big_simon 0.2.1 → 0.2.2
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/Gemfile.lock +1 -1
- data/exe/big_simon +2 -33
- data/lib/big_simon/runners.rb +1 -1
- data/lib/big_simon/version.rb +1 -1
- metadata +1 -1
checksums.yaml
CHANGED
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@@ -1,7 +1,7 @@
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---
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2
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SHA1:
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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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metadata.gz: 980c3ecda67dca9161c5b0c9f8585157a46305be
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4
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data.tar.gz: 26f3eee3f8758d738e8963ef514b9c555106e858
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: d4d93aeb93b23e4fb08ed1cb0a8d4b144f3ddab2d5cb521cdde25a278b779eb97431294f6f33166f16ff664cffd8bb6371194034fe4000ce1b5030c4e3641ba9
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7
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data.tar.gz: 5678b2858ebf3e586c8246aba357dc9b376494dd43d091acc4156421a54b6078612f5319b5a4c21bf641d8b84c9ce4eaf4f904be39c0adc180349adb561b2c67
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data/Gemfile.lock
CHANGED
data/exe/big_simon
CHANGED
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@@ -82,43 +82,19 @@ wish_outf = BigSimon::Runners.wish BigSimon::WISH, tmpdir_virus, tmpdir_host, tm
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vhm_outf = BigSimon::Runners.vir_host_matcher BigSimon::VHM, tmpdir_virus, tmpdir_host, tmpdir
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# TODO separate the parser from the runner for mummer.
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host_info_mummer = BigSimon::Runners.mummer BigSimon::MUMMER, tmpdir_virus, tmpdir_host, tmpdir, threads
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puts "mummer"
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pp host_info_mummer
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puts
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85
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host_info_mummer = BigSimon::Runners.mummer BigSimon::MUMMER, tmpdir_virus, tmpdir_host, tmpdir, threads, all_seq_lengths
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# TODO separate the parser from the runner for homology
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host_info_homology = BigSimon::Runners.homology tmpdir_virus, tmpdir_host, tmpdir, threads
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puts "homology"
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pp host_info_homology
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puts
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host_info_homology = BigSimon::Runners.homology tmpdir_virus, tmpdir_host, tmpdir, threads, all_seq_lengths
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host_info_wish = BigSimon::Parsers.wish wish_outf
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host_info_vhm = BigSimon::Parsers.vir_host_matcher vhm_outf
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puts "wish"
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pp host_info_wish
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puts
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puts "vhm"
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pp host_info_vhm
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puts
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host_info_simple_names = BigSimon::Pipeline.collate_host_results [host_info_wish, host_info_vhm, host_info_mummer, host_info_homology], programs
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host_info = BigSimon::Pipeline.map_taxa host_info_simple_names, name_map_virus, name_map_host
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puts
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pp host_info_simple_names
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puts
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puts
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pp host_info
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puts
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# Just a basic all info file
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# File.open all_predictions_fname, "w" do |f|
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@@ -137,8 +113,6 @@ end
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scores_files.each do |program, files|
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files.each do |name, file|
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puts "LALA 3: #{[program, name, file]} #{%w[virus host score].join}"
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file.puts %w[virus host score].join "\t"
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end
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end
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@@ -150,8 +124,6 @@ host_info.each do |virus, h1|
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h2[:scores].each do |program, score|
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lines[[virus, host, program]] = [score]
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puts "LALA: #{[virus, host, score]}"
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scores_files[program][:raw].puts [virus, host, score].join "\t"
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end
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@@ -159,9 +131,6 @@ host_info.each do |virus, h1|
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h2[:scaled_scores].each do |program, score|
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lines[[virus, host, program]] << score
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puts "LALA 2: #{[virus, host, score]}"
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scores_files[program][:scaled].puts [virus, host, score].join "\t"
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end
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data/lib/big_simon/runners.rb
CHANGED
data/lib/big_simon/version.rb
CHANGED