mizlab 0.1.0 → 0.1.2
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- checksums.yaml +4 -4
- data/.github/workflows/deploy.yml +1 -1
- data/lib/mizlab/version.rb +1 -1
- data/lib/mizlab.rb +3 -7
- metadata +1 -1
checksums.yaml
CHANGED
@@ -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:
|
3
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-
metadata.gz:
|
4
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-
data.tar.gz:
|
3
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+
metadata.gz: df8aef7891b1d4362295bf293deeab71c0df4b1acdb7e67d7fbc79fe01a7f047
|
4
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+
data.tar.gz: 836d63375f5b57f0dee6c8b52602870e1bec91e49a0af6caa7133c588bf8298f
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5
5
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SHA512:
|
6
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-
metadata.gz:
|
7
|
-
data.tar.gz:
|
6
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+
metadata.gz: 5a27e47c4d641c989a5c3d0d744f77316cd898a4172bc96e3231cc1d7b1c8f9421cf521f1c61d4af81c42f8e4acb5498702ba61c19b51200f2bb9b0a9b3d4a94
|
7
|
+
data.tar.gz: a62744a6682e782a68e729fecc00e31d3685768acb52a4e86243037de2a07b96de1527d6b0c91378e1c0245061815c6663c311cefdf7fdd1ba17b27cdcbcd333
|
data/lib/mizlab/version.rb
CHANGED
data/lib/mizlab.rb
CHANGED
@@ -3,6 +3,7 @@
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|
3
3
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require_relative "mizlab/version"
|
4
4
|
require "set"
|
5
5
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require "bio"
|
6
|
+
require "stringio"
|
6
7
|
|
7
8
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module Mizlab
|
8
9
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class << self
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@@ -106,7 +107,7 @@ module Mizlab
|
|
106
107
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end
|
107
108
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|
108
109
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def fetch_nucleotide(accession)
|
109
|
-
return Bio::NCBI::REST::EFetch.
|
110
|
+
return Bio::NCBI::REST::EFetch.nucleotide(accession)
|
110
111
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end
|
111
112
|
|
112
113
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# get patterns from filled pixs.
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@@ -200,14 +201,9 @@ module Mizlab
|
|
200
201
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# @param [String] entries Entries as string
|
201
202
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# @yield [Object] Object that match entry format.
|
202
203
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def parse(entries)
|
203
|
-
|
204
|
-
File.open(tmp_file_name, "w") do |f|
|
205
|
-
f.puts entries
|
206
|
-
end
|
207
|
-
Bio::FlatFile.auto(tmp_file_name).each_entry do |e|
|
204
|
+
Bio::FlatFile.auto(StringIO.new(entries)).each_entry do |e|
|
208
205
|
yield e
|
209
206
|
end
|
210
|
-
File.delete(tmp_file_name)
|
211
207
|
end
|
212
208
|
end
|
213
209
|
end
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