ncbi-taxonomy 0.2.9 → 0.2.11
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/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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---
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SHA1:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 927fee0b32e8a3664ca445a6b7f17de0de265a88
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data.tar.gz: 112683d6b58e993f6a62bbd3d8901fa97a41a35d
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SHA512:
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metadata.gz:
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data.tar.gz:
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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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# Actually this software does not use this table. Therefore, this error can be ignored.
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# Later, I should fix this.
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-
class Update
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+
class Update
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def initialize
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@home_dir = Dir.home
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@work_dir = @home_dir + "/.ncbi_taxonomy"
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@@ -53,13 +53,13 @@ class Update
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end
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def download_md5
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`curl -s
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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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end
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-
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+
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def download_dump
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`curl -s
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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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end
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-
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+
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# substitute some characters
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def substitution
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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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self.load_db
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self.release
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end
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-
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+
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def load_db
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sql = <<EOF
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PRAGMA page_size=4096;
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@@ -142,7 +142,7 @@ name_class VARCHAR(255)
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CREATE TABLE nodes (
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tax_id BIGINT,
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parent_tax_id BIGINT,
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rank VARCHAR(64),
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rank VARCHAR(64),
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embl_code VARCHAR(64),
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division_id INTEGER,
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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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.import merged.dmp.trim merged
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.import names.dmp.trim names
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.import nodes.dmp.trim nodes
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-
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+
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EOF
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`echo "#{sql}" | sqlite3 #{@taxdb} < /dev/stdin`
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end
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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: ncbi-taxonomy
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version: !ruby/object:Gem::Version
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version: 0.2.
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version: 0.2.11
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platform: ruby
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authors:
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- Seok-Won Kim
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autorequire:
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bindir: bin
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cert_chain: []
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date:
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date: 2017-03-30 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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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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version: '0'
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requirements: []
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rubyforge_project:
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rubygems_version: 2.
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rubygems_version: 2.6.10
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signing_key:
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specification_version: 4
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summary: NCBI Taxonomy search using local repository
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test_files: []
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has_rdoc:
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