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CHANGELOG.md

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Changelog

bigecyhmm v0.1.6 (2025-03-17)

Add

  • Draft of phosphorous cycles (with genes PhnD, PhnJ, PstS, PtxD, PitA, PNaS, PhnZ, PhnX, PhnA, PhnM, PhnW, PepM, Ppd, HtxB, HtxA and ptxB).
  • Template figure for phosphorous cycles (from https://doi.org/10.1038/s41467-024-47914-0).
  • Three test HMMs (HtxB, HtxA and ptxB created from https://doi.org/10.1038/s41467-024-47914-0).
  • HMMs for phosphorus cycle from https://doi.org/10.1016/j.soilbio.2022.108826: phoA, phoD, phoX, phoN, aphA, olpA, appA, phnG, phnH, phnI, phnK, phnL, ppa, ppx, ppk1, gcd, pqqC, phoB, phoR, phoU.
  • Creation of barplot showing the coverage of EsMeCaTa on each sample of a dataset.
  • Test for computing abundance of taxonomic rank (used to create the barplot showing the coverage of EsMeCaTa predicitons on the samples).
  • Cytochrome c oxidase in other cycle to highlight aerobic taxa. Update associated template.
  • Creation of HMM functional profile showing the abundance of each HMM in the sample of the dataset.
  • Motif validation step from METABOLIC.

Fix

  • Fix issue of function with zero abundance/occurrence not present in output files.
  • Fix several issues with threshold not being applied correctly.

bigecyhmm v0.1.5 (2025-01-29)

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  • 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.

bigecyhmm v0.1.4 (2025-01-08)

Fix

  • Try to fix issue in pyproject.toml with pypi publishing.

bigecyhmm v0.1.3 (2025-01-06)

Add

  • bigecyhmm_visualisation to create visualisation from esmecata and bigecyhmm outputs.

bigecyhmm v0.1.2 (2024-12-09)

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.

bigecyhmm v0.1.1 (2024-11-01)

Add

  • presence of formula for pathways.

Fix

  • issue in heterogeneity between HMMs presence in pathways, template and compressed file.
  • issue in pyproject.toml.

bigecyhmm v0.1.0 (2024-10-22)

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.

bigecyhmm v0.0.4 (2024-03-13)

Add

  • scripts to create diagram figures in Python using pillow.
  • pillow as dependency.
  • templates folder for biogeochemical diagram creation.

bigecyhmm v0.0.3 (2024-03-12)

Add

  • scripts folder with script create_hmm.py trying to create HMMs and draw_biogeochemical_cycles.R to draw geochemical cycle diagrams (modified from METABOLIC script).
  • R_diagram_pathways.tsv in database folder.
  • creation of metadata file.

Modify

  • update HMMs database with: aspA, nod, fthfs, mcrG, mtaB and mtbA.
  • set HMMs score threshold to 40 and evalue to 1e-5 to extract functions.

bigecyhmm v0.0.2 (2024-03-11)

Add

  • diagram files creation.
  • R_diagram_pathways.tsv in database folder.

Modify

  • multiprocessing: previously done using pyhmmer multiprocessing but it is much faster to use python multiprocessing on the different input fasta files and give 1 CPU to pyhmmer.

bigecyhmm v0.0.1 (2024-03-08)

First test release for bigecyhmm.

Add

  • bigecyhmm command line and python functions.
  • HMMs used in hmm_databases folder.
  • Readme.
  • CHANGELOG.
  • License.