akaviaLab
akaviaLab
Updated version of https://github.com/opencobra/cobrapy/pull/988. Tried to simplify and tidy the code in addition to merging. Modified according to @cdiener requests - Ignored changes in notes for now - renamed constructors...
Fix 673
* [X] fix #673 * [X] description of feature/fix Fix #673 by making reactions in species search the model fields, if this species is in a model. Added checks in...
* [ ] fix #(issue number) * [X] description of feature/fix Changed type hints in dictlist to be TypeVar(Object), because otherwise my linter would complain about expecting a Reaction and...
Very initial attempt at compartments. Just to see if I'm heading in the right direction. Will not be committed as is.
* [X] description of feature Added functions for comparing models, metabolites, reactions, groups, genes. This is an adaptation of a function I used to compare XML and MAT models of...
#### Problem description The model has groups that contain members (list of reactions). However, the reactions do not have a groups field, and the subsystems is always an empty string....
https://github.com/opencobra/cobratoolbox/blob/c72a7bd511f79ebc1b6b1e0421544b22b4a9335d/src/reconstruction/rBioNet/neighborRxn2data.m#L44 This is unclear, since it loads up existing data, instead of using the model. Was this perhaps meant to be "rxns"?
isSameCobraModel does not check subSystems. Should this be fixed? One way of fixing it is changing subSystems not to be cells within cell, but I'm not sure why that is...
**Describe the issue** Running PureCN on a sample fails with Detected overlapping gaps on chromosome , : INTERNAL ERROR: Detected overlapping gaps on chromosome 10 in argument gaps . Calls:...
### Have you checked the docs? - [x] [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting) - [x] [nf-core modules documentation](https://nf-co.re/docs/contributing/modules) ### Description of the bug The code in gProfiler module https://github.com/nf-core/differentialabundance/blob/3dd360fed0dca1780db1bdf5dce85e5258fa2253/modules/nf-core/gprofiler2/gost/templates/gprofiler2_gost.R#L222 seems to split...