Code

Update parsers#77

Code

Merged

fmaguire merged 35 commits intomasterpha4ge/hAMRonization:masterfrom update_parserspha4ge/hAMRonization:update_parsersCopy head branch name to clipboardAug 21, 2022

+1,265-1,277

Commits

Commits on Jun 2, 2021

• add schema as csv

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  f92768d

Commits on Jan 18, 2022

• update schema #27 #65

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  ccc05ab

• add versioning to schema (date in iso 8601 format)

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  b799d60

Commits on May 13, 2022

• Merge branch 'master' into update_schema

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• Update AMR gene & Variant specification - version 2022-05-13T15:07:33.790091

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  9fcc780

• update hAMRonizedResult class with AMR gene & Variant specification - version 2022-05-13T15:07:33.79

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  b554b10

• Update hAMRonizedResult.py

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• update abricate (and sanity test)

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  bc74a1d

Commits on May 16, 2022

• update amrfinder (and sanity test)

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  5b73fcc

• update amrplusplus (and sanity test)

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  a3b1fb5

• update ariba (and sanity test)

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  7993618

• update kmerresistance (and sanity tests)

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  a668793

• update resfinder (and sanity tests)

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  47b1922

• update resfinder 4 (and sanity tests)

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  d8caa26

• drop .py from software name

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  c1d2d4f

• Update test_sanity.py

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  711f9cb

• update RGI (and sanity tests)

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  1035acd

• update srax (and sanity tests)

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  8c846a1

• update groot (and sanity tests)

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  cedacb3

• update deeparg

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• update srst2

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  324f21d

• start tbprofiler (not working)

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  5e6ee3d

• Update StarAmrIO.py

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  e455be7

• Update MykrobeIO.py

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• Update ResFamsIO.py

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  465b11e

Commits on Jun 2, 2022

• fix mutation examples (aa and nt)

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  c24f6c7

• Merge branch 'update_schema' into update_parsers

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  2f571f5

Commits on Aug 17, 2022

• Add mutational parsing for AMRFinderPlus #70

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  fb977c2

• Fix tests, deprecate resfinder <4, convert genetic_variation_type to use constants

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  4352585

Commits on Aug 20, 2022

• Add pointfinder parser and tests

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  c3713c9

• Add RGI parsing for variants in main mode #70

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  c74a1b7

• Add Ariba variant parsing for #70

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  bc81a3d

Commits on Aug 21, 2022

• Add staramr variant and sanity #70

  fmaguire

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  4c502a7

• Add resfams sanity test

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  daee621

• Remove extraneous print in Ariba

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  ad6f193