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I'm downloading translated viral genomes initially via Blast - which had shortcomings - and now by efetch.

What I want to do is obtain a complete list of all translated protein ids from a nucleotide Genbank entry.

efetch -db nucleotide -format gpc -id MT039887 | xtract -insd ....

The protein id and the translated gene sequences are within the efetch -db nucleotide -format gpc -id MT039887 output ... but how do I use xtract to parse them?

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If you want the cds in fasta format, try:

esearch -db nucleotide -query MT039887 | efetch -format fasta_cds_na

And for the proteins sequence in fasta format:

elink -db nucleotide -target protein -id MT039887 | efetch -format fasta 
| improve this answer | |
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  • $\begingroup$ Wow!! and thank you. Thats the answer ... days like this BioSE works. @zorbax I owe you. "Acknowledgements" thank you heading your way (thats not a metaphor). $\endgroup$ – Michael Feb 27 at 16:33
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In case you are still interested in just getting the protein ids and not sequence, you can use xtract like this:

efetch -db nucleotide -format gpc -id MT039887 | xtract  -insd CDS gene product protein_id 
MT039887.1  orf1ab  orf1ab polyprotein           QHZ00388.1
MT039887.1  S       surface glycoprotein         QHZ00389.1
MT039887.1  orf3a   orf3a protein                QHZ00390.1
MT039887.1  E       envelope protein             QHZ00391.1
MT039887.1  M       membrane glycoprotein        QHZ00392.1
MT039887.1  orf6    orf6 protein                 QHZ00393.1
MT039887.1  orf7a   orf7a protein                QHZ00394.1
MT039887.1  orf8    orf8 protein                 QHZ00395.1
MT039887.1  N       nucleocapsid phosphoprotein  QHZ00396.1
MT039887.1  orf10   orf10 protein                QHZ00397.1
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