panCT

panCT is our pangenome complex trait toolkit, which implements command utilities for complex trait analyses using pangenomes

Warning

panCT is still under construction and has not yet been published to PyPI or bioconda, so it cannot yet be installed through pip or conda.

Commands

• panct complexity: Compute complexity scores for a GFA file

• panct walks: Create an efficient cache of the walks in a GFA file

Detailed information about each command can be found in the Commands section of our documentation. Examples there utilize a set of example files described here.

Logging

All commands output log messages to standard error. The universal --verbosity flag controls the level of detail in our logging messages. By default, this is set to INFO, which will yield errors, warnings, and info messages. To get more detailed messages, set it to DEBUG. To get only error messages, set it to ERROR. To get errors and warnings, set it to WARNING. Refer to the Python documentation on logging levels for more information.

Contributing

We gladly welcome any contributions to panct!

Please read our contribution guidelines and then submit a Github issue.

Citing

We do not yet have a manuscript for our toolkit.