rbbt-sources 3.0.21 → 3.0.22
Sign up to get free protection for your applications and to get access to all the features.
checksums.yaml
CHANGED
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
---
|
|
2
2
|
SHA1:
|
|
3
|
-
metadata.gz:
|
|
4
|
-
data.tar.gz:
|
|
3
|
+
metadata.gz: ce778ea86eac08aeec69eb5847f7ab609cc6bb9c
|
|
4
|
+
data.tar.gz: b910f1456e958aa74afdfe5bc26a8954fddbc4d1
|
|
5
5
|
SHA512:
|
|
6
|
-
metadata.gz:
|
|
7
|
-
data.tar.gz:
|
|
6
|
+
metadata.gz: d840ef81a8c9724dedfaf8fd586622c86248a5d114897a05e351a62e8c11ceabdee61f4c40225871c99aaf0acaba1038b1dc2924abb7cb9204354e8904b4ca15
|
|
7
|
+
data.tar.gz: da941fdec542e45598b2703370eed85968d107da44aa0ef3b8c649aaaf42eb08c427150340f7d1d87c483a40ca521f239a6e0ac81fe30aa60b3337056d67e9b7
|
data/lib/rbbt/sources/biomart.rb
CHANGED
|
@@ -82,7 +82,6 @@ module BioMart
|
|
|
82
82
|
url = Thread.current['archive_url'] ? Thread.current['archive_url'] + query.gsub(/\n/,' ') : BIOMART_URL + query.gsub(/\n/,' ')
|
|
83
83
|
|
|
84
84
|
begin
|
|
85
|
-
iii open_options
|
|
86
85
|
response = Open.read(url, open_options.dup)
|
|
87
86
|
rescue
|
|
88
87
|
Open.remove_from_cache url, open_options
|
|
@@ -16,7 +16,7 @@ def first(list)
|
|
|
16
16
|
end
|
|
17
17
|
|
|
18
18
|
def process_jochem
|
|
19
|
-
jochem = Open.open("http://www.biosemantics.org/
|
|
19
|
+
jochem = Open.open("http://www.biosemantics.org/downloads/file/Jochem/JochemV1_2.zip")
|
|
20
20
|
identifiers = File.open('identifiers', 'w')
|
|
21
21
|
|
|
22
22
|
identifiers.puts("#: :namespace=JoChem")
|
|
@@ -32,6 +32,7 @@ $biomart_probe_identifiers = [
|
|
|
32
32
|
$biomart_identifiers = [
|
|
33
33
|
[ 'Entrez Gene ID', "entrezgene"],
|
|
34
34
|
[ 'Ensembl Protein ID', "ensembl_peptide_id" ],
|
|
35
|
+
[ 'MGI ID' , "mgi_id"] ,
|
|
35
36
|
[ 'Associated Gene Name', "external_gene_name" ],
|
|
36
37
|
[ 'CCDS ID', "ccds" ],
|
|
37
38
|
[ 'Protein ID', "protein_id" ],
|
|
@@ -20,7 +20,7 @@ $biomart_lexicon = [
|
|
|
20
20
|
|
|
21
21
|
$biomart_identifiers = [
|
|
22
22
|
['Entrez Gene ID', "entrezgene"],
|
|
23
|
-
['Associated Gene Name' , "
|
|
23
|
+
['Associated Gene Name' , "rgd_symbol"],
|
|
24
24
|
['Protein ID' , "protein_id"] ,
|
|
25
25
|
['UniProt/SwissProt ID' , "uniprot_swissprot"] ,
|
|
26
26
|
['UniProt/SwissProt Accession' , "uniprot_swissprot_accession"] ,
|
|
@@ -28,18 +28,17 @@ $biomart_identifiers = [
|
|
|
28
28
|
['EMBL (Genbank) ID' , "embl"] ,
|
|
29
29
|
['RGD ID' , "rgd"] ,
|
|
30
30
|
['RGD Symbol' , "rgd_symbol"] ,
|
|
31
|
-
|
|
32
|
-
['Affy
|
|
33
|
-
['Affy
|
|
34
|
-
['Affy
|
|
35
|
-
['Affy
|
|
36
|
-
['Affy
|
|
37
|
-
['Affy rg
|
|
38
|
-
['Affy rg
|
|
39
|
-
['Affy
|
|
40
|
-
['Affy
|
|
41
|
-
['
|
|
42
|
-
['Codelink ID ', "codelink"],
|
|
31
|
+
#['Affy rae230a', "affy_rae230a"],
|
|
32
|
+
#['Affy rae230b', "affy_rae230b"],
|
|
33
|
+
#['Affy RaGene', "affy_ragene_1_0_st_v1"],
|
|
34
|
+
#['Affy rat230 2', "affy_rat230_2"],
|
|
35
|
+
#['Affy RaEx', "affy_raex_1_0_st_v1"],
|
|
36
|
+
#['Affy rg u34a', "affy_rg_u34a"],
|
|
37
|
+
#['Affy rg u34b', "affy_rg_u34b"],
|
|
38
|
+
#['Affy rg u34c', "affy_rg_u34c"],
|
|
39
|
+
#['Affy rn u34', "affy_rn_u34"],
|
|
40
|
+
#['Affy rt u34', "affy_rt_u34"],
|
|
41
|
+
#['Codelink ID ', "codelink"],
|
|
43
42
|
]
|
|
44
43
|
|
|
45
44
|
$namespace = File.basename(File.dirname(File.expand_path(__FILE__)))
|
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: 3.0.
|
|
4
|
+
version: 3.0.22
|
|
5
5
|
platform: ruby
|
|
6
6
|
authors:
|
|
7
7
|
- Miguel Vazquez
|
|
8
8
|
autorequire:
|
|
9
9
|
bindir: bin
|
|
10
10
|
cert_chain: []
|
|
11
|
-
date: 2015-
|
|
11
|
+
date: 2015-02-12 00:00:00.000000000 Z
|
|
12
12
|
dependencies:
|
|
13
13
|
- !ruby/object:Gem::Dependency
|
|
14
14
|
name: rbbt-util
|