Question: Esearch on Local nucleotide database
0
gravatar for Maxime B
3.7 years ago by
Maxime B0
Norway
Maxime B0 wrote:

I'm trying to download a marker sequence (ITS) for all the plant species using biopython and NCBI esearch/efetch.
It works well, however not only it is slow, but it stops after a few hundred downloads (my plant list is 86 000 species long), probably because of the NCBI download policy...

 

To prevent this, I'd like to use esearch/efetch on a local database, but how ? I know I can download the NCBI databases from ftp://ftp.ncbi.nlm.nih.gov/ but how to interface it with esearch/efetch/biopython locally ?

Thanks

ADD COMMENTlink modified 3.7 years ago • written 3.7 years ago by Maxime B0

Not really sure about why do you want to use biopython for such a task. You can just download the corresponding flatfiles and write up a custom parser for extracting the information you need.

ADD REPLYlink written 3.7 years ago by Cytosine440

Because it allows me to filter easily on the length of the sequence, and (mainly) because I had already written the piece of code a while ago.
But sure, I'll go with regexp if there is no esearch/efetch on local database...

ADD REPLYlink written 3.7 years ago by Maxime B0

Entrez utilities only work via the web.  There is no way to provide that exact functionality locally.  

ADD REPLYlink written 3.7 years ago by Sean Davis25k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1613 users visited in the last hour