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Filter HMMs update#1881

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mschecht wants to merge 28 commits intomastermerenlab/anvio:masterfrom filter-HMMs-updatemerenlab/anvio:filter-HMMs-updateCopy head branch name to clipboard

+191-84

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Commits on Jan 28, 2022

• Filter hmm hits table if it has not been done already

  mschecht

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  9042b89

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Commits on Jan 31, 2022

• adding a message to show that filter_HMMs already done

  mschecht

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  2b68b69

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• Merge branch 'master' into filter-HMMs-update

  mschecht

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  4b7302a

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• update EcoPhylo test

  mschecht

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  5683e92

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• parsing self values correctly

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  82a7d21

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Commits on Feb 2, 2022

• anvi-script-filter-hmm-hits-table records HMM domain filtering attributes

  mschecht

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  214c1c6

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• no needed

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  ecfb79c

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• updated EcoPhylo to use new contigsDB self attributes

  mschecht

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  f908ea0

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• fix

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Commits on Feb 3, 2022

• more clear

  mschecht

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  a14c999

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• remove whitespace & unused or redefined libraries

  meren

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  752b13d

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• suppress output messages

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  meren

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• the artifact name is contigs-db, not contigsDB :)

  meren

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  ae346be

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• cosmetics

  meren

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Commits on Feb 7, 2022

• should not load contigsDB before checking domtable path

  mschecht

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  21e4cef

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• fix

  mschecht

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  c04470f

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• warning to use hmmsearch with --domtblout if planning on using anvi-script-filter-hmm-hits-table

  mschecht

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  eed3714

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• sanity checks and better description of target and query coverage

  mschecht

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  3375156

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• sanity check to see if domtblout came from same HMM_source being filtered

  mschecht

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  8e2c02c

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• clear error message

  mschecht

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  99ce247

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• fix

  mschecht

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  2f69ff9

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• user may only provide one filtering parameter

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Commits on Feb 15, 2022

• better warning

  meren

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  8052c14

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• remove trailing whitespaces, contigsDBs, and unnecessary f-string

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  meren

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• make sure they are gene calls

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  3f5ea74

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• unused

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  f8d9b63

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• parameterize no_header variable

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  6f6855a

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• the DOM table we filter here HAS a header.

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  37c92d1

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