gene-matcher 0.1.7 → 0.1.9
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- checksums.yaml +4 -4
- data/lib/gene-matcher.rb +7 -3
- 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: 17b72e6c94dc3d82b5b48f8f1e223020ad32a83eaf2097cc728f4376365edd86
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4
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+
data.tar.gz: f4fa6a450071438398403caff25742f3164adf227cdf20586ba135516f59248c
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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: a1f1f01fae67f624e80d48b0bfc21f7e9d7372807204eac38fd4d47f599d27d4a4cf6ff425b0ebb5d7897f283768d66dca80f5deef8b5ec4c02d9af4ac6d4783
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7
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+
data.tar.gz: 1e64793c2c892d4dc7542505ae765f0849346b8776233f36ec0f4886981079dd42977ca556ad20acd0e1a0d79404163f901b6070cc02b848f1581691b9dd1a26
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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
6
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attr_reader :alignments
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7
7
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8
8
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def initialize(input_sequence, limit = 0.6)
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9
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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12
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end
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@@ -14,9 +15,12 @@ class Matcher
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15
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def scan(target_sequence,source = {})
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15
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sw = SmithWaterman.instance
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16
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a = sw.alignment(target_sequence, @input_sequence)
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17
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-
a.source = {target_sequence: target_sequence}.merge(source)
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18
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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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-
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19
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+
return if a.alignment_count == 0
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20
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+
return if a.score / a.alignment_count < @limit
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21
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+
a.source = {}.merge(source)
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22
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+
a.source[:target_sequence] = target_sequence if @reserve_target_sequence
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23
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+
@alignments += [a]
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20
24
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end
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21
25
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end
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26
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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: gene-matcher
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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: 0.1.
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4
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+
version: 0.1.9
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5
5
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platform: ruby
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6
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authors:
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7
7
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- ITO Yosei
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8
8
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autorequire:
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9
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bindir: bin
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10
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cert_chain: []
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11
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-
date: 2023-
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11
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+
date: 2023-10-03 00:00:00.000000000 Z
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12
12
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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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