mizlab 0.1.4 → 0.1.5
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- checksums.yaml +4 -4
- data/Rakefile +20 -0
- data/lib/mizlab/version.rb +1 -1
- data/lib/mizlab.rb +46 -5
- 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:
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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: 4407f6c76b786fe0c6bdc8a70ef04bbbd721bf247cf9d96de66be8300e137dbe
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4
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+
data.tar.gz: f404ba612019c0f19f28f7da7d660c31c7eb2a53bba962f1e495be25a19fe52e
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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: adbe76a35b85afff62667f50be8913936486ad9928edb51d9ded44ab20b4c9c30ecb3a106f8b92474c998d55630d85aeebe40aa678a2c4ec0ef81c887480c181
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7
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+
data.tar.gz: dee0b71988bb5b80103984d9f81b8cba8156d3ebce89728a423ee9e3517011444e4ac1ef13cd692ebb88caa3f1f2d8e6f44e839e5a812100211ba5326014d801
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data/Rakefile
CHANGED
@@ -16,4 +16,24 @@ YARD::Rake::YardocTask.new do |t|
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16
16
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t.stats_options = ["--list-undoc"]
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17
17
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end
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18
18
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19
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+
desc "Version up"
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20
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task :versionup do
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21
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version = ""
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22
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File.open("./lib/mizlab/version.rb") do |f|
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23
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version = f.read[(/(\d+\.\d+\.\d+)/)]
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24
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end
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25
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ver, minor_ver, hotfix = version.split(".")
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26
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hotfix = hotfix.to_i + 1
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27
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new_version = "#{ver}.#{minor_ver}.#{hotfix}"
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28
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cmd = "sed -E -i 's/[0-9]+\\.[0-9]+\\.[0-9]+/#{new_version}/' ./lib/mizlab/version.rb"
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29
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puts(cmd)
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30
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system(cmd)
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31
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cmd = "git add ./lib/mizlab/version.rb && git commit -m ':rocket: Version up'"
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32
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puts(cmd)
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33
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system(cmd)
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34
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cmd = "git tag v#{new_version}"
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35
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puts(cmd)
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36
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system(cmd)
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37
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end
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38
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+
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19
39
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task default: :test
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data/lib/mizlab/version.rb
CHANGED
data/lib/mizlab.rb
CHANGED
@@ -7,22 +7,63 @@ require "stringio"
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7
7
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8
8
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module Mizlab
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9
9
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class << self
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10
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+
# Get entry as String. You can also give a block.
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11
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# @param [String/Array] accessions Accession numbers like ["NC_012920", ...].
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12
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# @return [String] Entry as string.
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13
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# @yield [String] Entry as string.
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14
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def getent(accessions, is_protein = false)
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15
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accessions = accessions.is_a?(String) ? [accessions] : accessions
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16
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accessions.each do |acc|
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17
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ret = is_protein ? fetch_protein(acc) : fetch_nucleotide(acc)
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18
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if block_given?
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19
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yield ret
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20
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else
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21
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return ret
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22
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end
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23
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sleep(0.37) # Using 0.333... seconds, sometimes hit the NCBI rate limit
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24
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end
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25
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end
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26
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+
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10
27
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# Fetch data via genbank. You can also give a block.
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11
28
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# @param [String/Array] accessions Accession numbers Like ["NC_012920", ...].
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12
29
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# @param [Bool] is_protein wheather the accession is protein. Default to true.
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13
30
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# @return [Bio::GenBank] GenBank object.
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31
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+
# @yield [Bio::GenBank] GenBank object.
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14
32
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def getobj(accessions, is_protein = false)
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15
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-
accessions
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16
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-
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17
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-
ret = is_protein ? fetch_protein(acc) : fetch_nucleotide(acc)
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18
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-
parse(ret) do |o|
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33
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+
getent(accessions, is_protein) do |entry|
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34
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parse(entry) do |o|
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19
35
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if block_given?
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20
36
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yield o
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21
37
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else
|
22
38
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return o
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23
39
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end
|
24
40
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end
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25
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-
|
41
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+
end
|
42
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end
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43
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+
|
44
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# Save object.
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45
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# @param [String] filename Filepath from executed source.
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46
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# @param [Bio::DB] obj Object which inherits from `Bio::DB`.
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47
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# @return [nil]
|
48
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def savefile(filename, obj)
|
49
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if File.exists?(filename)
|
50
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yes = Set.new(["N", "n", "no"])
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51
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no = Set.new(["Y", "y", "yes"])
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52
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loop do
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53
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print("#{filename} exists already. Overwrite? [y/n] ")
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54
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inputed = gets.rstrip
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55
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if yes.include?(inputed)
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56
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return
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57
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elsif no.include?(inputed)
|
58
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break
|
59
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end
|
60
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puts("You should input 'y' or 'n'")
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61
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+
end
|
62
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+
end
|
63
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File.open(filename, "w") do |f|
|
64
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obj.tags.each do |t|
|
65
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f.puts(obj.get(t))
|
66
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+
end
|
26
67
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end
|
27
68
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end
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28
69
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