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Revamping the module for filling gaps #126
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enhancement
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refactoring
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first version of KEGG,MNX,BiGG reconstruction of metabolites and reactions
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Added functions for adding reac / metabs per database id
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some clean up, some new docstrings, started func for fill_model
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Update funcs + tested GeneGapFiller and KEGGapFiller with fill_model
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changed missing genes and reacs to attributes instead of return values
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- Adjusted due to new db_access set up - Started writing code for mapping from BioCyc IDs to other databases for the BioCycGapFiller
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- Also added Finn Mier as author as Reihaneh's script is og from him - Renamed all missing_reacs occurences to missing_reactions to fit subclasses to parent class
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Labels
enhancement
New feature or request
help wanted
Extra attention is needed
question
Further information is requested
refactoring
changes in the code functionality
For the following reasons the module for gap-filling needs to be revamped:
extension
SPECIMEN#9) and could, thus, be combined.Todo:
GapFiller
)KEGGapFiller
,BioCycGapFiller
,GeneGapFiller
gapfill_model
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