From eb8a180dafa4c53f198d63da3cd1acb6afa0b820 Mon Sep 17 00:00:00 2001 From: John Sterrett Date: Fri, 13 Jan 2023 10:25:24 -0700 Subject: [PATCH 1/3] quick patch symbol issue by adding symbol to not captured ko fields --- KEGG_parser/parsers.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/KEGG_parser/parsers.py b/KEGG_parser/parsers.py index ceb88f5..e475f2e 100644 --- a/KEGG_parser/parsers.py +++ b/KEGG_parser/parsers.py @@ -194,7 +194,7 @@ 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') From 398899c3221fc157bfdd267083049cc2364633e2 Mon Sep 17 00:00:00 2001 From: John Sterrett Date: Fri, 13 Jan 2023 12:42:00 -0700 Subject: [PATCH 2/3] add other not captured fields --- KEGG_parser/parsers.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/KEGG_parser/parsers.py b/KEGG_parser/parsers.py index e475f2e..f35a6b4 100644 --- a/KEGG_parser/parsers.py +++ b/KEGG_parser/parsers.py @@ -200,9 +200,10 @@ def split_module_reaction(current_dict, current_entry_name, current_entry_data): 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', 'INCLUDING') -NOT_CAPTURED_PATHWAY_FIELDS = ('GENE', 'ORGANISM', 'REFERENCE', 'AUTHORS', 'TITLE', 'JOURNAL') +NOT_CAPTURED_PATHWAY_FIELDS = ('GENE', 'ORGANISM', 'REFERENCE', 'AUTHORS', 'TITLE', 'JOURNAL', 'INCLUDING') NOT_CAPTURED_ORGANISM_FIELDS = ('AASEQ', 'NTSEQ') From ba9ba8b26a0c4511a2412bf92f012e2bcce46e8d Mon Sep 17 00:00:00 2001 From: John Sterrett Date: Fri, 13 Jan 2023 15:23:14 -0700 Subject: [PATCH 3/3] remove INLCUDING from CO fields, should have been in pathway fields --- KEGG_parser/parsers.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/KEGG_parser/parsers.py b/KEGG_parser/parsers.py index f35a6b4..94e792a 100644 --- a/KEGG_parser/parsers.py +++ b/KEGG_parser/parsers.py @@ -201,7 +201,7 @@ def split_module_reaction(current_dict, current_entry_name, current_entry_data): 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', - 'NETWORK', 'INCLUDING') + 'NETWORK') NOT_CAPTURED_PATHWAY_FIELDS = ('GENE', 'ORGANISM', 'REFERENCE', 'AUTHORS', 'TITLE', 'JOURNAL', 'INCLUDING')