refactor/feat: topUsedEnzymes, truncateValues and modifyKcats #61
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- instead of `nCols` referring to last number of columns, `cols` now contains directly which columns should have their value truncated.
- doc: explanation of input parameters - refactor: only generate table from cell array near end of function, for speed improvement and getting rid of warnings when new data was added to the table - feat: optional parameters: `writeFile` and `n` for number of top used enzymes, and now supporting `T` as command line output - feat: output table now contains additional column specifying the condition, this changes the output from before this commit
- indicated are now column indices, not number of columns
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In 2de6f02 (function topUsedEnzymes) the output variable T is not set in the script, this does not cause an error in the pipeline because the returned value is not required on its unique call (line 64 in getConstrainedModel), however this function is also useful for analyzing several flux distributions at once and therefore it might be called in different ways, out of the pipeline, by users.
Actually this is a bug that was already in the function.
- The output variable T is now set with a value (outputFile table). - The 'conditions' cell array is used for creating column names in the output table/file. - Documentation modified accordingly - Makes sure that the output size is never larger than the number of enzymes in the model. - Draw and/or exchange protein reactions are identified in the rxns field for avoiding ambiguities in the rxnNames field. - Function call changed accordingly
Merged
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topUsedEnzymesonly generate table from cell array near end of function, for speed improvement and getting rid of warnings when new data was added to the tabletopUsedEnzymesoptional parameters:writeFileandnfor number of top used enzymes, and now supportingTas command line outputtopUsedEnzymesoutput table now contains additional column specifying the condition, this changes the output from before this committruncateValuesdirectly uses column numbers: instead ofnColsreferring to last number of columns,colsnow contains directly which columns should have their value truncated.modifyKcatssupports newtruncateValuesbehaviour