bio-gggenome 0.1.0 → 0.2.0
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- data/VERSION +1 -1
- data/bin/gggenome +73 -0
- metadata +6 -4
data/VERSION
CHANGED
@@ -1 +1 @@
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1
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-
0.
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1
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+
0.2.0
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data/bin/gggenome
ADDED
@@ -0,0 +1,73 @@
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#!/usr/env ruby
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#
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# gggenome command-line tool
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#
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help = "
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gggenome: Command-line tool for GGGenome the Ultrafast DNA search,
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http://gggenome.dbcls.jp/en/
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Usage:
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gggenome hg19 1 TTCATTGACAACATTA
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gggenome hg19 0 TTCATTGACAACATTA
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gggenome hg19 TTCATTGACAACATTA
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gggenome 1 TTCATTGACAACATTA
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gggenome TTCATTGACAACATTA
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"
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require 'rubygems'
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require 'bio-gggenome'
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case ARGV.size
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when 1
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when 2
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when 3
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else
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puts help
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exit
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end
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hits = Bio::GGGenome.search(ARGV)
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puts "database: #{hits['database']}"
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puts "summary: #{hits['summary']}"
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puts "time: #{hits['time']}"
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puts "error: #{hits['error']}"
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puts "results:"
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chr = ""
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hits['results'].each do |hit|
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if hit['name'] != chr
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chr = hit['name']
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print "\n\t#{chr.rjust(20)} : #{hit['strand']}"
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else
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print hit['strand']
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end
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end
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puts
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puts
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hits['results'].each do |hit|
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case hit['strand']
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when "+"
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snippet = hit['snippet'].sub(hits['summary'][0]['query'], hits['summary'][0]['query'].downcase)
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when "-"
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snippet = hit['snippet'].sub(hits['summary'][1]['query'], hits['summary'][1]['query'].downcase)
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end
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left = hit['position'] - hit['snippet_pos']
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right = left + hit['position_end'] - hit['position']
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snippet = hit['snippet']
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left_part = snippet[0..(left-1)]
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hit_part = snippet[left..right]
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right_part = snippet[(right+1)..hit['snippet'].size]
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snippet = left_part + hit_part.downcase + right_part
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puts [hit['name'],
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hit['strand'],
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hit['position'].to_s.rjust(13), " " * (left_part.size-17) + hit['position'].to_s.rjust(13) + " " * 4 + hit_part + " " * 4 + hit['position_end'].to_s].join("\t")
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puts ["",
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hit['strand'],
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hit['snippet_pos'].to_s.rjust(13),
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snippet,
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hit['snippet_end'].to_s.rjust(13)].join("\t")
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end
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metadata
CHANGED
@@ -1,7 +1,7 @@
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1
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--- !ruby/object:Gem::Specification
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name: bio-gggenome
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version: !ruby/object:Gem::Version
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version: 0.
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version: 0.2.0
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prerelease:
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platform: ruby
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authors:
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@@ -9,7 +9,7 @@ authors:
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autorequire:
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bindir: bin
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cert_chain: []
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-
date: 2013-08-
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date: 2013-08-13 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: rdoc
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version: '3.12'
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description: A Ruby client for GGGenome the Ultrafast sequence search
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email: mitsuteru.nakao@gmail.com
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executables:
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executables:
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- gggenome
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extensions: []
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extra_rdoc_files:
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- LICENSE.txt
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@@ -108,6 +109,7 @@ files:
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- README.rdoc
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- Rakefile
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- VERSION
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- bin/gggenome
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- lib/bio-gggenome.rb
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- lib/bio-gggenome/gggenome.rb
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- test/helper.rb
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@@ -127,7 +129,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
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version: '0'
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segments:
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- 0
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hash:
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hash: -804717082175376756
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required_rubygems_version: !ruby/object:Gem::Requirement
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none: false
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requirements:
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