rbbt-util 5.19.7 → 5.19.8
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/etc/app.d/finder.rb +3 -0
- data/lib/rbbt/util/R/plot.rb +1 -0
- data/share/rbbt_commands/tsv/attach +9 -2
- 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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metadata.gz: 70a20a4985413f36348028410a914cb78fbf4795
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data.tar.gz: 52aef24051104d8a63c3c84839abb479964d1b08
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 7b45d1c76971f7450d105ac1a817f0bcc87d3dbbec0427de52921844b8ea485bda96c2eed28f3bcebb056e57165c3f66cdb6577ec8f9bd4d8e9944d0a6dd9100
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7
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data.tar.gz: 60203a5f62caf8993bb33e58e4720efa941307b791d1ca6be05cf67a63913d2f27e27d7ff1a584e2d60b288565151b8c2568325636cef551a289d77501cdb47f
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data/etc/app.d/finder.rb
CHANGED
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@@ -17,6 +17,9 @@ if ENV['RBBT_FINDER']
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organism_hash = {"organism" => /[A-Z][a-z]{2}(?:\/[a-z]{3}20\d\d)?/}
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finder.add_instance(organism_hash, :namespace => organism)
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+
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snp_hash = {"SNP" => /^rs\d+$/}
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finder.add_instance(snp_hash, :namespace => organism)
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end
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set :finder, finder
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Log.debug("Finder started with: #{finder.instances.length} instances")
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data/lib/rbbt/util/R/plot.rb
CHANGED
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@@ -14,6 +14,7 @@ $ rbbt tsv attach <file1> <file2> [<file3> ...] [options]
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Use - to read from STDIN
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-f--fields* Fields to attach (all if not specified)
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-i--identifiers* Identifier file
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-h--help Print this help
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EOF
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@@ -28,15 +29,21 @@ end
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file1, *rest = ARGV
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fields = options[:fields]
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identifiers = options[:identifiers]
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if identifiers.nil?
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require 'rbbt/sources/organism'
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Organism.identifiers(Organism.default_code("Hsa"))
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end
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fields = fields ? fields.split(/[,|]/).collect{|f| f.strip} : nil
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tsv = TSV.open(file1)
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tsv = TSV.open(file1, :unnamed => true)
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rest.each do |file2|
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file_fields = TSV.parse_header(file2).all_fields - tsv.all_fields
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these_fields = fields ? fields & file_fields : nil
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tsv = tsv.attach file2, :fields => these_fields
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tsv = tsv.attach file2, :fields => these_fields, :identifiers => identifiers
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end
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puts tsv.to_s
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metadata
CHANGED
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@@ -1,14 +1,14 @@
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--- !ruby/object:Gem::Specification
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name: rbbt-util
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version: !ruby/object:Gem::Version
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version: 5.19.
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version: 5.19.8
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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: 2015-
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date: 2015-12-14 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: rake
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