PyPedal

The PyPedal project is a Python module that provides a range of tools to manipulate pedigrees, visualize pedigrees, and calculate genetic diversity measures from pedigrees. The latest release includes some new features and bug fixes. The PyPedalError and PyPedalPedigreeInputFileNameError classes have been added, making the exception raised in NewPedigree::__init__() works correctly.

Some improvements have been made in pyp_newclasses/NewAnimal::__init__() to avoid calling string methods on non-strings. The string_to_int() method in pyp_newclasses/NewAnimal now utilizes a new hashing algorithm taken from "Data Structures and Algorithms with Object-Oriented Design Patterns in Python" by Bruno R. Preiss, which fixes the collision problem with the previous algorithm. Moreover, pyp_newclasses/NewAnimal::__init__() assigns animal, sire, and dam names correctly even if integral IDs are passed rather than strings.

Other bug fixes include turning off a bunch of debugging messages left on in pyp_utils/reorder(), fixing the error in pyp_utils/assign_offspring() due to errors introduced when the new object model conversion was made, and removing pyp_utils/reorder_list(). The new release also includes a new parameter, max_rounds, to pyp_utils/reorder(), with a default value of 100 rounds. Additionally, pyp_utils/reorder() will write error messages to the logfile and STDIO if a pedigree could not be renumbered in renumber_max_rounds of iteration.

In the latest release, a new function, pyp_io/write_ijk(), has been added, which saves an NRM to a disk in ijk format. The previously existing functions, pyp_nrm/*, have been improved, including fixing a bug in pyp_nrm/inbreeding() so that it correctly works with pre-calculated NRM. Finally, an error message in pyp_newclasses/NewPedigree::preprocess() has been rewritten to make more sense.