Pypgx

Latest version: v0.25.0

Safety actively analyzes 638466 Python packages for vulnerabilities to keep your Python projects secure.

Scan your dependencies

Page 1 of 4

0.25.0

-------------------

* Add 26 new genes: ACYP2, ADRA2A, ADRB2, ANKK1, APOE, ATM, BCHE, BDNF, DBH, DRD2, F2, GRIK1, GRIK4, GRIN2B, HTR1A, HTR2A, IFNL4, ITGB3, ITPA, OPRK1, OPRM1, RARG, SLC6A4, SLC28A3, SLC47A2, UGT1A6.

0.24.0

-------------------

* Change G6PD haplotype name from ``*MALE`` to ``MALE``, as the gene does not utilize star allele nomenclature.
* Update G6PD haplotype nomenclature in accordance with the latest CPIC version (2024-01-07).
* :issue:`119`: Add G6PD phenotype data in accordance with the latest CPIC version (2024-01-07).
* Update CYP4F2 haplotype nomenclature in accordance with the latest PharmVar version (2024-01-27).

0.23.0

-------------------

* :issue:`115`: Add new genes COMT and MTHFR (thanks `nbiesot <https://github.com/nbiesot>`__).
* :issue:`117`: Fix major bug in :meth:`api.utils.estimate_phase_beagle` method. The bug was introduced in version 0.22.0 (:issue:`113`) and carries significant implications, especially if the user's input VCF contains sample names that overlap with the reference panel or if there are differences in chromosome annotation compared to the reference panel (e.g. 'chr22' vs. '22').

0.22.0

-------------------

* :issue:`100`: Add new method :meth:`sdk.utils.get_bundle_path` to enable customization of the ``pypgx-bundle`` directory's location instead of the user's home directory.
* :issue:`114`: Fix bug in :meth:`api.core.get_recommendation` method where string ``'None'`` was treated as missing value by ``pandas.read_csv`` version 2.0 or higher.
* :issue:`113`: Fix bug in :meth:`api.utils.estimate_phase_beagle` method where Beagle's expectation-maximization algorithm estimated a parameter value that was outside the permitted range.

0.21.0

-------------------

* :issue:`96`: Fix bug in :command:`compute-copy-number` command where it threw an error "Different sample sets found" when the sample name consists of only numbers with one or more leading zeros.
* :issue:`97`: Fix bug in IFNL3 genotyping where certain variants were not considered because they were located outside of the target region.
* :issue:`99`: Refresh the CPIC table for :meth:`api.core.load_cpic_table` method. The table's latest update was on February 6, 2022.
* :issue:`63`: Fix bug in :meth:`api.utils.estimate_phase_beagle` method where Beagle throws an error "Window has only one position" even when multiple overlapping variants exist.

0.20.0

-------------------

* :issue:`73`: Fix bug in :command:`run-ngs-pipeline` command where empty VCF (i.e. no variants were found in the target gene) was causing error when plotting allele fraction. From now on, a warning will be produced telling users to specify ``--do-not-plot-allele-fraction`` to suppress this warning.
* :issue:`78`: Fix bug in :command:`compute-copy-number` command where it threw an error "Different sample sets found" when the sample name consists of only numbers.

Page 1 of 4

© 2024 Safety CLI Cybersecurity Inc. All Rights Reserved.