Final capture replace filtering #36
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Add a command-line option to exclude "unknown protein" or "unknown sequence family" from results
Currently, phrases, i.e. sub-sets of candidate descriptions, that only consist of non-informative words are still scored and might be assigned as the final annotation. This should be changed. If the set of informative words is empty, classify the protein or sequence family as "unknown".
The new option is '-x'
- Replaced standard Rust regex with fancy-regex in capture-replace-pairs, thus allowing for (named) backreferences. - Using named backreferences multiple occurrences of the same word are replaced with the first occurrence, i.e. any subsequent occurrence is deleted.
- Polishing iteratively applies capture-replace-pairs (fancy-regex, replace instruction) to the human readable descriptions (HRDs) assigned to the queries (families or proteins) - This is used among others to remove terminal non-informative words like '[...] and', or [...] the', or '[...] or' etc. - The polishing step can be suppressed (skipped) by providing the new command line option --polish-capture-replace-pairs (-d) with "none". Use the same option to provide custom capture-replace-pairs.
- problem was mutability and iteration over mutable references...
Example polish-capture-replace-pairs file in misc.
coeit
approved these changes
Aug 10, 2022
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Added option to polish human readable descriptions (HRDs) assigned to queries (proteins or sequence families) by prot-scriber's scoring mechanism. Polishing uses capture-replace-pairs, i.e. regular expressions (fancy-regex syntax) and replace instructions to iteratively process HRDs as a last step before writing the output table. Currently this is used to delete trailing non-informative words like
[...] and,[...] or,[...] the, etc. A command line option has been added allowing to either suppress this final polishing by provision of-d noneor or allow for custom polishing capture replace pairs. Also an example file with the default has been added to./misc.Closes #26 #33 #34