turning old shell ncbi querys into url querys
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5 weeks ago
Guelakais • 0

I used to work with a shell application for the eutils, which could do quite a lot and generated my querys with it. This no longer seems to work or has been outdated. I know that the url api can theoretically do just as much. Does anyone know how to translate the following query into a url?

esearch -db nuccore -query "Sclerotinia sclerotiorum 1980 [TITLE]"  | efilter -molecule mrna | efetch -format fasta > s_sclerot.fa

I also know what the beginning is. I am currently failing to plug the following query parts

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=nuccore&term=Sclerotinia/sclerotiorum/1980/[TITLE]
eutils ncbi • 166 views
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Entering edit mode
5 weeks ago
GenoMax 141k

This no longer seems to work or has been outdated.

Not yet any way.

Following still works :

$ esearch -db nuccore -query "Sclerotinia sclerotiorum 1980 [TITLE]"  | efilter -molecule mrna 
<ENTREZ_DIRECT>
  <Db>nuccore</Db>
  <QueryKey>2</QueryKey>
  <Count>14445</Count>
  <Step>2</Step>
</ENTREZ_DIRECT>

As for the URL the following works

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=nuccore&term=%22Sclerotinia%20sclerotiorum%201980%22TITLE

or

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=nuccore&term=Sclerotinia+sclerotiorum+1980
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