abl

Python package for managing case files.

Sub-packages

templates

Jinja templates for rendering case files

Functions

get_configfile()

Get path of the Snakemake configuration file for the current machine.

get_root()

Get the path to the current package, abl.

Classes

Output([sim])

Container and methods for getting paths of and copying case files.
class abl.Output(sim=None)[source]

Container and methods for getting paths of and copying case files.

A path object self.root points to the directory containing the case files.

copy(new_dir, force=False)[source]

Copy case files to a new directory. The directory does not have to be present.

Parameters

  • new_dir – A str or Path-like instance pointing to the new directory.

  • force – Force copy would overwrite if files already exist.

get_paths()[source]

Get a list of paths to all case files.

Returns

list

write_makefile_usr(fp=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='UTF-8'>, comments='')[source]

Write the makefile_usr.inc file which is required for compilation.

abl.get_configfile()[source]

Get path of the Snakemake configuration file for the current machine. All configuration files are stored under etc sub-package.

abl.get_root()[source]

Get the path to the current package, abl.