Question: some questions about edirect
0
gravatar for nicktfcn1
5 weeks ago by
nicktfcn10
nicktfcn10 wrote:

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 • 90 views
ADD COMMENTlink modified 4 weeks ago • written 5 weeks ago by nicktfcn10

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

ADD REPLYlink written 4 weeks ago by nicktfcn10
1
gravatar for genomax
5 weeks ago by
genomax85k
United States
genomax85k wrote:

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
ADD COMMENTlink modified 5 weeks ago • written 5 weeks ago by genomax85k
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