User: joe
joe • 140
- Reputation:
- 140
- Status:
- Trusted
- Location:
- Last seen:
- 3 months, 1 week ago
- Joined:
- 1 year, 1 month ago
- Email:
- i**************@gmail.com
Posts by joe
<prev
• 44 results •
page 1 of 5 •
next >
0
votes
0
answers
196
views
0
answers
... Thanks for the reply - this is just a ridiculous example. Downloading and filtering may be the best approach for me. ...
written 7 months ago by
joe • 140
1
vote
0
answers
196
views
0
answers
... 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 ...
written 7 months ago by
joe • 140
0
votes
2
answers
261
views
2
answers
... I'll just comment that the original issue of the incorrectly formatted XML was not addressed. ...
written 8 months ago by
joe • 140
0
votes
2
answers
261
views
2
answers
... 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 8 months ago by
joe • 140
0
votes
2
answers
261
views
2
answers
... My (original) issue was that the xml output was not correctly formatted, and I later realized the data returned was not correct. ...
written 8 months ago by
joe • 140
0
votes
2
answers
261
views
2
answers
... 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 8 months ago by
joe • 140
0
votes
2
answers
261
views
2
answers
... 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 8 months ago by
joe • 140
0
votes
2
answers
261
views
2
answers
... 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 8 months ago by
joe • 140
3
votes
2
answers
261
views
2
answers
... 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 ...
written 8 months ago by
joe • 140
0
votes
0
answers
234
views
0
answers
... 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 ...
written 9 months ago by
joe • 140
Latest awards to joe
Supporter
8 months ago,
voted at least 25 times.
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 947 users visited in the last hour