FEV_KEGG.quirks module

Sometimes, things do not work as expected. This is when quirk workarounds save the day.

Warning

These quirks are highly time-specific, they can change any moment! Be sure to re-evaluate the workarounds regularly.

FEV_KEGG.quirks.METABOLIC_PATHWAYS = ['01100', '01110', '01120', '01130', '01200', '01210', '01212', '01230', '01220', '00010', '00020', '00030', '00040', '00051', '00052', '00053', '00500', '00520', '00620', '00630', '00640', '00650', '00660', '00562', '00190', '00195', '00196', '00710', '00720', '00680', '00910', '00920', '00061', '00062', '00071', '00072', '00073', '00100', '00120', '00121', '00140', '00561', '00564', '00565', '00600', '00590', '00591', '00592', '01040', '00230', '00240', '00250', '00260', '00270', '00280', '00290', '00300', '00310', '00220', '00330', '00340', '00350', '00360', '00380', '00400', '00410', '00430', '00440', '00450', '00460', '00471', '00472', '00473', '00480', '00510', '00513', '00512', '00515', '00514', '00532', '00534', '00533', '00531', '00563', '00601', '00603', '00604', '00540', '00550', '00511', '00730', '00740', '00750', '00760', '00770', '00780', '00785', '00790', '00670', '00830', '00860', '00130', '00900', '00902', '00909', '00904', '00906', '00905', '00981', '00908', '00903', '00281', '01052', '00522', '01051', '01059', '01056', '01057', '00253', '00523', '01054', '01053', '01055', '00940', '00945', '00941', '00944', '00942', '00943', '00901', '00403', '00950', '00960', '01058', '00232', '00965', '00966', '00402', '00311', '00332', '00261', '00331', '00521', '00524', '00525', '00231', '00401', '00404', '00405', '00333', '00254', '00362', '00627', '00364', '00625', '00361', '00623', '00622', '00633', '00642', '00643', '00791', '00930', '00351', '00363', '00621', '00626', '00624', '00365', '00984', '00980', '00982', '00983', '00970']

KEGG PATHWAY does not provide a reliable naming convention for pathways which are part of metabolism and actually do contain ‘Compounds’ and Enzymes/Genes.

This is the list of all pathway names which currently provide usable information about metabolism.

Warning

It may change any time! Compare with KEGG PATHWAY to see whether you want to categorise different pathways as ‘metabolic’.

FEV_KEGG.quirks.NON_EXISTING_ORGANISMS = ['lni', 'scla', 'pavl', 'our', 'rox', 'dei', 'miq', 'phz', 'mela', 'simp', 'grs', 'deo', 'mdv', 'hag', 'ema', 'pset', 'stro', 'bmur', 'malk', 'lyb', 'ptc', 'pamg', 'vit', 'syo', 'thas', 'paih', 'otk', 'laca', 'pio', 'fsa', 'lcy', 'mgg', 'psai', 'bzg', 'cbae', 'git', 'aue', 'mbas', 'kit', 'vdb', 'aid', 'smur', 'phr', 'melm', 'mee']

Some organisms in KEGG supposedly exist, but when retrieved, their data returns empty, which raises an Error.

Warning

Today, some organisms might be in this list without reason, others might be missing. Please try to fetch the organisms in this list by executing

org = FEV_KEGG.Organism.Organism('lni')
org.getPathways()

If this fails, then lni still belongs in this list.