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Issue #123: Add anib #338

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Issue #123: Add anib #338

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Commits on Jul 15, 2021

  1. Initial split of v2 ANIb code into anib.py and aniblastall.py files 

    Including changing the parameter `mode` to `method`
    @baileythegreen
    baileythegreen committed Jul 15, 2021
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Commits on Jul 21, 2021

  1. Updated comments/logging

    @baileythegreen
    baileythegreen committed Jul 21, 2021
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  2. Added sysexit when adding genomes to the database fails

    @baileythegreen
    baileythegreen committed Jul 21, 2021
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  3. Added initial versions of functions and comments about needed code 

    `run_anib_jobs()`, `update_comparison_results()`
    @baileythegreen
    baileythegreen committed Jul 21, 2021
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  4. Rename fraglens to fragsizes for consistency with anib.py

    @baileythegreen
    baileythegreen committed Jul 21, 2021
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Commits on Sep 13, 2021

  1. Add add_blastdb() to pyani_orm.py

    @baileythegreen
    baileythegreen committed Sep 13, 2021
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  2. Change default for maxmatch from None to False 

    If this is not a boolean, it prevents sqlite from recognising duplicate 
entries
    @baileythegreen
    baileythegreen committed Sep 13, 2021
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  3. Add/expand code to process input genomes 

    Up to adding them to the database
    @baileythegreen
    baileythegreen committed Sep 13, 2021
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  4. Split genome files into contiguous fragments

    @baileythegreen
    baileythegreen committed Sep 13, 2021
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  5. Implement generate_joblist()

    @baileythegreen
    baileythegreen committed Sep 13, 2021
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  6. Implement run_anib_jobs()

    @baileythegreen
    baileythegreen committed Sep 13, 2021
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  7. Implement update_comparisons_results() and commit to database

    @baileythegreen
    baileythegreen committed Sep 13, 2021
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  8. Update call to generate_joblist() 

    Now passes the lists of all `fragfiles` and `fraglens`
    @baileythegreen
    baileythegreen committed Sep 13, 2021
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  9. Update name of output file in fragment_fasta_file()

    @baileythegreen
    baileythegreen committed Sep 13, 2021
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  10. Update value passed for maxmatch to a boolean 

    Necessary for sqlite to recognise duplicate values
    @baileythegreen
    baileythegreen committed Sep 13, 2021
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  11. Implement remainder of subcmd_anib()

    @baileythegreen
    baileythegreen committed Sep 13, 2021
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  12. Add a commented question

    @baileythegreen
    baileythegreen committed Sep 13, 2021
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  13. Alter generate_blastn_commands() to only take one query/subject pair

    @baileythegreen
    baileythegreen committed Sep 13, 2021
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  14. Alter construct_blastn_cmdline() for a single query/subject pair

    @baileythegreen
    baileythegreen committed Sep 13, 2021
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  15. Remove method parameter from process_blast() call

    @baileythegreen
    baileythegreen committed Sep 13, 2021
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  16. Change outfilename in `construct_makeblastdb_cmd() 

    `
    @baileythegreen
    baileythegreen committed Sep 13, 2021
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  17. Move aniblastall-specific tests to test_aniblastall.py

    @baileythegreen
    baileythegreen committed Sep 13, 2021
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  18. Change call to parse_blast_tab() to not use method parameter

    @baileythegreen
    baileythegreen committed Sep 13, 2021
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  19. Skip tests as a result of changes to how command lines are generated 

    Currently, we don't pass a list of genome pairs to `anib.py`.
    @baileythegreen
    baileythegreen committed Sep 13, 2021
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  20. Add get_version() tests and boilerplate

    @baileythegreen
    baileythegreen committed Sep 13, 2021
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  21. Merge branch 'master' of https://github.com/widdowquinn/pyani into an… 

    …ib_123
    @baileythegreen
    baileythegreen committed Sep 13, 2021
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Commits on Sep 14, 2021

  1. Make changes to reflect splitting of anib and aniblastall 

    - remove `mode` or `method` arguments in function calls/definitions
- change references to module names from `anib` to `aniblastall` where 
necessary
    @baileythegreen
    baileythegreen committed Sep 14, 2021
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Commits on Sep 21, 2021

  1. Add tests for get_version() 

    These got removed somewhere?
    @baileythegreen
    baileythegreen committed Sep 21, 2021
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Commits on Sep 22, 2021

  1. Fixed typos and put one variable name in camelcase

    @baileythegreen
    baileythegreen committed Sep 22, 2021
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  2. Fix which file is passed as input and which as blastdb

    @baileythegreen
    baileythegreen committed Sep 22, 2021
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  3. Move serialisation of fragment dictionary to primary function

    @baileythegreen
    baileythegreen committed Sep 22, 2021
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  4. Added useful debugging lines to anib.py 

    May be removed later on
    @baileythegreen
    baileythegreen committed Sep 22, 2021
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  5. Add long versions of CLI flags to anib_parser.py

    @baileythegreen
    baileythegreen committed Sep 22, 2021
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  6. Comment out (likely) unnecessary function 

    Will be removed later
    @baileythegreen
    baileythegreen committed Sep 22, 2021
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  7. Update docstrings to reflect new comparison handling

    @baileythegreen
    baileythegreen committed Sep 22, 2021
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  8. Add useful debugging lines 

    May be removed later
    @baileythegreen
    baileythegreen committed Sep 22, 2021
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  9. Populate aniblastall_parser.py

    @baileythegreen
    baileythegreen committed Sep 22, 2021
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  10. Comment out (likely) unnecessary function 

    Will be removed later
    @baileythegreen
    baileythegreen committed Sep 22, 2021
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  11. Simplify generation of command lines and update supporting docstrings

    @baileythegreen
    baileythegreen committed Sep 22, 2021
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  12. Update command name referenced in docstrings

    @baileythegreen
    baileythegreen committed Sep 22, 2021
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  13. Fix which files are passed as input and blastdb in command generation

    @baileythegreen
    baileythegreen committed Sep 22, 2021
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  14. Add useful debugging lines 

    May be removed later
    @baileythegreen
    baileythegreen committed Sep 22, 2021
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  15. Add imports and convenience struct for ComparisonJob

    @baileythegreen
    baileythegreen committed Sep 22, 2021
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  16. Add initial code for starting a run and adding it to the database

    @baileythegreen
    baileythegreen committed Sep 22, 2021
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  17. Add genomes for the ru to the database

    @baileythegreen
    baileythegreen committed Sep 22, 2021
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  18. Get genomes for the run and create output directories

    @baileythegreen
    baileythegreen committed Sep 22, 2021
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  19. Add code to fragment fasta files

    @baileythegreen
    baileythegreen committed Sep 22, 2021
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  20. Add code to create blastdb

    @baileythegreen
    baileythegreen committed Sep 22, 2021
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  21. Add code to generate list of comparisons and filter existing ones

    @baileythegreen
    baileythegreen committed Sep 22, 2021
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  22. Add code for case where all comparisons have been run already

    @baileythegreen
    baileythegreen committed Sep 22, 2021
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  23. Add code for recovery mode

    @baileythegreen
    baileythegreen committed Sep 22, 2021
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  24. Rename blastcmd to blastallcmd

    @baileythegreen
    baileythegreen committed Sep 22, 2021
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  25. Add generate_joblist()

    @baileythegreen
    baileythegreen committed Sep 22, 2021
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  26. Add code to generate joblist

    @baileythegreen
    baileythegreen committed Sep 22, 2021
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  27. Add code to run comparisons

    @baileythegreen
    baileythegreen committed Sep 22, 2021
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  28. Add code to update database

    @baileythegreen
    baileythegreen committed Sep 22, 2021
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  29. Remove or rename things specific to anib to aniblastall

    @baileythegreen
    baileythegreen committed Sep 22, 2021
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  30. Skip unnecessary tests 

    Will probably be removed
    @baileythegreen
    baileythegreen committed Sep 22, 2021
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  31. Add dir_aniblastall_in() fixture

    @baileythegreen
    baileythegreen committed Sep 22, 2021
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Commits on Sep 30, 2021

  1. Add lines debugging 

    May be removed later
    @baileythegreen
    baileythegreen committed Sep 30, 2021
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Commits on Oct 5, 2021

  1. Fix naming of elements in `test_subcmd_anib" namespace

    @baileythegreen
    baileythegreen committed Oct 5, 2021
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  2. Update naming of TestANIbSubcommand()

    @baileythegreen
    baileythegreen committed Oct 5, 2021
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  3. Switch to use NamedTuple

    @baileythegreen
    baileythegreen committed Oct 5, 2021
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  4. Add test_subcmd_10_aniblastall.py

    @baileythegreen
    baileythegreen committed Oct 5, 2021
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  5. Make test_subcmd_04_anim.py match other method subcommand tests

    @baileythegreen
    baileythegreen committed Oct 5, 2021
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  6. Fix names of executable variables

    @baileythegreen
    baileythegreen committed Oct 5, 2021
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Commits on Oct 7, 2021

  1. Pass both stdout and stderr to the regex version search

    @baileythegreen
    baileythegreen committed Oct 7, 2021
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  2. Set indir and outdir to required in anib_parser.py

    @baileythegreen
    baileythegreen committed Oct 7, 2021
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  3. Add docs/subcmd_anib.rst

    @baileythegreen
    baileythegreen committed Oct 7, 2021
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  4. Add documentation for aniblastall

    @baileythegreen
    baileythegreen committed Oct 7, 2021
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Commits on Dec 12, 2021

  1. Merge branch 'master' of https://github.com/widdowquinn/pyani into an… 

    …ib_123
    @baileythegreen
    baileythegreen committed Dec 12, 2021
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  2. Replace f-strings in logging statements

    @baileythegreen
    baileythegreen committed Dec 12, 2021
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Commits on Apr 13, 2022

  1. Update .gitignore

    @baileythegreen
    baileythegreen committed Apr 13, 2022
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  2. Merge branch 'master' of https://github.com/widdowquinn/pyani into an… 

    …ib_123
    @baileythegreen
    baileythegreen committed Apr 13, 2022
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  3. Update call to add_run() to fit the function's new return value

    @baileythegreen
    baileythegreen committed Apr 13, 2022
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  4. Remove f-strings from logging calls

    @baileythegreen
    baileythegreen committed Apr 13, 2022
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Commits on May 11, 2022

  1. Merge branch 'master' of https://github.com/widdowquinn/pyani into an… 

    …ib_123
    @baileythegreen
    baileythegreen committed May 11, 2022
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Commits on May 16, 2022

  1. Merge branch 'master' of https://github.com/widdowquinn/pyani into an… 

    …ib_123
    @baileythegreen
    baileythegreen committed May 16, 2022
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Commits on Jun 7, 2022

  1. update deprecated behaviours in pandas 

    - the sort_index() call now needs axis as an explicit keyword
- pandas.utils.testing is now pandas.testing
    @widdowquinn
    widdowquinn committed Jun 7, 2022
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  2. remove unused import 

    If an import is no longer required, it should be removed, rather
than commented as "probably not required" or similar.
    @widdowquinn
    widdowquinn committed Jun 7, 2022
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Commits on Jun 16, 2022

  1. Merge branch 'master' of https://github.com/widdowquinn/pyani into an… 

    …ib_123
    @baileythegreen
    baileythegreen committed Jun 16, 2022
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