mizlab 0.1.4 → 0.1.5
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- 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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---
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SHA256:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 4407f6c76b786fe0c6bdc8a70ef04bbbd721bf247cf9d96de66be8300e137dbe
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data.tar.gz: f404ba612019c0f19f28f7da7d660c31c7eb2a53bba962f1e495be25a19fe52e
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: adbe76a35b85afff62667f50be8913936486ad9928edb51d9ded44ab20b4c9c30ecb3a106f8b92474c998d55630d85aeebe40aa678a2c4ec0ef81c887480c181
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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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t.stats_options = ["--list-undoc"]
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end
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desc "Version up"
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task :versionup do
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version = ""
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File.open("./lib/mizlab/version.rb") do |f|
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version = f.read[(/(\d+\.\d+\.\d+)/)]
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end
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ver, minor_ver, hotfix = version.split(".")
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hotfix = hotfix.to_i + 1
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new_version = "#{ver}.#{minor_ver}.#{hotfix}"
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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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puts(cmd)
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system(cmd)
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cmd = "git add ./lib/mizlab/version.rb && git commit -m ':rocket: Version up'"
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puts(cmd)
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system(cmd)
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cmd = "git tag v#{new_version}"
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puts(cmd)
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system(cmd)
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end
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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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module Mizlab
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class << self
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# Get entry as String. You can also give a block.
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# @param [String/Array] accessions Accession numbers like ["NC_012920", ...].
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# @return [String] Entry as string.
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# @yield [String] Entry as string.
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def getent(accessions, is_protein = false)
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accessions = accessions.is_a?(String) ? [accessions] : accessions
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accessions.each do |acc|
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ret = is_protein ? fetch_protein(acc) : fetch_nucleotide(acc)
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if block_given?
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yield ret
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else
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return ret
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end
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sleep(0.37) # Using 0.333... seconds, sometimes hit the NCBI rate limit
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end
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end
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# Fetch data via genbank. You can also give a block.
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# @param [String/Array] accessions Accession numbers Like ["NC_012920", ...].
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# @param [Bool] is_protein wheather the accession is protein. Default to true.
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# @return [Bio::GenBank] GenBank object.
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# @yield [Bio::GenBank] GenBank object.
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def getobj(accessions, is_protein = false)
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accessions
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ret = is_protein ? fetch_protein(acc) : fetch_nucleotide(acc)
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parse(ret) do |o|
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getent(accessions, is_protein) do |entry|
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parse(entry) do |o|
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if block_given?
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yield o
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else
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return o
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end
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end
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-
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end
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end
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# Save object.
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# @param [String] filename Filepath from executed source.
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# @param [Bio::DB] obj Object which inherits from `Bio::DB`.
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# @return [nil]
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def savefile(filename, obj)
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if File.exists?(filename)
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yes = Set.new(["N", "n", "no"])
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no = Set.new(["Y", "y", "yes"])
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loop do
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print("#{filename} exists already. Overwrite? [y/n] ")
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inputed = gets.rstrip
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if yes.include?(inputed)
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return
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elsif no.include?(inputed)
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break
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end
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puts("You should input 'y' or 'n'")
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end
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end
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File.open(filename, "w") do |f|
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obj.tags.each do |t|
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f.puts(obj.get(t))
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end
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end
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end
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