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Project description
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 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.
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