Metage2Metabo v1.6.1

Fix

• Fix an issue with host keys ("host_prodtargets", "host_scope", "comhost_scope" and "host_unprodtargets") not appearing in comm_scopes.json file. But these keys used the old behavior of Metage2Metabo (possible unproducible seeds are contained in them). Host handling by Metage2Metabo will be modified in a future release.

Metage2Metabo v1.6.0

WARNING: change for individual and community scopes:

• for individual scope: only seeds that are producible, ie associated with activated reactions are now shown in the results. Additional information on producible, non-producible and absent seeds are available in the json output. This requires MeneTools version >= 3.4.0.
• for community scope: use of miscoto focus for computation in order to retrieve the metabolite producers in community. This requires MiSCoTo version >= 3.2.0.

Add

• Test in m2m_analysis to check if combination of powergraph predicted by bubbletools is the same as the ones found in minimal communities.
• Creation of boolean equation summarizing the powergraph if it is simple enough.
• New option --target-com-scope to use all the community scope as targets for minimal community prediction (issue #21).
• Add a function to modify xml created by Pathway Tools (issue #60).
• Troubleshooting page in readthedocs (issue #24 and #25).
• Metadata json file created when using command line (both for m2m and m2m_analysis).
• Essential and alternative symbiont in producibility_targets.json (issue #19).
• Test for host for m2m metacom.

Fix

• Fix potential error when reading taxon_id file (issue #22).
• Fix issue with etree in reconstruction.
• Issues with readthedocs.
• GitHub Actions not working.

Modify

• Better deal with seeds that are absent from networks or not produced in iscope and also the seeds that are produced through interactions in cscope (issue #53).
• Exit m2m_analysis when there are unproducible targets (issue #23).
• Check forbidden characters during targets file creation.
• Do not allow abbreviation in command arguments by argparse (issue #54).
• Sanitize use of tarfile extractall (issue #55).
• Remove unused dependency.
• First step in replacing pkg_resources (which will become deprecated in the future) with importlib.metadata or import of __version__.
• Move from setup.py/setup.cfg to pyproject.toml.
• Update tutorial.
• Update docs and readme.
• Update license year and affiliation.
• Move support for CI to Python 3.8 and 3.9.
• Remove import in __init__.py to avoid loading m2m_analysis dependencies when using only m2m.
• Avoid using os.unlink() function on Windows as it can lead to Permission Error.

Metage2Metabo v1.5.4

Fix

• Issues in html powergraph creation:
  • some nodes are not indicated as alternative symbionts.
  • colors are not applied to some nodes.
  • the names of the nodes contain unicode ints.

Modify

• Update license year.

Metage2Metabo v1.5.3

Fix

• Correctly fix the issue with the colors used for the powergraph.

Metage2Metabo v1.5.2

Modify

• Change the shapes of the nodes in the html output of m2m_analysis: circle for essential symbionts and square for alternative symbionts.

Fix

• Issue with the number of colors used to color the taxon in the powergraph.

Metage2Metabo v1.5.1

Fix

• issue in m2m_analysis where clyngor module uses the clingo module producing ValueError.
• issue in m2m_analysis when incorrect paths for seed and/or target files were given as input.

Metage2Metabo v1.5.0

This release focuses on m2m_analysis by adding new option, new output files,more documentation and refactoring some functions and output files.

There is also a complete refactoring on the structure of m2m repository: the two big scripts (m2m_workflow.py and m2m_analysis.py) are now split in multiple scripts in two folders ( m2m and m2m_analysis).

Add

• New option for m2m_analysis: --level to select the taxonomy level (phylum, class, order, family, genus or species) that will be used in the following steps of m2m_analysis, by default, it is phylum.
• HTML output for m2m_analysis. HTML visualization is interactive and nodes are coloured (by key species types or taxon).
• Error message with incorrect SBML file format.
• Log files for m2m_analysis.
• New tests for m2m_analysis.
• Documentation about m2m_analysis output files.
• Citation to eLife article.
• Tutorial with a jupyter notebook about m2m metacom methods.

Modify

• Add colours (by key species types or taxon) to m2m_analysis svg.
• Modify m2m_analysis output files.
• Replace GPL license by LGPL license.
• Complete refactoring of m2m repository structure: m2m_workflow.py and m2m_analysis.py have been split into multiple scripts contained inside m2m and m2m_analysis folders.

Remove

• Delete m2m_analysis stats because it is no more useful with the changes made to m2m_analysis.

Metage2Metabo v1.4.1

Add

• Clarified logs when some target metabolites are also part of the seeds. Indications to which file one must refer in order to check the individual producibility of such seeds by organisms.

Metage2Metabo v1.4.0

Warning: the version 1.4.0 of m2m needs updated version of its dependencies:

• menetools >= 3.1.0.
• miscoto >= 3.0.3.
• mpwt >= 0.6.0.

Add

• Multiprocessing for m2m iscope and m2m metacom, wich can be called using the options -c.
• New option --pwt-xml for m2m recon and m2m workflow: this option extracts the XML file created by MetaFlux (a module of Pathway Tools) so it can be used as input for m2m instead of extracting the .dat files and using padmet to create the SBML input (using mpwt 0.6.0).
• Scripts and data for diversity analysis in article data.
• New output file "indiv_produced_seeds.json" showing if seeds are producible by individual organisms (using menetools 3.1.0).

Fix

• Issue with seeds in individual_producers.
• SBML and padmet stats computation for m2m recon and m2m workflow so it can count correctly reactions, metabolites and genes in XML from MetaFlux.

Modify

• Update article data, scripts and jupyter notebook.
• Update readme and docs.
• Update requirements.txt and delete redundant files.
• Replace keystone species by key species (also modified in miscoto 3.0.3).

Metage2Metabo v1.3.5

Add

• Windows and MacOS tests in GitHub Actions.
• Windows compatibility for m2m metacom using menetools 3.0.2 and miscoto 3.0.2.