gene-matcher 0.1.6 → 0.1.8
Sign up to get free protection for your applications and to get access to all the features.
- checksums.yaml +4 -4
- data/lib/alignment.rb +1 -0
- data/lib/gene-matcher.rb +4 -2
- metadata +2 -2
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
|
---
|
2
2
|
SHA256:
|
3
|
-
metadata.gz:
|
4
|
-
data.tar.gz:
|
3
|
+
metadata.gz: 5771710c52d3dbbae5d62459a0dc1d8252b328efd052b0237e12e70afea7fd3a
|
4
|
+
data.tar.gz: '0548219e592497aafbe4c906bf1e516734cd491eb944a4ef42afa867c4f57a0f'
|
5
5
|
SHA512:
|
6
|
-
metadata.gz:
|
7
|
-
data.tar.gz:
|
6
|
+
metadata.gz: 83ce39ab33b72100ed8bf91e9721fe327a7c4276f6ee778d166e263f4758278b24c6ea4f2b9f6a94348461c318af21748b52c20f8f6b2042323ea17c5cfcf8c7
|
7
|
+
data.tar.gz: 882d7151d85c3e8c9f2437a4d7f29c078e643335abe1287a7991996542a30696c0fec2ead401773dc97c26b6757b22a273da5f56eae5f11365ff5e5771b99592
|
data/lib/alignment.rb
CHANGED
data/lib/gene-matcher.rb
CHANGED
@@ -2,11 +2,12 @@
|
|
2
2
|
require_relative 'smith-waterman'
|
3
3
|
|
4
4
|
class Matcher
|
5
|
-
attr_accessor :input_sequence, :limit
|
5
|
+
attr_accessor :input_sequence, :limit, :reserve_target_sequence
|
6
6
|
attr_reader :alignments
|
7
7
|
|
8
8
|
def initialize(input_sequence, limit = 0.6)
|
9
9
|
@limit = limit
|
10
|
+
@reserve_target_sequence = false
|
10
11
|
@input_sequence = input_sequence
|
11
12
|
@alignments = []
|
12
13
|
end
|
@@ -14,7 +15,8 @@ class Matcher
|
|
14
15
|
def scan(target_sequence,source = {})
|
15
16
|
sw = SmithWaterman.instance
|
16
17
|
a = sw.alignment(target_sequence, @input_sequence)
|
17
|
-
a.source = {
|
18
|
+
a.source = {}.merge(source)
|
19
|
+
a.source[:target_sequence] = target_sequence if @reserve_target_sequence
|
18
20
|
puts "#{a.score} / #{a.alignment_count} = #{a.score / a.alignment_count}" if ENV["DEBUG"]
|
19
21
|
@alignments += [a] if a.score / a.alignment_count >= @limit
|
20
22
|
end
|
metadata
CHANGED
@@ -1,14 +1,14 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: gene-matcher
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 0.1.
|
4
|
+
version: 0.1.8
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- ITO Yosei
|
8
8
|
autorequire:
|
9
9
|
bindir: bin
|
10
10
|
cert_chain: []
|
11
|
-
date: 2023-09-
|
11
|
+
date: 2023-09-12 00:00:00.000000000 Z
|
12
12
|
dependencies: []
|
13
13
|
description: Algorithm for determining similar regions between nucleic acid sequences.
|
14
14
|
email: y-itou@lumber-mill.co.jp
|