rbbt-sources 3.1.30 → 3.1.32
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- checksums.yaml +4 -4
- data/etc/xena_hubs +2 -0
- data/lib/rbbt/sources/Xena.rb +109 -0
- data/lib/rbbt/sources/organism.rb +16 -0
- data/share/install/Organism/organism_helpers.rb +3 -2
- data/test/rbbt/sources/test_organism.rb +4 -0
- metadata +4 -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
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+
metadata.gz: 0c4f4b556028ce477969e38d0b4a1d8a05b01305
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4
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data.tar.gz: 208e92cf212d96dc3333000d350e598ec45f6361
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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: 1f3e8855b0a233a6d97b80193a92fd90c45e1bfefb0f5b074a4aad2ec7151d9de1dd1c1eae842a84a9f15aeb436af4b97330845ec4ee8defe03735e65de1037f
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7
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+
data.tar.gz: a3f529915268806ac18920cfea3786ec2ab906b8492f3f8d6fd7786480a07bf1b17d6b4f5963a6175a1ff231a1697e53099fda66628e5d1fea9f7d525d7cf44e
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data/etc/xena_hubs
ADDED
@@ -0,0 +1,109 @@
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1
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+
require 'rbbt-util'
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2
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require 'rbbt/resource'
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3
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require 'rest-client'
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4
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+
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5
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module Xena
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6
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extend Resource
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7
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self.subdir = 'share/databases/Xena'
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8
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+
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9
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DEFAULT_XENA_HUB = "https://ucscpublic.xenahubs.net"
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10
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TCGA_HUB = "https://tcga.xenahubs.net/"
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11
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#def self.organism(org="Hsa")
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12
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# Organism.default_code(org)
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13
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#end
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14
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+
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15
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#self.search_paths = {}
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16
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#self.search_paths[:default] = :lib
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17
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18
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def self.query(query, hub = DEFAULT_XENA_HUB)
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19
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url = File.join(hub, 'data/')
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20
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21
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uri = URI.parse(url)
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22
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http = Net::HTTP.new(uri.host, uri.port)
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23
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http.use_ssl = true
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24
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25
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header = {'Content-Type': 'text/plain'}
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26
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request = Net::HTTP::Post.new(uri.request_uri, header)
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27
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request.body = query
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28
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response = http.request(request)
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29
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+
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30
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JSON.parse(response.body)
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31
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end
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32
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+
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33
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def self.tsv(file, hub = DEFAULT_XENA_HUB)
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34
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url = "#{hub}/download/#{file}"
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35
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TSV.open(url, :monitor => true, :header_hash => '')
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end
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37
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38
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def self.cohorts(hub = DEFAULT_XENA_HUB)
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query =<<-EOF
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40
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(;allCohorts
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41
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(fn []
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(map :cohort
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43
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(query
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{:select [[#sql/call [:distinct #sql/call [:ifnull :cohort "(unassigned)"]] :cohort]]
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:from [:dataset]})))
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)
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EOF
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self.query query, hub
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50
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end
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51
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52
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def self.cohort_dataset(cohort, hub = DEFAULT_XENA_HUB)
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53
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query =<<-EOF
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(; datasetList
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55
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(fn [cohorts]
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56
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(let [count-table {:select [[:dataset.name :dname] [:%count.value :count]]
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57
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:from [:dataset]
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:join [:field [:= :dataset.id :dataset_id]
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:code [:= :field.id :field_id]]
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:group-by [:dataset.name]
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:where [:= :field.name "sampleID"]}]
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(query {:select [:d.name :d.longtitle :count :d.type :d.datasubtype :d.probemap :d.text :d.status [:pm-dataset.text :pmtext]]
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:from [[:dataset :d]]
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:left-join [[:dataset :pm-dataset] [:= :pm-dataset.name :d.probemap]
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count-table [:= :dname :d.name]]
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:where [:in :d.cohort cohorts]})
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))
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["#{ cohort }"])
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EOF
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self.query(query, hub)
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end
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Xena.claim Xena.data, :proc do
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end
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end
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if __FILE__ == $0
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Xena.cohorts(Xena::TCGA_HUB).each do |cohort|
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puts Log.color :magenta, cohort
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Xena.cohort_dataset(cohort, Xena::TCGA_HUB).each do |info|
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puts Log.color(:blue, "Name: ") + Log.color(:yellow, info["name"].to_s)
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puts Log.color(:blue, "Title: ") + info["longtitle"].to_s
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86
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puts Log.color(:blue, "Type: ") + info["type"].to_s
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puts
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88
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end
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puts
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end
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91
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|
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raise "STOP"
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query_str =<<-EOF
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(;allCohorts
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96
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(fn []
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(map :cohort
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(query
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{:select [[#sql/call [:distinct #sql/call [:ifnull :cohort "(unassigned)"]] :cohort]]
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:from [:dataset]}))))
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EOF
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103
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Log.severity = 0
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iii Xena.query(query_str, 'https://ucscpublic.xenahubs.net/')
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105
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raise "STOP"
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106
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file = "GTEx_Analysis_v6_RNA-seq_RNA-SeQCv1.1.8_gene_rpkm_log.gz"
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107
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Log.tsv Xena.tsv(file)
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108
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end
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109
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@@ -259,4 +259,20 @@ module Organism
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259
259
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260
260
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Misc.total_length(exon_ranges)
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261
261
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end
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262
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+
|
263
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def self.chromosome_sizes(organism = Organism.default_code("Hsa"))
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264
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chromosome_sizes = {}
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265
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|
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Organism[organism].glob_all("chromosome_*").each do |file|
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267
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chromosome = file.split("_").last.split(".").first
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268
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size = if Open.gzip?(file) || Open.bgzip?(file)
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269
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CMD.cmd("zcat '#{ file }' | wc -c ").read
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else
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File.size(file)
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272
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end
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273
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chromosome_sizes[chromosome] = size.to_i
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end
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275
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|
276
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chromosome_sizes
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end
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262
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end
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@@ -573,12 +573,13 @@ end
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573
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#{{{ Special files
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require 'bio'
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575
575
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576
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-
file 'transcript_sequence' => ["exons", "transcript_exons"] do |t|
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576
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+
file 'transcript_sequence' => ["exons", "transcript_exons", "blacklist_chromosomes"] do |t|
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577
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exon_info = TSV.open('exons', :type => :list, :fields => ["Exon Strand", "Exon Chr Start", "Exon Chr End", "Chromosome Name"], :unnamed => true)
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578
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579
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chr_transcript_ranges ||= {}
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transcript_strand = {}
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581
581
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582
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blacklist_chromosomes = Path.setup(File.expand_path('blacklist_chromosomes')).list
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transcript_exons = Path.setup(File.expand_path('transcript_exons'))
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584
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TSV.traverse transcript_exons do |transcript,values|
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585
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transcript = transcript.first if Array === transcript
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@@ -604,7 +605,7 @@ file 'transcript_sequence' => ["exons", "transcript_exons"] do |t|
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604
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transcript_sequence = {}
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606
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chr_transcript_ranges.each do |chr, transcript_ranges|
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607
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begin
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607
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-
raise "LRG, GL, HG, NT, KI, and HSCHR chromosomes not supported: #{chr}" if chr
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608
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raise "LRG, GL, HG, NT, KI, and HSCHR chromosomes not supported: #{chr}" if blacklist_chromosomes.include? chr
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608
609
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p = File.expand_path("./chromosome_#{chr}")
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610
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Organism.root.annotate p
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611
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p.sub!(%r{.*/organisms/},'share/organisms/')
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@@ -66,6 +66,10 @@ class TestOrganism < Test::Unit::TestCase
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66
66
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assert_equal ["ENSG00000133703"], Gene.setup("Kras", "Associated Gene Name", "Mmu/jun2011").ensembl.ortholog(Organism.default_code("Hsa"))
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end
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68
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69
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def test_chr_sizes
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assert Organism.chromosome_sizes["2"].to_i > 10_000_000
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end
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72
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#def test_genes_at_chromosome
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# pos = [12, 117799500]
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# assert_equal "ENSG00000089250", Organism::Hsa.genes_at_chromosome_positions(pos.first, pos.last)
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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
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4
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-
version: 3.1.
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4
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+
version: 3.1.32
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5
5
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platform: ruby
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6
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authors:
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- Miguel Vazquez
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autorequire:
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bindir: bin
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cert_chain: []
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-
date: 2018-
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+
date: 2018-08-03 00:00:00.000000000 Z
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dependencies:
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13
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- !ruby/object:Gem::Dependency
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14
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name: rbbt-util
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@@ -89,6 +89,7 @@ files:
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- etc/allowed_biomart_archives
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- etc/biomart/missing_in_archive
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- etc/organisms
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- etc/xena_hubs
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92
93
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- lib/rbbt/sources/CASCADE.rb
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93
94
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- lib/rbbt/sources/COREAD_phospho_proteome.rb
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95
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- lib/rbbt/sources/COSTART.rb
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@@ -101,6 +102,7 @@ files:
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- lib/rbbt/sources/PRO.rb
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- lib/rbbt/sources/PSI_MI.rb
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104
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- lib/rbbt/sources/STITCH.rb
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105
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- lib/rbbt/sources/Xena.rb
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104
106
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- lib/rbbt/sources/array_express.rb
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105
107
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- lib/rbbt/sources/barcode.rb
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106
108
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- lib/rbbt/sources/bibtex.rb
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