User: joe

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joe130
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Posts by joe

<prev • 44 results • page 1 of 5 • next >
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Comment: C: NCBI e-utilities: timeout and restart
... Thanks for the reply - this is just a ridiculous example. Downloading and filtering may be the best approach for me. ...
written 28 days ago by joe130
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NCBI e-utilities: timeout and restart
... Let's say I have a large NCBI query which I get disconnected from (example below) - is there a way to restart the query from a known # in the list? Or to break apart the `esearch` query into a few lists to pipe into `esummary` or `efetch`? Thanks! esearch -db 'protein' -query 'CRISPR' | esummar ...
ncbi esummary esearch efetch e-utilities written 28 days ago by joe130
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Comment: C: XML from entrez not formatted correctly
... I'll just comment that the original issue of the incorrectly formatted XML was not addressed. ...
written 4 weeks ago by joe130
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Comment: C: XML from entrez not formatted correctly
... Nice! ...next time. Now I'm more familiar with `rentrez`. I was calling this as part of a bigger function on a list of a few hundred SRA accessions, so yes, in the case I needed (wanted) to work from R. ...
written 4 weeks ago by joe130
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Comment: C: XML from entrez not formatted correctly
... My (original) issue was that the xml output was not correctly formatted, and I later realized the data returned was not correct. ...
written 4 weeks ago by joe130
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Answer: A: XML from entrez not formatted correctly
... Thanks everyone for the responses. In the end I did the below, not exactly what I wanted but I got by... this.runID <- "SRR10025068" # entrez.cmd <- paste0("esearch -db 'sra' -query '", this.runID,"' | esummary -db 'all' -format runinfo") entrez.cmd [1] "esearch -db 'sra' ...
written 4 weeks ago by joe130
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Comment: C: XML from entrez not formatted correctly
... Wow, so I just realized that the issue isn't the XML, it's also the data returned is incorrect - a much bigger issue. ...
written 4 weeks ago by joe130
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Comment: C: XML from entrez not formatted correctly
... Thanks, I tried the entrez e-utils as well, but the data returned between the two functions is similar but different, and unfortunately I'm looking at the different stuff. ...
written 4 weeks ago by joe130
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XML from entrez not formatted correctly
... Hi all, I'm hoping someone might advise on the XML text output from `rentrez` following the below workflow. It seems that the output does not open/close all tags properly and I'm not sure how I can clean this up. For example, in the below the open tag "Platform" isn't annotated `>` and therefore ...
R rxml entrez rentrez xml written 4 weeks ago by joe130
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JGI IMG/M bulk download to AWS S3 bucket
... Is there any documentation for a CLI/API download of JGI IMG/M to S3? Maybe someone has created a workflow of their own they're willing to share? I tried to create something following the [API instructions][1] but unfortunately it seems the XML links are dead. [1]: https://genome.jgi.doe.gov/po ...
jgi img metagenomics img/m written 9 weeks ago by joe130

Latest awards to joe

Student 15 days ago, asked a question with at least 3 up-votes. For NCBI SRA AWS AMI
Supporter 4 weeks ago, voted at least 25 times.
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: mclapply on AWS
Scholar 11 weeks ago, created an answer that has been accepted. For A: mclapply on AWS
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: mclapply on AWS
Scholar 4 months ago, created an answer that has been accepted. For A: mclapply on AWS

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