rbbt-util 5.17.73 → 5.17.74
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- checksums.yaml +4 -4
- data/share/rbbt_commands/system/optimize +82 -0
- metadata +2 -1
checksums.yaml
CHANGED
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@@ -1,7 +1,7 @@
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1
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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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3
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metadata.gz: 60cd54c17004ef80456c9a69b1c2f5f9b8c5f175
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4
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data.tar.gz: d7e91f9c4beeda66383edb73e5c1db647d30af59
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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: 69c7cbb4d618f5830df5bf91e8927712884bb83ca7f95e0179522e9c0a49e694d85de0efc6c28ed40d3faecc9f3dbc6932944bd703fdfa67faa9fb08894b6061
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7
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data.tar.gz: 27a0fdd194de5180300fe37d0b888130c23a91132ebef7c84ddd6d62954575a7f173cab3f46a984b4bd0cdbc5392ee8bf668642f9678a057870f4165af23433c
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@@ -0,0 +1,82 @@
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1
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#!/usr/bin/env ruby
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2
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3
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require 'rbbt-util'
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4
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require 'rbbt/util/simpleopt'
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5
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6
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$0 = "rbbt #{$previous_commands*""} #{ File.basename(__FILE__) }" if $previous_commands
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7
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8
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options = SOPT.setup <<EOF
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9
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10
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Optimize the files in a directory.
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11
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12
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$ rbbt system optimize [options] <directory>
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13
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14
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Compresses the chromosome files with BGZ and optimizes TokyoCabinet databases. Some files
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15
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do not compress correctly with BGZ and are left un-compressed.
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16
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17
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-h--help Print this help
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18
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-k--keep Keep original files
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19
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20
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EOF
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21
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if options[:help]
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22
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if defined? rbbt_usage
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23
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rbbt_usage
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else
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25
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puts SOPT.usage
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26
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end
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27
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exit 0
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28
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end
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29
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30
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directory = ARGV.shift
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31
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raise ParameterException, "No directory given" if directory.nil?
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32
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33
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raise ParameterException, "Not a valid directory" unless File.directory? directory
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34
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35
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directory = Path.setup directory.dup
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36
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keep = options[:keep]
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37
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38
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Log.info Log.color(:magenta, "Processing chromosomes")
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39
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chromosome_files = directory.glob('**/chromosome_*')
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40
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TSV.traverse chromosome_files, :type => :array, :bar => "Processing chromosomes" do |chr_file|
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41
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next if chr_file =~ /.bgz$/
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42
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compressed_file = chr_file + '.bgz'
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43
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Log.info "Compressing #{ chr_file } into #{ compressed_file }"
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44
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CMD.cmd("bgzip '#{ chr_file }' -c > #{ compressed_file }")
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45
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begin
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46
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Open.read(compressed_file)
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47
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if keep
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48
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Log.info "File #{ chr_file } was correctly compressed. Keeping original"
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49
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else
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50
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Log.info "File #{ chr_file } was correctly compressed. Removing original"
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51
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FileUtils.rm chr_file
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52
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end
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53
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rescue
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54
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Log.warn "File #{ chr_file } was not correctly compressed. Removing compressed version and leaving original"
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55
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FileUtils.rm compressed_file
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56
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end
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57
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end
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58
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59
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Log.info Log.color(:magenta, "Processing Tokyo Cabinet files")
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60
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61
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all_files = directory.glob('**/*')
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62
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TSV.traverse all_files, :type => :array, :bar => "Processing Tokyo Cabinet files" do |file|
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63
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cmd = 'file "' << file << '"'
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64
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file_type = CMD.cmd(cmd).read.strip.partition(/:\s+/).last
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65
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next unless file_type =~ /Tokyo/
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66
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type = file_type.split(", ")[1]
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67
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case type
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68
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when "Hash"
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69
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cmd = 'tchmgr optimize "' << file << '"'
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70
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when "B+ tree"
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71
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cmd = 'tcbmgr optimize "' << file << '"'
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else
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73
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next
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74
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end
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75
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size = File.size(file)
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76
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cmd << ' -td -tl' if size > 2_000_000_000 or file_type =~ /deflate/
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Log.info "Optimizing #{type} database #{file}"
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io = CMD.cmd(cmd)
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79
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while line = io.gets
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80
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Log.debug line
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81
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end
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82
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end
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metadata
CHANGED
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@@ -1,7 +1,7 @@
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1
1
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--- !ruby/object:Gem::Specification
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2
2
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name: rbbt-util
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3
3
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version: !ruby/object:Gem::Version
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4
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-
version: 5.17.
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4
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version: 5.17.74
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5
5
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platform: ruby
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6
6
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authors:
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7
7
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- Miguel Vazquez
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@@ -308,6 +308,7 @@ files:
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308
308
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- share/rbbt_commands/study/task
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309
309
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- share/rbbt_commands/system/clean
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310
310
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- share/rbbt_commands/system/deleted_files
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311
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- share/rbbt_commands/system/optimize
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311
312
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- share/rbbt_commands/system/purge
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312
313
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- share/rbbt_commands/system/report
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313
314
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- share/rbbt_commands/system/status
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