* Complete refactoring of `bigecyhmm_visualisation` with two new subcommands `bigecyhmm_visualisation esmecata` for input from EsMeCaTa or `bigecyhmm_visualisation genomes` if the inputs are genomes. * Handle abundance data with `bigecyhmm_visualisation`. * In `bigecyhmm_visualisation`, add the possibility to create heatmap, polar plot and diagrams showing abundance of specific function categories. Also creates tabulated files indicating the ratio of organisms associated with functions for each sample. * Add creation of metadata file for `bigecyhmm_visualisation`. * Numerous tests for the visualisation. * HMM associated with formate fermentation (formate lyase, hycE, `K15830`).
Modify
* Rename pathway `C-S-10:Acetogenesis` into `C-S-10:Acetogenesis WL` and make it focus on Wood–Ljungdahl pathway. * Update readme to better explain outputs and `bigecyhmm_visualisation`.
Fix
* Fix issue when computing abundance where abundances were not normalised by total abundance.
0.1.4
Fix
* Try to fix issue in pyproject.toml with pypi publishing.
0.1.3
Add
* `bigecyhmm_visualisation` to create visualisation from esmecata and bigecyhmm outputs.
0.1.2
Add
* `pathway_presence.tsv` showing the presence of pathways in each taxon of the communities. * file associated with hydrogen consumption `hydrogen_consumption.tsv`. * test for carbon cycle. * missing HMMs (and other HMMs for hydrogenases).
Modify
* move `Total.R_input.txt` outside of `diagram_input` folder.
Fix
* typo in metadata.
0.1.1
Add
* presence of formula for pathways.
Fix
* issue in heterogeneity between HMMs presence in pathways, template and compressed file. * issue in pyproject.toml.
0.1.0
Add
* use of threshold with pyhmmer.
Modify
* information for several HMMs: `acsB`, `mcrC`, `mcrG`, `mtaB`, `mtbA`, `rubisco_form_II_III`, `rubisco_form_III`, `rubisco_form_IV`, `fthfs`, `fhs`, `nod`, `apsA`, `apsK`, `arsC (trx)`, `cysN`.