rbbt-sources 3.1.46 → 3.1.47
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- checksums.yaml +4 -4
- data/etc/biomart/missing_in_archive +4 -0
- data/lib/rbbt/sources/biomart.rb +5 -0
- data/share/install/Organism/Hsa/Rakefile +1 -1
- data/share/install/Organism/Mmu/Rakefile +1 -1
- data/share/install/Organism/Rno/Rakefile +1 -1
- data/share/install/Organism/organism_helpers.rb +2 -2
- metadata +2 -2
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
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1
1
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---
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2
2
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SHA256:
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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: 6cecde427390fc444e5ef5b6bef42072bf87714b404647c6c086da92a1eaa13a
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4
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+
data.tar.gz: 673429c8eab433ec9854c81d52450f8885c57e4b3f8b6779ded44585e6f88343
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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: e39a3a6418bfb514ec786da0128f6fb8437da9728224dacd41b837300680c6d34e821f08954820cb5b7fd064546fee21fd0557d179c469eda969485ffd5cd965
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7
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+
data.tar.gz: 9f332f35fcd9c66db7506875efcc7c5276b1f588dd3b70ca299aaa2a7f25c33a650e496ba207af4e12e3bb2a6dfbc9ec8b1f0729e3acedc354145572dd268836
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data/lib/rbbt/sources/biomart.rb
CHANGED
@@ -134,11 +134,14 @@ module BioMart
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134
134
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# cause an error if the BioMart WS does not allow filtering with that
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135
135
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# attribute.
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136
136
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def self.query(database, main, attrs = nil, filters = nil, data = nil, open_options = {})
|
137
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+
IndiferentHash.setup(open_options)
|
137
138
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open_options = Misc.add_defaults open_options, :nocache => false, :filename => nil, :field_names => nil, :by_chr => false
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138
139
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filename, field_names, by_chr = Misc.process_options open_options, :filename, :field_names, :by_chr
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139
140
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attrs ||= []
|
140
141
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open_options = Misc.add_defaults open_options, :keep_empty => false, :merge => true
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141
142
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|
143
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+
IndiferentHash.setup(open_options)
|
144
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+
|
142
145
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Log.low "BioMart query: '#{main}' [#{(attrs || []) * ', '}] [#{(filters || []) * ', '}] #{open_options.inspect}"
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143
146
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144
147
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max_items = 2
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@@ -167,6 +170,7 @@ module BioMart
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167
170
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end
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168
171
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169
172
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open_options[:filename] = "BioMart[#{main}+#{attrs.length}]"
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173
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+
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170
174
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if filename.nil?
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171
175
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results = TSV.open data, open_options
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172
176
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results.key_field = main
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@@ -200,6 +204,7 @@ module BioMart
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|
200
204
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missing+=v if Organism.compare_archives(current_archive, t) == -1
|
201
205
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elsif k=~ /^>(.*)/
|
202
206
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t = $1.strip
|
207
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+
iii [current_archive, t, Organism.compare_archives(current_archive, t)]
|
203
208
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missing+=v if Organism.compare_archives(current_archive, t) == 1
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204
209
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end
|
205
210
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end
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@@ -5,7 +5,7 @@ require File.join(File.dirname(__FILE__), '../../lib/helpers')
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5
5
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6
6
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$taxs = [9606]
|
7
7
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$scientific_name = "Homo sapiens"
|
8
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-
$ortholog_key = "
|
8
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+
$ortholog_key = "hsapiens_homolog_ensembl_gene"
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9
9
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10
10
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$biomart_db = 'hsapiens_gene_ensembl'
|
11
11
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$biomart_db_germline_variation = 'hsapiens_snp'
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@@ -5,7 +5,7 @@ require File.join(File.dirname(__FILE__), '../../lib/helpers')
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5
5
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6
6
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$taxs = [10090]
|
7
7
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$scientific_name = "Mus musculus"
|
8
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-
$ortholog_key = "
|
8
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+
$ortholog_key = "mmusculus_homolog_ensembl_gene"
|
9
9
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|
10
10
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$biomart_db = 'mmusculus_gene_ensembl'
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11
11
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$biomart_db_germline_variation = 'mmusculus_snp'
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@@ -9,7 +9,7 @@ $scientific_name = "Rattus norvegicus"
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9
9
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$biomart_db = 'rnorvegicus_gene_ensembl'
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10
10
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$biomart_db_germline_variation = 'rnorvegicus_snp'
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11
11
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$biomart_db_somatic_variation = 'rnorvegicus_snp_som'
|
12
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-
$ortholog_key = "
|
12
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+
$ortholog_key = "rnorvegicus_homolog_ensembl_gene"
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13
13
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|
14
14
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$biomart_lexicon = [
|
15
15
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[ 'Associated Gene Name' , "external_gene_id"],
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@@ -547,13 +547,13 @@ end
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|
547
547
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rule /^possible_ortholog_(.*)/ do |t|
|
548
548
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other = t.name.match(/ortholog_(.*)/)[1]
|
549
549
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other_key = Organism.ortholog_key(other).produce.read
|
550
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-
BioMart.tsv($biomart_db, $biomart_ensembl_gene, [["Ortholog Ensembl Gene ID", "inter_paralog_" + other_key]], [], nil, :keep_empty => false, :type => :
|
550
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+
BioMart.tsv($biomart_db, $biomart_ensembl_gene, [["Ortholog Ensembl Gene ID", "inter_paralog_" + other_key]], [], nil, :keep_empty => false, :type => :double, :filename => t.name, :namespace => Thread.current['namespace'])
|
551
551
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end
|
552
552
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|
553
553
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rule /^ortholog_(.*)/ do |t|
|
554
554
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other = t.name.match(/ortholog_(.*)/)[1]
|
555
555
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other_key = Organism.ortholog_key(other).produce.read
|
556
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-
BioMart.tsv($biomart_db, $biomart_ensembl_gene, [["Ortholog Ensembl Gene ID", other_key]], [], nil, :keep_empty => false, :type => :
|
556
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+
BioMart.tsv($biomart_db, $biomart_ensembl_gene, [["Ortholog Ensembl Gene ID", other_key]], [], nil, :keep_empty => false, :type => :double, :filename => t.name, :namespace => Thread.current['namespace'])
|
557
557
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end
|
558
558
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559
559
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rule /[a-z]{3}[0-9]{4}\/.*/i do |t|
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metadata
CHANGED
@@ -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
|
3
3
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version: !ruby/object:Gem::Version
|
4
|
-
version: 3.1.
|
4
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+
version: 3.1.47
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5
5
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platform: ruby
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6
6
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authors:
|
7
7
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- Miguel Vazquez
|
8
8
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autorequire:
|
9
9
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bindir: bin
|
10
10
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cert_chain: []
|
11
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-
date: 2020-
|
11
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+
date: 2020-07-14 00:00:00.000000000 Z
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12
12
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dependencies:
|
13
13
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- !ruby/object:Gem::Dependency
|
14
14
|
name: rbbt-util
|