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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1
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+
#!/usr/env ruby
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2
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#
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3
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# gggenome command-line tool
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4
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#
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5
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help = "
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6
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+
gggenome: Command-line tool for GGGenome the Ultrafast DNA search,
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7
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+
http://gggenome.dbcls.jp/en/
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8
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+
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9
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+
Usage:
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10
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gggenome hg19 1 TTCATTGACAACATTA
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11
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gggenome hg19 0 TTCATTGACAACATTA
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12
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gggenome hg19 TTCATTGACAACATTA
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13
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gggenome 1 TTCATTGACAACATTA
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14
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gggenome TTCATTGACAACATTA
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15
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16
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"
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17
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18
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require 'rubygems'
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19
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require 'bio-gggenome'
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20
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+
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21
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case ARGV.size
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22
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when 1
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23
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when 2
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24
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when 3
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25
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else
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26
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puts help
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27
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exit
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28
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end
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29
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+
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30
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hits = Bio::GGGenome.search(ARGV)
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31
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32
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puts "database: #{hits['database']}"
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33
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puts "summary: #{hits['summary']}"
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34
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puts "time: #{hits['time']}"
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35
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puts "error: #{hits['error']}"
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36
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puts "results:"
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37
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+
|
38
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chr = ""
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39
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hits['results'].each do |hit|
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40
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if hit['name'] != chr
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41
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chr = hit['name']
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42
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print "\n\t#{chr.rjust(20)} : #{hit['strand']}"
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43
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else
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44
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print hit['strand']
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45
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end
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46
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end
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47
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puts
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48
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puts
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49
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+
|
50
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hits['results'].each do |hit|
|
51
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case hit['strand']
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52
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when "+"
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53
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snippet = hit['snippet'].sub(hits['summary'][0]['query'], hits['summary'][0]['query'].downcase)
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54
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when "-"
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55
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snippet = hit['snippet'].sub(hits['summary'][1]['query'], hits['summary'][1]['query'].downcase)
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56
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end
|
57
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+
left = hit['position'] - hit['snippet_pos']
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58
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+
right = left + hit['position_end'] - hit['position']
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59
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snippet = hit['snippet']
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60
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left_part = snippet[0..(left-1)]
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61
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hit_part = snippet[left..right]
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62
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right_part = snippet[(right+1)..hit['snippet'].size]
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63
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snippet = left_part + hit_part.downcase + right_part
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64
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+
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65
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puts [hit['name'],
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66
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hit['strand'],
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67
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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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68
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puts ["",
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69
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hit['strand'],
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70
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hit['snippet_pos'].to_s.rjust(13),
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71
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snippet,
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72
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hit['snippet_end'].to_s.rjust(13)].join("\t")
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73
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end
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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: bio-gggenome
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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: 0.
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4
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+
version: 0.2.0
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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: 2013-08-
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12
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+
date: 2013-08-13 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: rdoc
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@@ -93,7 +93,8 @@ dependencies:
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93
93
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version: '3.12'
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94
94
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description: A Ruby client for GGGenome the Ultrafast sequence search
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95
95
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email: mitsuteru.nakao@gmail.com
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96
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-
executables:
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96
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+
executables:
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97
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+
- gggenome
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97
98
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extensions: []
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98
99
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extra_rdoc_files:
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99
100
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- LICENSE.txt
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@@ -108,6 +109,7 @@ files:
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108
109
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- README.rdoc
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109
110
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- Rakefile
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110
111
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- VERSION
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112
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+
- bin/gggenome
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111
113
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- lib/bio-gggenome.rb
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112
114
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- lib/bio-gggenome/gggenome.rb
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113
115
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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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127
129
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version: '0'
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128
130
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segments:
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129
131
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- 0
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130
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-
hash:
|
132
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+
hash: -804717082175376756
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131
133
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required_rubygems_version: !ruby/object:Gem::Requirement
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132
134
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none: false
|
133
135
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requirements:
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