Fix "what SYMBOL" issue #10
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
kthurimella
approved these changes
Feb 16, 2023
|
|
||
| NOT_CAPTURED_PATHWAY_FIELDS = ('GENE', 'ORGANISM', 'REFERENCE', 'AUTHORS', 'TITLE', 'JOURNAL') | ||
| NOT_CAPTURED_PATHWAY_FIELDS = ('GENE', 'ORGANISM', 'REFERENCE', 'AUTHORS', 'TITLE', 'JOURNAL', 'INCLUDING') |
There was a problem hiding this comment.
This makes sense and it looks like it must have been added afterwards. I'm wondering if there is a case where we can capture fields that may get added, but we don't update the not captured fields, just to keep a bit less of a dependency on keeping up with KEGG fields.
There was a problem hiding this comment.
I agree. Hopefully we can discuss ways to do this during our next code review! @JTFouquier @bsantan @acolorado1 @albatalavera @jboconnor13 (tagging you all so we can discuss at some point)
There was a problem hiding this comment.
Didn't have a chance to specifically discuss a better fix, but did decide to go ahead and merge.
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
parse_ko()has been raising an error for my use (through AMON, consistent with AMON issue #13. When runningtest_parse_KEGG.py, tests for this function fail.A typical error message would be
ValueError: What is SYMBOL in K00001?fromraise ValueError('What is {} in {}?'.format(current_entry_name, ko_dict['ENTRY']))at line 212.To circumvent this issue, I added SYMBOL to
NOT_CAPTURED_KO_FIELDS. But then I got a similar issue at each of the next steps with the CO fields and PATHWAY fields, so I added NETWORK and INCLUDING to those (respectively). After these changes, all tests pass, and AMON is no longer erroring.I could be wrong, but I'm guessing these fields have been added to the KEGG reports since KEGG_Parser was last updated? Any ideas on if this is the right approach to fixing this issue?