rbbt-sources 2.0.1 → 2.0.2
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data/lib/rbbt/sources/dbSNP.rb
CHANGED
@@ -9,7 +9,7 @@ module DbSNP
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9
9
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10
10
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URL = "ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/VCF/common_all.vcf.gz"
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11
11
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12
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-
DbSNP.claim DbSNP.
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12
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+
DbSNP.claim DbSNP.mutations_ncbi, :proc do
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13
13
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tsv = TSV.setup({}, :key_field => "RS ID", :fields => ["Genomic Mutation"], :type => :single)
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14
14
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file = Open.open(URL, :nocache => true)
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15
15
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while line = file.gets do
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@@ -28,8 +28,9 @@ module DbSNP
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28
28
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tsv.to_s
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29
29
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end
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30
30
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31
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-
DbSNP.claim DbSNP.
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31
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+
DbSNP.claim DbSNP.mutations, :proc do
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32
32
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ftp = Net::FTP.new('ftp.broadinstitute.org')
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33
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+
ftp.passive = true
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33
34
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ftp.login('gsapubftp-anonymous', 'devnull@nomail.org')
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34
35
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ftp.chdir('/bundle/2.3/hg19')
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35
36
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@@ -23,6 +23,7 @@ module Ensembl
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23
23
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release = Ensembl.releases[build]
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24
24
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name = Organism.scientific_name(organism)
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25
25
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ftp = Net::FTP.new(Ensembl::FTP::SERVER)
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26
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+
ftp.passive = true
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26
27
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ftp.login
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27
28
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ftp.chdir(File.join('pub', release, 'mysql'))
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28
29
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file = ftp.list(name.downcase.gsub(" ",'_') + "_core_*").collect{|l| l.split(" ").last}.last
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metadata
CHANGED
@@ -1,7 +1,7 @@
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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
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3
3
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version: !ruby/object:Gem::Version
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4
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-
version: 2.0.
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4
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+
version: 2.0.2
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5
5
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prerelease:
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6
6
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platform: ruby
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7
7
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authors:
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@@ -9,7 +9,7 @@ authors:
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9
9
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autorequire:
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10
10
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bindir: bin
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11
11
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cert_chain: []
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12
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-
date: 2013-01-
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12
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+
date: 2013-01-09 00:00:00.000000000 Z
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13
13
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dependencies:
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14
14
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- !ruby/object:Gem::Dependency
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15
15
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name: rbbt-util
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