Dear reader!
I intend to retrieve the taxonomy for some accession numbers in NCBI using the following command:
Using the following example:
www.ncbi.nlm.nih.gov/protein/XP_018619665.1
I run this command:
esearch -db protein -query "XP_018619665.1" | elink -target taxonomy | efetch -format native -mode xml | grep ScientificName | awk -F ">|<" 'BEGIN{ORS=", ";}{print $3;}'
The above example returns:
"QueryKey value not found in fetch input"
I believe the reason is that the sequence has been updated.
I am now wondering how I can handle this kind of error within the terminal or within R?
This command is used within R in part of my code.