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some questions about edirect

esearch -db nucleotide -query PRJNA257197 | efetch -format fasta > ebola.fasta enter image description here this should download all sequence which is about 200+, but i only got the result like below which is only 10+. enter image description here

i think it`s maybe a net error and it cause it only download part of them. But how can i change that.

I need all of them not part of them. Please help me!!

software error
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written by nicktfcn1 • nicktfcn1

tx, guys. it works now. i guess elink -target nuccore do some work.

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written by nicktfcn1 • nicktfcn1

1 answer

You have a bioproject ID so you ideally should do the following to get the sequences you need:

$ esearch -db bioproject -query "PRJNA257197" | elink -target nuccore | efetch -format fasta | grep ">" | wc -l
251

There appear to be 251 genomes. To save the sequences to a file 

$ esearch -db bioproject -query "PRJNA257197" | elink -target nuccore | efetch -format fasta > ebola.fa

That said, following does seem to work (have not checked why there is a difference of 2 compared to search above). 

$ esearch -db nuccore -query "PRJNA257197" | efetch -format fasta | grep ">" | wc -l
249
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written by GenoMax GenoMax

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