Releases · zhanglab/psamm

07 Dec 22:18

jonls

PSAMM 0.17

When loading native models, PSAMM now uses the PyYAML safe loader and also uses the optimized CSafeLoader if present. This speeds up the start time of commands.
Various additional optimizations to model loading have been added. This speeds up the start time of some commands.
The fba command now shows the genes associated with each reaction for a quick overview of which genes influence the flux solution.
The sbmlexport command now properly exports gene association information.
All commands better handle output that contains unicode characters. In previous versions this would often fail when using Python 2.

Assets 2

01 Dec 20:49

jonls

PSAMM 0.16

Add an option to randomsparse to perform the deletion based on genes instead of reactions. This uses the gene association expression defined in the reaction property genes.
Add threshold option to fva command.
Fix bugs in gapfill that resulted in the procedure not detecting reactions that could be reversed, and sometimes failing to find a result at all.
Add epsilon option to chargecheck and ignore charge imbalances below the epsilon value.
Allow the search command to find reactions containing a specific compound even when the compartment is not specified.
Output more information is the result of the search command.
Improved handling of flux bounds at infinity (e.g. with default_flux_limit = .inf in model.yaml).

Assets 2

19 Oct 19:28

jonls

PSAMM 0.15

Add support for reading flux bounds and objectives from SBML files that are
using the FBC extension.
Add a tutorial to the documentation at https://psamm.rtfd.org/.
Add command tableexport to export various parts of the model as a TSV file.
Add command excelexport to export all parts of the model as an Excel file.
Allow various parameters that take a reaction as an argument to also be able
to take a list of reactions from a file, using the @ prefix. For example,
given a file r.txt with each reaction ID on a separate line, the reactions
can be excluded from the masscheck command by specifying
--exclude @r.txt.
Allow reactions to be excluded from the formulacheck and chargecheck
commands.