turning old shell ncbi querys into url querys
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 This no longer seems to work or has been outdated.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]
• 612 views
•
link
1 answer
This no longer seems to work or has been outdated.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
• 0 views
•
link
Log in to answer this question.