ncbi-taxonomy 0.2.9 → 0.2.11
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- checksums.yaml +4 -4
- data/lib/ncbi_taxonomy_update.rb +8 -8
- metadata +3 -4
checksums.yaml
CHANGED
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@@ -1,7 +1,7 @@
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1
1
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---
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2
2
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SHA1:
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3
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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: 927fee0b32e8a3664ca445a6b7f17de0de265a88
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4
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+
data.tar.gz: 112683d6b58e993f6a62bbd3d8901fa97a41a35d
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5
5
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SHA512:
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6
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-
metadata.gz:
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7
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-
data.tar.gz:
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6
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+
metadata.gz: 101f8a73f55b9294ac4b8b97cd54f0c2e0049bef2490fdfe80a966f83a6eaf6b5d2095937248416ea2ca09df4dc65e0fd3dac60cfbd0c74297f11a43942b07ed
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7
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+
data.tar.gz: 80cec6af65bb1e7c1ce32cbc11d230dcf62ade6bf8b9914bb094814286f8e8c199cc078fd084feb58da71de07fb7c6d46b23b1819331bbf5d56c0c24accd0de8
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data/lib/ncbi_taxonomy_update.rb
CHANGED
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@@ -5,7 +5,7 @@ require 'fileutils'
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5
5
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# Actually this software does not use this table. Therefore, this error can be ignored.
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6
6
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# Later, I should fix this.
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7
7
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8
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-
class Update
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8
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+
class Update
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9
9
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def initialize
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10
10
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@home_dir = Dir.home
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11
11
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@work_dir = @home_dir + "/.ncbi_taxonomy"
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@@ -53,13 +53,13 @@ class Update
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53
53
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end
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54
54
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55
55
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def download_md5
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56
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-
`curl -s
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56
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+
`curl -s https://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz.md5 > taxdump.tar.gz.md5 2>/dev/null`
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57
57
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end
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58
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-
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58
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+
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59
59
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def download_dump
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60
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-
`curl -s
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60
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+
`curl -s https://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz 2>/dev/null | tar zxf - `
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61
61
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end
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62
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-
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62
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+
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63
63
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# substitute some characters
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64
64
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def substitution
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65
65
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Dir.entries(@work_dir).each do |file|
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@@ -90,7 +90,7 @@ class Update
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90
90
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self.load_db
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91
91
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self.release
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92
92
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end
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93
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-
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93
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+
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94
94
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def load_db
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95
95
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sql = <<EOF
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96
96
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PRAGMA page_size=4096;
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@@ -142,7 +142,7 @@ name_class VARCHAR(255)
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142
142
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CREATE TABLE nodes (
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143
143
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tax_id BIGINT,
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144
144
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parent_tax_id BIGINT,
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145
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-
rank VARCHAR(64),
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145
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+
rank VARCHAR(64),
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146
146
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embl_code VARCHAR(64),
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147
147
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division_id INTEGER,
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148
148
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inherited_div_flag BOOLEAN,
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@@ -172,7 +172,7 @@ CREATE INDEX nodes_idx ON nodes(tax_id,parent_tax_id,rank,embl_code,division_id,
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172
172
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.import merged.dmp.trim merged
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173
173
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.import names.dmp.trim names
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174
174
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.import nodes.dmp.trim nodes
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175
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-
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175
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+
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176
176
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EOF
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177
177
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`echo "#{sql}" | sqlite3 #{@taxdb} < /dev/stdin`
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178
178
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end
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metadata
CHANGED
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@@ -1,14 +1,14 @@
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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: ncbi-taxonomy
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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: 0.2.
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4
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+
version: 0.2.11
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5
5
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platform: ruby
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6
6
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authors:
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7
7
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- Seok-Won Kim
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8
8
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autorequire:
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9
9
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bindir: bin
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10
10
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cert_chain: []
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11
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-
date:
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11
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+
date: 2017-03-30 00:00:00.000000000 Z
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12
12
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dependencies:
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13
13
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- !ruby/object:Gem::Dependency
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14
14
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name: sqlite3
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@@ -61,9 +61,8 @@ required_rubygems_version: !ruby/object:Gem::Requirement
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61
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version: '0'
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62
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requirements: []
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63
63
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rubyforge_project:
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64
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-
rubygems_version: 2.
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64
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+
rubygems_version: 2.6.10
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65
65
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signing_key:
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66
66
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specification_version: 4
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67
67
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summary: NCBI Taxonomy search using local repository
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68
68
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test_files: []
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69
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-
has_rdoc:
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