rbbt-sources 3.1.32 → 3.1.33
Sign up to get free protection for your applications and to get access to all the features.
- checksums.yaml +4 -4
- data/lib/rbbt/sources/CASCADE.rb +32 -45
- data/lib/rbbt/sources/MCLP.rb +1 -1
- data/lib/rbbt/sources/go.rb +0 -2
- data/share/install/Organism/organism_helpers.rb +10 -0
- metadata +2 -2
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
|
---
|
2
2
|
SHA1:
|
3
|
-
metadata.gz:
|
4
|
-
data.tar.gz:
|
3
|
+
metadata.gz: 1bc10d05cb25aa6e8c21a838af30f8e910915411
|
4
|
+
data.tar.gz: 5c1443c4088a393a33513884813ef3eb9b276ff7
|
5
5
|
SHA512:
|
6
|
-
metadata.gz:
|
7
|
-
data.tar.gz:
|
6
|
+
metadata.gz: 9c2c009324e163840751e84ec0b2eeaff7ed02588637140f26563814183ef43666c2118b92c560cf5fff56c30d9913160e0a940092b4327259f1b18d66efa7fd
|
7
|
+
data.tar.gz: dc09879abc9d3b1f60ff9ecc68f4a2d34da8dfbc19aa6cfcc5640d773d8412b8aa5e3a630dba0b8a8f54c1753dfd88d61c5b50bec8a94694798e0ab376a5804d
|
data/lib/rbbt/sources/CASCADE.rb
CHANGED
@@ -12,18 +12,8 @@ module CASCADE
|
|
12
12
|
#self.search_paths = {}
|
13
13
|
#self.search_paths[:default] = :lib
|
14
14
|
|
15
|
-
|
16
|
-
|
17
|
-
CASCADE.claim CASCADE.interactions, :proc do
|
18
|
-
io = nil
|
19
|
-
TmpFile.with_file do |tmp|
|
20
|
-
Misc.in_dir tmp do
|
21
|
-
Log.warn "Please enter bitbucket credentials to access the asmundf/cascade repo"
|
22
|
-
`git clone #{URL}`
|
23
|
-
io = Open.open("cascade/cascade.tsv")
|
24
|
-
end
|
25
|
-
end
|
26
|
-
|
15
|
+
def self.process_interactions(file)
|
16
|
+
io = Open.open(file)
|
27
17
|
tsv = TSV.open(io, :merge => true, :header_hash => '')
|
28
18
|
|
29
19
|
new_fields = ["ENTITYB"] + (tsv.fields - ["ENTITYB"])
|
@@ -36,33 +26,19 @@ module CASCADE
|
|
36
26
|
values.collect{|v| v.scan(/\d+/) * ";;"}
|
37
27
|
end
|
38
28
|
|
39
|
-
tsv
|
29
|
+
tsv
|
40
30
|
end
|
41
31
|
|
42
|
-
|
43
|
-
|
44
|
-
TmpFile.with_file do |tmp|
|
45
|
-
Misc.in_dir tmp do
|
46
|
-
Log.warn "Please enter bitbucket credentials to access the asmundf/cascade repo"
|
47
|
-
`git clone #{URL}`
|
48
|
-
io = Open.open("cascade/cascade_translation.tsv")
|
49
|
-
end
|
50
|
-
end
|
51
|
-
|
52
|
-
tsv = TSV.open(io, :merge => true, :header_hash => '', :type => :flat, :sep2 => /[,.]\s*/)
|
53
|
-
|
32
|
+
def self.process_members(file)
|
33
|
+
TSV.open(file, :merge => true, :header_hash => '', :type => :flat, :sep2 => /[,.]\s*/)
|
54
34
|
end
|
55
35
|
|
56
|
-
|
57
|
-
|
58
|
-
tsv = CASCADE.interactions.tsv
|
59
|
-
members = CASCADE.members.tsv
|
60
|
-
|
36
|
+
def self.process_paradigm(interactions, members)
|
61
37
|
proteins = Set.new members.values.flatten.uniq
|
62
38
|
outputs = Set.new
|
63
39
|
associations = {}
|
64
40
|
|
65
|
-
|
41
|
+
interactions.through do |source, values|
|
66
42
|
values.zip_fields.each do |target,typea,ida,databasea,typeb,idb,databaseb,effect|
|
67
43
|
next if typea == 'gene'
|
68
44
|
|
@@ -129,24 +105,35 @@ module CASCADE
|
|
129
105
|
str
|
130
106
|
end
|
131
107
|
|
132
|
-
CASCADE.claim CASCADE["topology.sif"], :proc do
|
133
|
-
|
134
|
-
tsv = CASCADE.interactions.tsv
|
135
|
-
|
136
|
-
str = StringIO.new
|
137
108
|
|
138
|
-
|
139
|
-
|
140
|
-
|
141
|
-
|
142
|
-
|
109
|
+
URL = 'https://bitbucket.org/asmundf/cascade'
|
110
|
+
CASCADE.claim CASCADE.interactions, :proc do
|
111
|
+
io = nil
|
112
|
+
TmpFile.with_file do |tmp|
|
113
|
+
Misc.in_dir tmp do
|
114
|
+
Log.warn "Please enter bitbucket credentials to access the asmundf/cascade repo"
|
115
|
+
`git clone #{URL}`
|
116
|
+
process_interactions("cascade/cascade.tsv")
|
117
|
+
end
|
118
|
+
end
|
119
|
+
end
|
143
120
|
|
144
|
-
|
121
|
+
CASCADE.claim CASCADE.members, :proc do
|
122
|
+
TmpFile.with_file do |tmp|
|
123
|
+
Misc.in_dir tmp do
|
124
|
+
Log.warn "Please enter bitbucket credentials to access the asmundf/cascade repo"
|
125
|
+
`git clone #{URL}`
|
126
|
+
process_members("cascade/cascade_translation.tsv")
|
145
127
|
end
|
146
128
|
end
|
129
|
+
end
|
147
130
|
|
148
|
-
|
149
|
-
|
131
|
+
CASCADE.claim CASCADE.paradigm, :proc do
|
132
|
+
|
133
|
+
interactions = CASCADE.interactions.tsv
|
134
|
+
members = CASCADE.members.tsv
|
135
|
+
|
136
|
+
process_paradigm(interactions, members)
|
150
137
|
end
|
151
138
|
|
152
139
|
CASCADE.claim CASCADE.output_nodes, :proc do
|
@@ -173,5 +160,5 @@ iif CASCADE.interactions.produce.find if __FILE__ == $0
|
|
173
160
|
iif CASCADE.members.produce.find if __FILE__ == $0
|
174
161
|
iif CASCADE.paradigm.produce.find if __FILE__ == $0
|
175
162
|
iif CASCADE["topology.sif"].produce.find if __FILE__ == $0
|
176
|
-
iif CASCADE.output_nodes.produce
|
163
|
+
iif CASCADE.output_nodes.produce.find if __FILE__ == $0
|
177
164
|
|
data/lib/rbbt/sources/MCLP.rb
CHANGED
data/lib/rbbt/sources/go.rb
CHANGED
@@ -6,7 +6,6 @@ require 'rbbt/persist/tsv'
|
|
6
6
|
# now all it does is provide a translation form id to the actual names.
|
7
7
|
module GO
|
8
8
|
|
9
|
-
extend Resource
|
10
9
|
|
11
10
|
extend Resource
|
12
11
|
self.subdir = 'share/databases/GO'
|
@@ -270,4 +269,3 @@ if defined? Entity
|
|
270
269
|
end
|
271
270
|
end
|
272
271
|
|
273
|
-
|
@@ -32,6 +32,10 @@ $biomart_transcript = [
|
|
32
32
|
$biomart_ensembl_gene
|
33
33
|
]
|
34
34
|
|
35
|
+
$biomart_transcript_cds = [
|
36
|
+
['CDS Start','cdna_coding_start'],
|
37
|
+
]
|
38
|
+
|
35
39
|
$biomart_transcript_sequence = [
|
36
40
|
['cDNA','cdna'],
|
37
41
|
]
|
@@ -209,6 +213,12 @@ file 'transcripts' => 'gene_positions' do |t|
|
|
209
213
|
Misc.sensiblewrite(t.name, transcripts.to_s)
|
210
214
|
end
|
211
215
|
|
216
|
+
file 'transcript_cds' do |t|
|
217
|
+
cds = BioMart.tsv($biomart_db, $biomart_ensembl_transcript, $biomart_transcript_cds, [], nil, :type => :single, :namespace => Thread.current['namespace'], :cast => :to_i)
|
218
|
+
|
219
|
+
Misc.sensiblewrite(t.name, cds.to_s)
|
220
|
+
end
|
221
|
+
|
212
222
|
file 'gene_positions' do |t|
|
213
223
|
sequences = BioMart.tsv($biomart_db, $biomart_ensembl_gene, $biomart_gene_positions, [])
|
214
224
|
|
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: 3.1.33
|
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: 2019-02-20 00:00:00.000000000 Z
|
12
12
|
dependencies:
|
13
13
|
- !ruby/object:Gem::Dependency
|
14
14
|
name: rbbt-util
|