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Enhance the polish
module
#58
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Additionally: - Cleaned up some code - Added more comments - Resolved issues regarding empty `protein_fasta` parameter
I just detected that currently the function |
At least in my models the growth function has the id # Get ID and remove 'R_'
current_id = entity.getId()
if current_id[:2] == 'R_':
current_id = current_id[2:] |
Regarding the ID for growth, this seems to vary between models a lot. We could also just change the regex to include |
…58 (1) Added more comments (2) Restructured functions (3) Removed BUG
As mentioned in these comments #52 (comment) and #52 (comment). It would indeed make sense to add compartment specifications for all reactions which happen in the same compartment within |
COBRApy manipulates IDs back and forth. This prefix is only there in the SBML export. Upon import |
In |
Of course not. This entire ID manipulation is nonsense and causes chaos. There should be separate fields for every piece of information that the BiGG ID ships. |
I think the |
But for the polishing module we mostly use |
While investigating models from Heinken et al.[1] I realised that improving the function [1] |
This module now can: - Remove NaN containing URIs or at least return them - Check if the vmhreaction identifiers found are also BiGG Identifiers if 'id_db:' is set to 'VMH'
* Changed PyPI version badge For the next release the PyPI version badge stems now from 'shields.io' and not from 'badge.fury.io'. * Changed colour for refineGEMs version badge * Adjusted handling of BioCyc identifiers in polish_annotations #95 #58 * Added requirement for importlib_resources=5.13.0 to Pipfile * Added code to cope with missing sub-database prefixes for BioCyc identifiers #95 * Changed NaN identifier handling #95 * Fixed issue III: None prefix identifier pairs in invalid_curies.tsv #95 * Adjusted files with version for release 1.2.2
This issue was opened to collect all enhancements for the
polish
module.biomass.test_biomass_presence
polish
#53polish
module to the bioregistry API #91polish_carveme.py
for package #24polish_carveme
doubles rdf descriptions for sbml:annotation tags #39polish
needs to define default units and compartment structures #38add_reac
to handlegrowth|_*biomass\d*_*
IDs properlyThe text was updated successfully, but these errors were encountered: