Code

Add Dayhoff encoding of amino acids#689

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Merged

luizirber merged 53 commits intosourmash-bio:mastersourmash-bio/sourmash:masterfrom czbiohub-sf:olgabot/dayhoffCopy head branch name to clipboardAug 26, 2019

+509-47

Commits

Commits on Jun 29, 2019

• Initial commit of dayhoff encoding

  olgabot

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  df1d637

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• Pad end of codon with ambiguous nucleotides

  olgabot

  committed
  602a395

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• Add ambiguous bases

  olgabot

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  dc379fa

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• Add dayhoff encoding

  olgabot

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  482f4d2

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• Add more checks of dayhoff type

  olgabot

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  9885571

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Commits on Jun 30, 2019

• hopefully fix tests to get the Cpp to build

  olgabot

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  1ca5bfe

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Commits on Jul 1, 2019

• --no-protein --> --no-dayhoff

  olgabot

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  4c992e6

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• set dayhoff to default to false

  olgabot

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  fc28322

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• Add dayhoff to construct_moltype_args

  olgabot

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  c4a7a08

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• track_abundance is now 6th parameter instead of 5th

  olgabot

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  0bbaa67

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• "scaled" is now 7th parameter

  olgabot

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  2544000

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• use 'dayhoff' as molecule name

  olgabot

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  d1e7328

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• Actually compute a dayhoff signature

  olgabot

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  119eed8

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• Add simple test for computing dayhoff

  olgabot

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  5668449

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• Set dayhoff as molecule type when writing

  olgabot

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  7867b26

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• don't compute dna signature for simplicity

  olgabot

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  588f5d1

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• Check if dayhoff is set if protein is set

  olgabot

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  7d714df

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• Test for dna + dayhoff

  olgabot

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  dbaf9a3

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• Fix logic of obtaining molecule type

  olgabot

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  6e8b370

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• Add test for molecule type

  olgabot

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  189ac42

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Commits on Jul 4, 2019

• Add dayhoff test for sourmash sig describe

  olgabot

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  559b6a4

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Commits on Jul 7, 2019

• Merge branch 'master' into olgabot/dayhoff

  olgabot

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  2cd1fcc

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• fix segfault in linux

  luizirber

  committed
  c485ce0

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Commits on Jul 9, 2019

• Merge pull request #3 from luizirber/olgabot/dayhoff

  Show description for d4ab126
  olgabot

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  d4ab126

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• Add args.dayhoff to add_sequence

  olgabot

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  61136df

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• Use class's value of dayhoff

  olgabot

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  6ea480d

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• Try to add dayhoff option for when input is protein

  olgabot

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  c38eb64

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• Don't need to pass dayhoff=True to add_sequence

  olgabot

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  e5e6aa9

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• Add dayhoff fixture for testing

  olgabot

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  3f8b89a

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• Add low level tests of dayhoff hashes

  olgabot

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  44e9d33

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• Both signatures need to be dayhoff to be comparable

  olgabot

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  463c9ff

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• Use class's value of dayhoff variable to drive logic

  olgabot

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  bb90f77

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• Don't pass dayhoff to add_sequence

  olgabot

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  0d82ce2

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• Add nonworking test to make sure dayhoff and protein hashes are distinct

  olgabot

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  c0ff22b

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• Add public method of converting amino acid letter to dayhoff

  olgabot

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  5b4f16b

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• Add 'for' to list comprehension

  olgabot

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  1bcd1ae

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• Remove dayhoff boolean from add_sequence

  olgabot

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  3ded344

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• aa_to_dayhoff as const?!?

  olgabot

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  7de2b42

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• Maybe need to instantiate the return string first??

  olgabot

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  e2bc460

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• Don't do list comprehension for now for debugging purposes

  olgabot

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  3f6403a

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Commits on Jul 11, 2019

• Now KmerMinHash actually has aa_to_dayhoff method

  olgabot

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Commits on Jul 15, 2019

• Convert python string to bytes to input to aa_to_dayhoff

  olgabot

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  e338dc5

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• aa_to_dayhoff returns type 'string'

  olgabot

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  1dc49fa

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• Allow for int as input to to_bytes and convert to bytes properly

  olgabot

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  c3e5004

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• Add option to run only tests using a particular fixture

  olgabot

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  89e0cf3

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• Fix test output for 'sig describe' so dayhoff md5 != protein md5

  olgabot

  committed
  aae410b

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• Add json_iter test for molecule types

  olgabot

  committed
  4c07abb

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• Add check for dayhoff signature output

  olgabot

  committed
  2d1681b

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Commits on Jul 23, 2019

• Reorganized amino acid translation and dayhoff encoding

  olgabot

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• check for message in stderr, not stdout

  olgabot

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  34f81db

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Commits on Jul 24, 2019

• Expose translate_codon method for testing

  olgabot

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  a5626a4

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Commits on Aug 24, 2019

• Merge branch 'master' into olgabot/dayhoff

  luizirber

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  4db8a1f

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Commits on Aug 26, 2019

• Merge branch 'master' into olgabot/dayhoff

  luizirber

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