rbbt-sources 3.0.14 → 3.0.16
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- checksums.yaml +4 -4
- data/lib/rbbt/sources/organism.rb +4 -0
- data/share/install/Organism/organism_helpers.rb +4 -3
- data/share/install/STITCH/Rakefile +2 -2
- data/share/install/STRING/Rakefile +1 -1
- data/test/rbbt/sources/test_biomart.rb +1 -1
- data/test/rbbt/sources/test_organism.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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SHA1:
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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
|
+
metadata.gz: 62838e9efa3c3cbab442302949e74407a46dbe15
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4
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+
data.tar.gz: 0c43d26fec66e78ef09d7dec5ad0d06b4502a189
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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: 72afc70a5edfe98c9bbc13efc80c3d3cde8a73167d33036cef6afa8f3afc41bc930ca3d4402308ec6545bd4ccfc9d9feb0c100967872599be1dce865f54e4022
|
7
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+
data.tar.gz: 529fec12bdfc2cdae42129659600eaa5c1bec7dc95b12d0342a633334ff25163ee2f0abf7077267db19871e3a25e28be37d8b962818dfd67410fe62310b0b6e0
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@@ -6,6 +6,10 @@ module Organism
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6
6
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self.pkgdir = "rbbt"
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7
7
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self.subdir = "share/organisms"
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8
8
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9
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+
def self.default_code(organism = "Hsa")
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10
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+
organism.split("/").first << "/feb2014"
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11
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+
end
|
12
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+
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9
13
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def self.organism_codes(organism = nil)
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10
14
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if organism
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11
15
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Rbbt.etc.allowed_biomart_archives.list.collect{|build| [organism, build] * "/" }
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@@ -540,8 +540,8 @@ file 'transcript_sequence' => ["exons", "transcript_exons"] do |t|
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540
540
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chr_transcript_ranges ||= {}
|
541
541
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transcript_strand = {}
|
542
542
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|
543
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-
|
544
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-
TSV.traverse
|
543
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+
transcript_exons = Path.setup(File.expand_path('transcript_exons'))
|
544
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+
TSV.traverse transcript_exons do |transcript,values|
|
545
545
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transcript = transcript.first if Array === transcript
|
546
546
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transcript_ranges = []
|
547
547
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@@ -572,7 +572,8 @@ file 'transcript_sequence' => ["exons", "transcript_exons"] do |t|
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572
572
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p.sub!(%r{.*/organisms/},'share/organisms/')
|
573
573
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chr_str = p.produce.read
|
574
574
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rescue Exception
|
575
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-
Log.debug("Chr #{ chr } failed (#{transcript_ranges.length} transcripts not covered)")
|
575
|
+
Log.debug("Chr #{ chr } failed (#{transcript_ranges.length} transcripts not covered): #{$!.message}")
|
576
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+
Log.exception $!
|
576
577
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next
|
577
578
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end
|
578
579
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@@ -1,7 +1,7 @@
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1
1
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require File.join(File.dirname(__FILE__),'../lib/rake_helper')
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2
2
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|
3
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-
define_source_tasks "protein_chemicals" => "http://stitch.embl.de/download/protein_chemical.links.
|
4
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-
"chemicals" => "http://stitch.embl.de/download/chemicals.
|
3
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+
define_source_tasks "protein_chemicals" => "http://stitch.embl.de/download/protein_chemical.links.v4.0.tsv.gz",
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4
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+
"chemicals" => "http://stitch.embl.de/download/chemicals.v4.0.tsv.gz"
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5
5
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|
6
6
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process_tsv :protein_chemical, 'protein_chemicals',
|
7
7
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:key => 1,
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@@ -1,6 +1,6 @@
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1
1
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require File.join(File.dirname(__FILE__),'../lib/rake_helper')
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2
2
|
|
3
|
-
define_source_tasks "protein_protein" => "http://string-db.org/newstring_download/protein.links.v9.
|
3
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+
define_source_tasks "protein_protein" => "http://string-db.org/newstring_download/protein.links.v9.1.txt.gz"
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4
4
|
|
5
5
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process_tsv :protein_protein, 'protein_protein', :grep => '9606\.ENSP', :fix => lambda{|l| l.gsub(/9606\./,'')}, :merge => true, :sep => "\s" do
|
6
6
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headers ['Ensembl Protein ID', 'Interactor Ensembl Protein ID', 'Score']
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@@ -54,7 +54,7 @@ class TestOrganism < Test::Unit::TestCase
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|
54
54
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def test_lift_over
|
55
55
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mutation_19 = "19:21131664:T"
|
56
56
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mutation_18 = "19:20923504:T"
|
57
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-
source_build = "Hsa
|
57
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+
source_build = Organism.default_code("Hsa")
|
58
58
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target_build = "Hsa/may2009"
|
59
59
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|
60
60
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assert_equal mutation_18, Organism.liftOver([mutation_19], source_build, target_build).first
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@@ -63,7 +63,7 @@ class TestOrganism < Test::Unit::TestCase
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|
63
63
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|
64
64
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def _test_orhtolog
|
65
65
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require 'rbbt/entity/gene'
|
66
|
-
assert_equal ["ENSG00000133703"], Gene.setup("Kras", "Associated Gene Name", "Mmu/jun2011").ensembl.ortholog("Hsa
|
66
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+
assert_equal ["ENSG00000133703"], Gene.setup("Kras", "Associated Gene Name", "Mmu/jun2011").ensembl.ortholog(Organism.default_code("Hsa"))
|
67
67
|
end
|
68
68
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|
69
69
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#def _test_genes_at_chromosome
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metadata
CHANGED
@@ -1,14 +1,14 @@
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1
1
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--- !ruby/object:Gem::Specification
|
2
2
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name: rbbt-sources
|
3
3
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version: !ruby/object:Gem::Version
|
4
|
-
version: 3.0.
|
4
|
+
version: 3.0.16
|
5
5
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platform: ruby
|
6
6
|
authors:
|
7
7
|
- Miguel Vazquez
|
8
8
|
autorequire:
|
9
9
|
bindir: bin
|
10
10
|
cert_chain: []
|
11
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-
date: 2014-08-
|
11
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+
date: 2014-08-26 00:00:00.000000000 Z
|
12
12
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dependencies:
|
13
13
|
- !ruby/object:Gem::Dependency
|
14
14
|
name: rbbt-util
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