gene-matcher 0.1.6 → 0.1.8
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- checksums.yaml +4 -4
- data/lib/alignment.rb +1 -0
- data/lib/gene-matcher.rb +4 -2
- metadata +2 -2
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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SHA256:
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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: 5771710c52d3dbbae5d62459a0dc1d8252b328efd052b0237e12e70afea7fd3a
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4
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+
data.tar.gz: '0548219e592497aafbe4c906bf1e516734cd491eb944a4ef42afa867c4f57a0f'
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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: 83ce39ab33b72100ed8bf91e9721fe327a7c4276f6ee778d166e263f4758278b24c6ea4f2b9f6a94348461c318af21748b52c20f8f6b2042323ea17c5cfcf8c7
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7
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+
data.tar.gz: 882d7151d85c3e8c9f2437a4d7f29c078e643335abe1287a7991996542a30696c0fec2ead401773dc97c26b6757b22a273da5f56eae5f11365ff5e5771b99592
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data/lib/alignment.rb
CHANGED
data/lib/gene-matcher.rb
CHANGED
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@@ -2,11 +2,12 @@
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2
2
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require_relative 'smith-waterman'
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3
3
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4
4
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class Matcher
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5
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-
attr_accessor :input_sequence, :limit
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5
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+
attr_accessor :input_sequence, :limit, :reserve_target_sequence
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6
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attr_reader :alignments
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7
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def initialize(input_sequence, limit = 0.6)
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9
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@limit = limit
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10
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+
@reserve_target_sequence = false
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10
11
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@input_sequence = input_sequence
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11
12
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@alignments = []
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end
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@@ -14,7 +15,8 @@ class Matcher
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15
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def scan(target_sequence,source = {})
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sw = SmithWaterman.instance
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a = sw.alignment(target_sequence, @input_sequence)
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17
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-
a.source = {
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18
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+
a.source = {}.merge(source)
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19
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+
a.source[:target_sequence] = target_sequence if @reserve_target_sequence
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puts "#{a.score} / #{a.alignment_count} = #{a.score / a.alignment_count}" if ENV["DEBUG"]
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19
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@alignments += [a] if a.score / a.alignment_count >= @limit
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20
22
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end
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metadata
CHANGED
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@@ -1,14 +1,14 @@
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1
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--- !ruby/object:Gem::Specification
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name: gene-matcher
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version: !ruby/object:Gem::Version
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4
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-
version: 0.1.
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4
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+
version: 0.1.8
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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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- ITO Yosei
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8
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autorequire:
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bindir: bin
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cert_chain: []
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11
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-
date: 2023-09-
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11
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+
date: 2023-09-12 00:00:00.000000000 Z
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dependencies: []
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description: Algorithm for determining similar regions between nucleic acid sequences.
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email: y-itou@lumber-mill.co.jp
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