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2 hours ago by

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.

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Asaf6.9k

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2 hours ago
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Fardokht20



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