bio-gggenome 0.1.0 → 0.2.0
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.
- data/VERSION +1 -1
- data/bin/gggenome +73 -0
- metadata +6 -4
data/VERSION
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
0.
|
|
1
|
+
0.2.0
|
data/bin/gggenome
ADDED
|
@@ -0,0 +1,73 @@
|
|
|
1
|
+
#!/usr/env ruby
|
|
2
|
+
#
|
|
3
|
+
# gggenome command-line tool
|
|
4
|
+
#
|
|
5
|
+
help = "
|
|
6
|
+
gggenome: Command-line tool for GGGenome the Ultrafast DNA search,
|
|
7
|
+
http://gggenome.dbcls.jp/en/
|
|
8
|
+
|
|
9
|
+
Usage:
|
|
10
|
+
gggenome hg19 1 TTCATTGACAACATTA
|
|
11
|
+
gggenome hg19 0 TTCATTGACAACATTA
|
|
12
|
+
gggenome hg19 TTCATTGACAACATTA
|
|
13
|
+
gggenome 1 TTCATTGACAACATTA
|
|
14
|
+
gggenome TTCATTGACAACATTA
|
|
15
|
+
|
|
16
|
+
"
|
|
17
|
+
|
|
18
|
+
require 'rubygems'
|
|
19
|
+
require 'bio-gggenome'
|
|
20
|
+
|
|
21
|
+
case ARGV.size
|
|
22
|
+
when 1
|
|
23
|
+
when 2
|
|
24
|
+
when 3
|
|
25
|
+
else
|
|
26
|
+
puts help
|
|
27
|
+
exit
|
|
28
|
+
end
|
|
29
|
+
|
|
30
|
+
hits = Bio::GGGenome.search(ARGV)
|
|
31
|
+
|
|
32
|
+
puts "database: #{hits['database']}"
|
|
33
|
+
puts "summary: #{hits['summary']}"
|
|
34
|
+
puts "time: #{hits['time']}"
|
|
35
|
+
puts "error: #{hits['error']}"
|
|
36
|
+
puts "results:"
|
|
37
|
+
|
|
38
|
+
chr = ""
|
|
39
|
+
hits['results'].each do |hit|
|
|
40
|
+
if hit['name'] != chr
|
|
41
|
+
chr = hit['name']
|
|
42
|
+
print "\n\t#{chr.rjust(20)} : #{hit['strand']}"
|
|
43
|
+
else
|
|
44
|
+
print hit['strand']
|
|
45
|
+
end
|
|
46
|
+
end
|
|
47
|
+
puts
|
|
48
|
+
puts
|
|
49
|
+
|
|
50
|
+
hits['results'].each do |hit|
|
|
51
|
+
case hit['strand']
|
|
52
|
+
when "+"
|
|
53
|
+
snippet = hit['snippet'].sub(hits['summary'][0]['query'], hits['summary'][0]['query'].downcase)
|
|
54
|
+
when "-"
|
|
55
|
+
snippet = hit['snippet'].sub(hits['summary'][1]['query'], hits['summary'][1]['query'].downcase)
|
|
56
|
+
end
|
|
57
|
+
left = hit['position'] - hit['snippet_pos']
|
|
58
|
+
right = left + hit['position_end'] - hit['position']
|
|
59
|
+
snippet = hit['snippet']
|
|
60
|
+
left_part = snippet[0..(left-1)]
|
|
61
|
+
hit_part = snippet[left..right]
|
|
62
|
+
right_part = snippet[(right+1)..hit['snippet'].size]
|
|
63
|
+
snippet = left_part + hit_part.downcase + right_part
|
|
64
|
+
|
|
65
|
+
puts [hit['name'],
|
|
66
|
+
hit['strand'],
|
|
67
|
+
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")
|
|
68
|
+
puts ["",
|
|
69
|
+
hit['strand'],
|
|
70
|
+
hit['snippet_pos'].to_s.rjust(13),
|
|
71
|
+
snippet,
|
|
72
|
+
hit['snippet_end'].to_s.rjust(13)].join("\t")
|
|
73
|
+
end
|
metadata
CHANGED
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
|
2
2
|
name: bio-gggenome
|
|
3
3
|
version: !ruby/object:Gem::Version
|
|
4
|
-
version: 0.
|
|
4
|
+
version: 0.2.0
|
|
5
5
|
prerelease:
|
|
6
6
|
platform: ruby
|
|
7
7
|
authors:
|
|
@@ -9,7 +9,7 @@ authors:
|
|
|
9
9
|
autorequire:
|
|
10
10
|
bindir: bin
|
|
11
11
|
cert_chain: []
|
|
12
|
-
date: 2013-08-
|
|
12
|
+
date: 2013-08-13 00:00:00.000000000 Z
|
|
13
13
|
dependencies:
|
|
14
14
|
- !ruby/object:Gem::Dependency
|
|
15
15
|
name: rdoc
|
|
@@ -93,7 +93,8 @@ dependencies:
|
|
|
93
93
|
version: '3.12'
|
|
94
94
|
description: A Ruby client for GGGenome the Ultrafast sequence search
|
|
95
95
|
email: mitsuteru.nakao@gmail.com
|
|
96
|
-
executables:
|
|
96
|
+
executables:
|
|
97
|
+
- gggenome
|
|
97
98
|
extensions: []
|
|
98
99
|
extra_rdoc_files:
|
|
99
100
|
- LICENSE.txt
|
|
@@ -108,6 +109,7 @@ files:
|
|
|
108
109
|
- README.rdoc
|
|
109
110
|
- Rakefile
|
|
110
111
|
- VERSION
|
|
112
|
+
- bin/gggenome
|
|
111
113
|
- lib/bio-gggenome.rb
|
|
112
114
|
- lib/bio-gggenome/gggenome.rb
|
|
113
115
|
- test/helper.rb
|
|
@@ -127,7 +129,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
|
|
|
127
129
|
version: '0'
|
|
128
130
|
segments:
|
|
129
131
|
- 0
|
|
130
|
-
hash:
|
|
132
|
+
hash: -804717082175376756
|
|
131
133
|
required_rubygems_version: !ruby/object:Gem::Requirement
|
|
132
134
|
none: false
|
|
133
135
|
requirements:
|