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Fix "what SYMBOL" issue #10

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merged 3 commits into from
Mar 3, 2023
Merged

Fix "what SYMBOL" issue #10

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eb8a180
quick patch symbol issue by adding symbol to not captured ko fields
sterrettJD Jan 13, 2023
398899c
add other not captured fields
sterrettJD Jan 13, 2023
ba9ba8b
remove INLCUDING from CO fields, should have been in pathway fields
sterrettJD Jan 13, 2023
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7 changes: 4 additions & 3 deletions KEGG_parser/parsers.py
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Original file line number Diff line number Diff line change
Expand Up @@ -194,15 +194,16 @@ def split_module_reaction(current_dict, current_entry_name, current_entry_data):
'COMPOUND': add_module_orthology, 'COMMENT': return_self, 'DBLINKS': add_nested_dict
}

NOT_CAPTURED_KO_FIELDS = ('REFERENCE', 'AUTHORS', 'TITLE', 'JOURNAL', 'SEQUENCE', 'BRITE')
NOT_CAPTURED_KO_FIELDS = ('REFERENCE', 'AUTHORS', 'TITLE', 'JOURNAL', 'SEQUENCE', 'BRITE', 'SYMBOL')

NOT_CAPTURED_RN_FIELDS = ('REFERENCE', 'AUTHORS', 'TITLE', 'JOURNAL')

NOT_CAPTURED_CO_FIELDS = ('BRITE', 'ATOM', 'BOND', 'BRACKET', 'ORIGINAL', 'REPEAT', 'NODE', 'EDGE', 'SEQUENCE',
'GENE', 'ORGANISM', 'TYPE', 'EFFICACY', 'PRODUCT', 'CLASS', 'DISEASE', 'TARGET',
'METABOLISM', 'INTERACTION', 'STR_MAP', 'REFERENCE', 'AUTHORS', 'TITLE', 'JOURNAL')
'METABOLISM', 'INTERACTION', 'STR_MAP', 'REFERENCE', 'AUTHORS', 'TITLE', 'JOURNAL',
'NETWORK')

NOT_CAPTURED_PATHWAY_FIELDS = ('GENE', 'ORGANISM', 'REFERENCE', 'AUTHORS', 'TITLE', 'JOURNAL')
NOT_CAPTURED_PATHWAY_FIELDS = ('GENE', 'ORGANISM', 'REFERENCE', 'AUTHORS', 'TITLE', 'JOURNAL', 'INCLUDING')
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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.

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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)

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Didn't have a chance to specifically discuss a better fix, but did decide to go ahead and merge.


NOT_CAPTURED_ORGANISM_FIELDS = ('AASEQ', 'NTSEQ')

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