miga-base 0.7.22.0 → 0.7.25.0

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Files changed (66) hide show
  1. checksums.yaml +4 -4
  2. data/Gemfile +3 -0
  3. data/README.md +1 -1
  4. data/Rakefile +1 -0
  5. data/lib/miga/cli/action/add.rb +10 -8
  6. data/lib/miga/cli/action/classify_wf.rb +12 -11
  7. data/lib/miga/cli/action/derep_wf.rb +3 -9
  8. data/lib/miga/cli/action/edit.rb +0 -1
  9. data/lib/miga/cli/action/find.rb +1 -1
  10. data/lib/miga/cli/action/generic.rb +1 -1
  11. data/lib/miga/cli/action/get.rb +7 -2
  12. data/lib/miga/cli/action/get_db.rb +16 -21
  13. data/lib/miga/cli/action/index_wf.rb +4 -2
  14. data/lib/miga/cli/action/init.rb +93 -144
  15. data/lib/miga/cli/action/init/daemon_helper.rb +1 -2
  16. data/lib/miga/cli/action/init/files_helper.rb +119 -0
  17. data/lib/miga/cli/action/ncbi_get.rb +1 -1
  18. data/lib/miga/cli/action/new.rb +15 -9
  19. data/lib/miga/cli/action/option.rb +44 -0
  20. data/lib/miga/cli/action/preproc_wf.rb +7 -5
  21. data/lib/miga/cli/action/quality_wf.rb +3 -3
  22. data/lib/miga/cli/action/tax_dist.rb +1 -1
  23. data/lib/miga/cli/action/tax_test.rb +1 -1
  24. data/lib/miga/cli/action/wf.rb +71 -53
  25. data/lib/miga/cli/base.rb +17 -5
  26. data/lib/miga/cli/objects_helper.rb +23 -18
  27. data/lib/miga/common.rb +4 -2
  28. data/lib/miga/common/net.rb +74 -0
  29. data/lib/miga/common/with_option.rb +83 -0
  30. data/lib/miga/common/with_result.rb +3 -2
  31. data/lib/miga/dataset/base.rb +20 -2
  32. data/lib/miga/dataset/result.rb +5 -3
  33. data/lib/miga/metadata.rb +25 -13
  34. data/lib/miga/project/base.rb +82 -2
  35. data/lib/miga/project/result.rb +4 -4
  36. data/lib/miga/remote_dataset.rb +2 -0
  37. data/lib/miga/result/stats.rb +2 -2
  38. data/lib/miga/version.rb +4 -2
  39. data/scripts/essential_genes.bash +18 -3
  40. data/scripts/miga.bash +8 -2
  41. data/scripts/mytaxa.bash +6 -5
  42. data/scripts/mytaxa_scan.bash +8 -7
  43. data/scripts/ogs.bash +2 -3
  44. data/scripts/ssu.bash +16 -2
  45. data/test/dataset_test.rb +5 -5
  46. data/test/lair_test.rb +1 -2
  47. data/test/net_test.rb +34 -0
  48. data/test/with_option_test.rb +115 -0
  49. data/utils/FastAAI/00.Libraries/01.SCG_HMMs/Archaea_SCG.hmm +41964 -0
  50. data/utils/FastAAI/00.Libraries/01.SCG_HMMs/Bacteria_SCG.hmm +32439 -0
  51. data/utils/FastAAI/00.Libraries/01.SCG_HMMs/Complete_SCG_DB.hmm +62056 -0
  52. data/utils/FastAAI/FastAAI/FastAAI +1336 -0
  53. data/utils/FastAAI/README.md +84 -0
  54. data/utils/FastAAI/kAAI_v1.0_virus.py +1296 -0
  55. data/utils/cleanup-databases.rb +2 -3
  56. data/utils/distance/base.rb +9 -0
  57. data/utils/distance/commands.rb +183 -81
  58. data/utils/distance/database.rb +69 -10
  59. data/utils/distance/pipeline.rb +15 -21
  60. data/utils/distance/runner.rb +27 -49
  61. data/utils/distance/temporal.rb +4 -2
  62. data/utils/distances.rb +2 -2
  63. data/utils/index_metadata.rb +1 -2
  64. data/utils/requirements.txt +6 -5
  65. data/utils/subclade/runner.rb +10 -11
  66. metadata +18 -6

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