{"id":25359578,"url":"https://github.com/monarch-initiative/phenotype2phenopacket","last_synced_at":"2025-10-29T23:31:26.551Z","repository":{"id":166843990,"uuid":"629956962","full_name":"monarch-initiative/phenotype2phenopacket","owner":"monarch-initiative","description":"Phenotype2Phenopacket is a command-line tool that converts a phenotype annotation into GA4GH Phenopackets, facilitating standardised phenotypic data 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Phenotype2Phenopacket\n\n_Phenotype2Phenopacket_ is a command-line interface (CLI) application for the construction of phenopackets\nfrom a phenotype annotation file.\n\n## Installation\n\nPhenotype2Phenopacket can be installed from PyPi.\n\n```shell\npip install phenotype2phenopacket\n```\n\n## Usages\n\nTo convert all OMIM diseases in a phenotype annotation file to disease phenopackets, where all phenotypes are retained:\n\n```shell\np2p convert --phenotype-annotation /path/to/phenotype.hpoa --output-dir /path/to/output-dir\n```\n\nTo convert all OMIM diseases in a phenotype annotation file to lightweight disease phenopackets (without phenotypic features):\n```shell\np2p convert --phenotype-annotation /path/to/phenotype.hpoa --output-dir /path/to/output-dir --skip-phenotypic-features\n```\n\nTo create synthetic patient disease phenopackets, where the dataset is more variable and frequencies are taken\ninto account and constrained noise is applied :\n\n```shell\np2p create --phenotype-annotation /path/to/phenotype.hpoa --output-dir /path/to/output-dir\n```\n\nYou can also limit the number of disease phenopackets converted/created:\n\n```shell\np2p convert --phenotype-annotation /path/to/phenotype.hpoa --output-dir /path/to/output-dir --num-diseases 100\n```\n\nOr limit for a specific OMIM disease:\n\n```shell\np2p create --phenotype-annotation /path/to/phenotype.hpoa --output-dir /path/to/output-dir --omim-id OMIM:619340\n```\n\nOr limit for a list of OMIM IDs specified in a text file, with each ID separated by a new line:\n\n```shell\np2p create --phenotype-annotation /path/to/phenotype.hpoa --output-dir /path/to/output-dir --omim-id-list /path/to/list.txt\n```\n\nTo add known gene-to-phenotype relationships to phenopackets:\n\n```shell\np2p 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\n```\n\n\u003e **_NOTE:_** To add known gene-to-phenotype the genes_to_disease.txt is expected. It can be downloaded [here](https://hpo.jax.org/data/annotations).","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmonarch-initiative%2Fphenotype2phenopacket","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmonarch-initiative%2Fphenotype2phenopacket","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmonarch-initiative%2Fphenotype2phenopacket/lists"}