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switch to using gather exclusively, away from LCA methods. #110

Merged
merged 36 commits into from
Aug 26, 2020
Merged

switch to using gather exclusively, away from LCA methods. #110

merged 36 commits into from
Aug 26, 2020

Commits on Jun 1, 2020

  1. augment analysis of clean contigs with indication of contaminants

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Commits on Jun 8, 2020

  1. Merge branch 'master' of github.com:dib-lab/charcoal into whole_genom… 

    …e_clean
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Commits on Jun 9, 2020

  1. more/better reporting

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Commits on Jul 9, 2020

  1. Merge branch 'master' of github.com:dib-lab/charcoal into whole_genom… 

    …e_clean
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  2. don't eliminate contigs because of only a few gather matches

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Commits on Jul 11, 2020

  1. switch away from LCA for initial classify

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  2. redo clean/dirty breakdowns with gather

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  3. deal properly with no lineage at all

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    ctb committed Jul 11, 2020
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  4. do clever gather things

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Commits on Jul 12, 2020

  1. improve report.txt output

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    ctb committed Jul 12, 2020
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  2. cleanup on aisle 2

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    ctb committed Jul 12, 2020
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  3. remove unused bad_hashes

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  4. move gather_at_rank to utils

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  5. rename lca_lineage to guessed_lineage

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  6. try evaluating GTDB contamination (#122) 

    * add explicit moltype to config

* add protein conf file

* first full successful run

* add gather_scaled to do faster searches

* adjust thresholds for protein

* use search rather than gather so we can look at GTDB 25k genomes

* upd

* refactor exact removal a bit

* improve reporting

* improve reporting

* silence lineages file warnings

* add gtdb conf

* require provided lineage to remove exact match

* flag identical matches removed

* clean up reporting etc
    @ctb
    ctb authored Jul 12, 2020
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Commits on Jul 15, 2020

  1. adjust lineages to just eukaryota

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  2. sourmash 3.4, yay

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Commits on Jul 17, 2020

  1. simple post-summary script

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Commits on Aug 22, 2020

  1. Add snakemake tests that actually run snakemake (#129) 

    * initial attempt to add snakemake tests

* snakemake tests working

* add test on protein side, too
    @ctb
    ctb authored Aug 22, 2020
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Commits on Aug 23, 2020

  1. misc

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  2. Merge branch 'whole_genome_clean' of https://github.com/dib-lab/charcoal 

     into whole_genome_clean
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Commits on Aug 25, 2020

  1. Refactor whole genome gather into a multistage pipeline (#130) 

    * attempted refactor try 1

* look at many genomes at once

* tentatively working?

* start generating summaries

* do progress elimination/reporting

* add summarize rule

* add provided lin to ibd2

* output CSV

* recover comment

* add f_major and f_ident to output

* update for tara-delmont

* remove lineage split

* get protein working

* fix provided lineage bug

* fix self-matching

* fix snakemake tests

* write actual genome cleaning code

* make min_f_ident and min_f_major configurable

* swizzle f_match and f_ident rows to later; sort output by total_bad_bp

* clean up imports a bit

* 'fix' tests by commenting many of them out

* pyflakes cleanup

* refactor and cleanup

* refactor and cleanup

* refactor and cleanup

* require genus-level match rank, for now.

* eliminate match_rank as a configurable parameter

* make use of gather threshold in contig classification

* more refactoring and cleanup

* rescue contigs that still have significant matches to correct lineage
    @ctb
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  2. move contigs loading into utils

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  3. move contigs loading into utils

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    ctb committed Aug 25, 2020
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Commits on Aug 26, 2020

  1. fix mistake around 'found'

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  2. misc cleanup of Snakefile

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  3. a very simple test for contigs_search.py

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    ctb committed Aug 26, 2020
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  4. add regression test for contigs_search

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  5. add a stub makefile to run tests easily

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    ctb committed Aug 26, 2020
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  6. typo

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    ctb committed Aug 26, 2020
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  7. pyflakes cleanup

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    ctb committed Aug 26, 2020
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  8. fix tests and remove some deprecations

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    ctb committed Aug 26, 2020
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  9. tests for clean_genome; general clean up

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    ctb committed Aug 26, 2020
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  10. minor cleanup

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    ctb committed Aug 26, 2020
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  11. revamp docs a bit

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    ctb committed Aug 26, 2020
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  12. a bit more info

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    ctb committed Aug 26, 2020
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