rbbt-sources 3.2.13 → 3.2.14
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 +6 -3
- metadata +12 -12
checksums.yaml
CHANGED
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@@ -1,7 +1,7 @@
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---
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2
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SHA256:
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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: 476a20bf7be9718acce0355dccc7f88105e168247348de1895491bbf7189b7d2
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4
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data.tar.gz: a434af060363f85fe565f9f394aa0a64acae7bf58bf98859159536c59be51a11
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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: e9f09c7a4514edaf3aabd89a5980d6be18d4761d72676da8be74625617f330b36816f66054fc6af5913ed9d94f6427391dec951307be23a2846225e1c840a813
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7
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data.tar.gz: 4b07413c9c8e8c6dd64180a1cdbb86407f81b86db8b14c63ff330a17d766b5604014f34dd3346bc6062029dd3c1dd4c1a2bdcaabb3b8cfa96434ba0170da32d6
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@@ -72,10 +72,14 @@ module Organism
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Open.mkdir File.dirname(file) unless File.directory?(file)
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url = "http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/liftOver"
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CMD.cmd_log("wget '#{url}' -O '#{file}'")
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-
CMD.cmd("chmod
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CMD.cmd("chmod 0755 '#{file}'")
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nil
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end
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CMD.tool :liftOver, Rbbt.software.opt.bin.liftOver
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+
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81
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Rbbt.set_software_env
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+
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def self.hg_build(organism)
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require 'rbbt/sources/ensembl_ftp'
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organism = organism.strip
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@@ -176,8 +180,7 @@ module Organism
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Open.write(map_file, Open.read(map_url))
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new_mutations = TmpFile.with_file do |target_bed|
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-
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CMD.cmd("#{Rbbt.software.opt.bin.liftOver.find} '#{source_bed}' '#{map_file}' '#{target_bed}' '#{unmapped_file}'").read
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CMD.cmd_log(:liftOver, "'#{source_bed}' '#{map_file}' '#{target_bed}' '#{unmapped_file}'")
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Open.read(target_bed) do |line|
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chr, position_alt, position, name = line.chomp.split("\t")
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chr.sub! /chr/, ''
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metadata
CHANGED
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@@ -1,7 +1,7 @@
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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: 3.2.
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version: 3.2.14
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platform: ruby
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authors:
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- Miguel Vazquez
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@@ -178,24 +178,24 @@ required_rubygems_version: !ruby/object:Gem::Requirement
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- !ruby/object:Gem::Version
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version: '0'
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requirements: []
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rubygems_version: 3.
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rubygems_version: 3.3.26
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signing_key:
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specification_version: 4
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summary: Data sources for the Ruby Bioinformatics Toolkit (rbbt)
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test_files:
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186
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+
- test/rbbt/sources/test_HPRD.rb
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- test/rbbt/sources/test_biomart.rb
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- test/rbbt/sources/test_entrez.rb
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- test/rbbt/sources/test_go.rb
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-
- test/rbbt/sources/
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-
- test/rbbt/sources/
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-
- test/rbbt/sources/
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- test/rbbt/sources/test_gscholar.rb
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- test/rbbt/sources/test_kegg.rb
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- test/rbbt/sources/test_matador.rb
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- test/rbbt/sources/test_organism.rb
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- test/rbbt/sources/
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- test/rbbt/sources/
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- test/rbbt/sources/test_pharmagkb.rb
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- test/rbbt/sources/test_pina.rb
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- test/rbbt/sources/test_pubmed.rb
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- test/rbbt/sources/test_stitch.rb
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- test/rbbt/sources/test_biomart.rb
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- test/rbbt/sources/test_HPRD.rb
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- test/rbbt/sources/test_string.rb
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- test/rbbt/sources/
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- test/rbbt/sources/test_synapse.rb
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- test/rbbt/sources/test_tfacts.rb
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- test/rbbt/sources/test_matador.rb
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- test/rbbt/sources/test_gscholar.rb
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- test/test_helper.rb
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