rbbt-sources 3.1.34 → 3.1.35
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/lib/rbbt/sources/organism.rb +16 -10
- data/share/Ensembl/release_dates +6 -0
- data/share/install/Organism/organism_helpers.rb +13 -0
- metadata +2 -2
checksums.yaml
CHANGED
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@@ -1,7 +1,7 @@
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---
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SHA1:
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-
metadata.gz:
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data.tar.gz:
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3
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metadata.gz: ff1cc882305d8bc0a5e81407d78870177f500537
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4
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data.tar.gz: 260dcaa7cb7e84de2aaf0293027fecb59712c2ba
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SHA512:
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metadata.gz:
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data.tar.gz:
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6
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metadata.gz: e63dd46454833e824492e6116b732df01166d87a89d49536d15bda6ce9bf826ef5712ed1a04a3f673a4aad1fc233089071c074fcd3cbbca5fafcf99c08c5f7e7
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7
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data.tar.gz: c57c92936d4a2afce719d488ad1d5a8e800c13e1d64e01085ca2835f288a2d208ca2e2cbc8badf432b338e38b8fdc8f25dc9b2d1d700a944a21b187950cc3bfd
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@@ -8,6 +8,7 @@ module Organism
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ARCHIVE_MONTH_INDEX = {}
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%w(jan feb mar apr may jun jul aug sep oct nov dec).each_with_index{|d,i| ARCHIVE_MONTH_INDEX[d] = i }
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11
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+
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def self.compare_archives(a1, a2)
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a1 = a1.partition("/").last if a1 and a1.include? "/"
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a2 = a2.partition("/").last if a2 and a2.include? "/"
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@@ -65,21 +66,26 @@ module Organism
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def self.hg_build(organism)
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require 'rbbt/sources/ensembl_ftp'
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69
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return 'hg19' unless organism =~ /\//
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-
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species, date = organism.split("/")
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-
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-
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case species
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when "Hsa"
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date = organism.split("/")[1]
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-
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release = Ensembl.releases[date]
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-
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-
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-
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-
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-
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release_number = release.sub(/.*-/,'').to_i
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if release_number <= 54
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'hg18'
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elsif release_number <= 75
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'hg19'
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else
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'hg38'
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end
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else
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'
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raise "Only organism 'Hsa' (Homo sapiens) supported" unless organism =~ /^Hsa/
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end
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end
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data/share/Ensembl/release_dates
CHANGED
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@@ -784,3 +784,16 @@ file 'uniprot2ensembl' => ["protein_sequence", "protein_identifiers"] do |t|
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784
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end
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785
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Misc.sensiblewrite(t.name, dumper.stream)
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786
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end
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787
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file 'gene_set' do |t|
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789
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path = File.expand_path(t.name)
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dirname = File.dirname(path)
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organism = File.basename(dirname)
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release = Ensembl.org2release(organism)
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794
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num = release.split("-").last
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795
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build_code = num.to_i > 75 ? "GRCh38" : "GRCh37"
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796
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url = "ftp://ftp.ensembl.org/pub/release-#{num}/gtf/homo_sapiens/Homo_sapiens.#{build_code}.#{num}.gtf.gz"
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797
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CMD.cmd("wget '#{url}' -O #{t.name}.gz")
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nil
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end
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metadata
CHANGED
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@@ -1,14 +1,14 @@
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1
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--- !ruby/object:Gem::Specification
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name: rbbt-sources
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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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version: 3.1.35
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platform: ruby
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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: 2019-03-
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date: 2019-03-28 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: rbbt-util
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