Dears, I have a group of Bioproject IDs and need to retrieve their corresponding SRA IDs. I tried to retrieve the whole data from SRA using
kywrds <- entrez_search(db = "sra", retmax = 20000,
term = "Homo sapiens[ORGN] AND Homo sapiens[orgn:__txid9606]")
However, the result of the whole homosapien is more than 4 million records, so I should use "retstart" with the "web_history" arguments with the retmax argument, but unfortunately, I couldn't do that.
The result I want to obtain is data frame of SRA IDs with their corresponding bioproject IDs
Could you help me to do that?
Thanks
You can search SRA directly using a BioProject ID. Shown below are EntrezDirect commands that you should be able to change the syntax to match that of BioPython.
esearch -db sra -query 'PRJEB4337[bioproject]'
You can then pass those results along to esummary and extract relevant information from the output XML. For example,
esearch -db sra -query 'PRJEB4337[bioproject]' | esummary | xtract -pattern DocumentSummary -element Bioproject Biosample Run@acc
will give you a 3-column, tab-delimited table with BioProject, BioSample and SRA Run accessions.
Thank you for your informative answer. I got the XML result from esummary but I need to access study ACC in ExpXml as attached I tried to make as following
esearch -db sra -query 'PRJEB4337[bioproject]' | esummary | xtract -pattern DocumentSummary -element Bioproject ExpXml@Study acc Run@acc
But it doesn't work
No result should be a simple table not XML that you show. Do not change the command posted by vkkodali_ncbi .
Three columns produced are bioproject ID, biosample ID and SRA Accession.
$ esearch -db sra -query 'PRJEB4337[bioproject]' | esummary | xtract -pattern DocumentSummary -element Bioproject Biosample Run@acc
PRJEB4337 SAMEA2145774 ERR315468
PRJEB4337 SAMEA2154125 ERR315343
PRJEB4337 SAMEA2145893 ERR315339
PRJEB4337 SAMEA2156266 ERR315348
I got what I want by the following command:
esearch -db sra -query 'PRJEB4337[bioproject]' | esummary | xtract -pattern DocumentSummary -element Study@acc Bioproject Biosample Run@acc
and produced:
ERP003613 PRJEB4337 SAMEA2145774 ERR315468
Thank you for your help :)
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