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Gapfill update #61

Merged
merged 23 commits into from
Feb 10, 2023
Merged

Gapfill update #61

merged 23 commits into from
Feb 10, 2023

Commits on Feb 2, 2023

  1. Created analysis_biocyc.py #52

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  2. Created entities.py #52

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  3. Created gapfill.py #52

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  4. Renamed genecomp to analysis_kegg.py #52

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  5. Updated __init__.py due to module changes #52

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  6. Adjusted code in curate #52

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  7. Adjusted code in analysis_kegg #52 

    Removed a function that was generalised to work with KEGG and BioCyc and is now in gapfill.
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Commits on Feb 8, 2023

  1. Added code for function gapfill_analysis #52

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  2. Updated analysis_biocyc #52

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  3. Updated analysis_kegg due to refactoring #52

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  4. Updated entities due to refactoring #52

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  5. Added InChI-Key to metabol_db_dict in cvterms #52 #59

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  6. Created analysis_db due to refactoring #52

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  7. Created parse due to refactoring #52

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  8. Updated __init__ due to new modules #52

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  9. Updated main due to new function gapfill_analysis #52

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  10. Added bigg_models_metabolites.txt for gapfill #52

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  11. Updated config due to new function gapfill_analysis #52

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Commits on Feb 9, 2023

  1. Fixed problems in analysis_biocyc #52 

    This function runs now properly and as intended.
    @GwennyGit
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  2. Improved BiGG ID to other ID mapping #52

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  3. Changed create_gp as preparation of analysis_biocyc #52

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  4. Added column name to parse_fasta_headers result #52

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  5. Removed test outpath from main #52

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