2019-07-22 00:00:00.000000000 Z
|
12
12
|
dependencies:
|
13
13
|
- !ruby/object:Gem::Dependency
|
14
14
|
name: rbbt-util
|