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phenopolis / phenopolis

An Open Platform for Harmonisation & Analysis of Sequencing & Phenotype Data
https://www.phenopolis.org
MIT License
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Add export to csv to /my_patients page #115

Open pontikos opened 7 years ago

pontikos commented 7 years ago

This would be useful for export our data and importing it in to DECIPHER for example.

IsmailM commented 7 years ago

what data would this include? And would it be one file per patient or for all patients?

Easiest solution would be to create another endpoint for the CSV (maybe using csv.DictWriter) and then I can add the UI button and the accomplying JS...

pontikos commented 7 years ago

DECIPHER requires, but a few of these will be blank for us:

Internal reference number or ID HGVS code   Genome assembly Transcript  Gene name   Intergenic  Chromosomal sex Open-access consent Age at last clinical assessment Prenatal age in weeks   Note    Mother's phenotype  Father's phenotype  Inheritance Pathogenicity   Phenotypes  Genotype    Responsible contact
pat1    chr7:g.103969467C>G GRCh37/hg19 NM_199000   LHFPL3  No  46XX    Yes 5       Some free text note Shares similar phenotype (dominant inheritance plausible)   Shares similar phenotype (dominant inheritance plausible)   De novo constitutive    Definitely pathogenic   1249, 252, 1518, 1892   Homozygous  Please see instructions
pontikos commented 7 years ago

I agree I'll write an endpoint to export the data.