Phenotype2Phenopacket

Phenotype2Phenopacket is a command-line interface (CLI) application for the construction of phenopackets from a phenotype annotation file.

Installation

Phenotype2Phenopacket can be installed from PyPi.

pip install phenotype2phenopacket

Usages

To convert all OMIM diseases in a phenotype annotation file to disease phenopackets, where all phenotypes are retained:

p2p convert --phenotype-annotation /path/to/phenotype.hpoa --output-dir /path/to/output-dir

To convert all OMIM diseases in a phenotype annotation file to lightweight disease phenopackets (without phenotypic features):

p2p convert --phenotype-annotation /path/to/phenotype.hpoa --output-dir /path/to/output-dir --skip-phenotypic-features

To create synthetic patient disease phenopackets, where the dataset is more variable and frequencies are taken into account and constrained noise is applied :

p2p create --phenotype-annotation /path/to/phenotype.hpoa --output-dir /path/to/output-dir

You can also limit the number of disease phenopackets converted/created:

p2p convert --phenotype-annotation /path/to/phenotype.hpoa --output-dir /path/to/output-dir --num-diseases 100

Or limit for a specific OMIM disease:

p2p create --phenotype-annotation /path/to/phenotype.hpoa --output-dir /path/to/output-dir --omim-id OMIM:619340

Or limit for a list of OMIM IDs specified in a text file, with each ID separated by a new line:

p2p create --phenotype-annotation /path/to/phenotype.hpoa --output-dir /path/to/output-dir --omim-id-list /path/to/list.txt

To add known gene-to-phenotype relationships to phenopackets:

p2p add-genes --phenopacket-dir /path/to/synthetic-phenopackets --genes-to-disease /path/to/genes_to_disease.txt --hgnc-data /path/to/hgnc_complete_set.txt --output-dir /path/to/output-dir

NOTE: To add known gene-to-phenotype the genes_to_disease.txt is expected. It can be downloaded here.