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Old 02-02-2019, 04:36 PM   #1
roliwilhelm
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Location: Ithaca, NY

Join Date: Jun 2012
Posts: 38
Question Downloading 'RunInfo Table' from SRA Run Selector

Hello,

I would like to download the metadata for a given BioProject from the SRA. I am able to get exactly what I need by hitting the download 'RunInfo Table' through the SRA Run Selector web interface (example). It should be relatively straightforward to perform this action from the command line using "wget".

By clicking on the 'RunInfo Table' button, the page loads the following address, which is stable link to download the information:

https://www.ncbi.nlm.nih.gov/Traces/...416ada018b1ea1

BUT, I have no idea where that hash information is coming from. Can anyone help there?

Alternatively, I've tried a series of efetch commands, but none provide me a '.tsv' (or '.csv' would be fine) of the complete BioProject metadata.

This command provides only the information about sequencing:
wget -O PRJNA308986.csv 'http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?save=efetch&db=sra&rettype=runinfo&term=PRJNA308986'

This command provides the full BioProject information sought, but in an .xml format which I haven't been able to parse.

wget -O PRJNA496337.xml 'http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?save=efetch&db=sra&rettype=bioproject&term=PRJNA496337'

Thanks in advance,
Roli
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