How to download advance search results from ICGC data portal?
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2.5 years ago
Boboboe ▴ 40

Hi,

I was trying to download data from ICGC data portal, specifically this result: https://dcc.icgc.org/search/g?filters=%7B%22donor%22:%7B%22projectId%22:%7B%22is%22:%5B%22MELA-AU%22%5D%7D,%22state%22:%7B%22is%22:%5B%22live%22%5D%7D,%22id%22:%7B%22is%22:%5B%22ES:2e7cad48-34e9-48fb-9cd1-4aa38b5cd12d%22%5D%7D%7D,%22gene%22:%7B%22type%22:%7B%22is%22:%5B%22protein_coding%22%5D%7D%7D%7D&donors=%7B%22sort%22:%22primarySite%22,%22order%22:%22desc%22%7D&genes=%7B%22size%22:50,%22from%22:1,%22sort%22:%22symbol%22,%22order%22:%22asc%22%7D

The table has > 20000 rows, and I would like to at least have the column " symbol" and " # of donor affected".

I have tried the export button associated with the table, but that's only exporting the first 50 rows I have tried save/edit gene results, but that only exports the name of genes I also used this https://github.com/icgc-dcc/icgc-python with the PQL shown on the page, but none of this have worked. could someone please help?

Thanks!

mutation ICGC ICGCDCC • 821 views
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The export csv/json button only exporting 50 results because the current view of the table only allowed to display 50 rows max per page.

The PQL query shown on the page will only get only the first 50 results because of limit(50). Try changing the limit.

select(*),in(gene.type,'protein_coding'),nested(donor,in(donor.projectId,'MELA-AU'),in(donor.state,'live'),indonor.id,'ES:2e7cad48-34e9-48fb-9cd1-4aa38b5cd12d')),sort(+symbol),limit(50)
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Hi! have you managed to work it out? I'm having the same problems

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