Running Entrez Direct-like commands on local or on custom mirror

Question

[p6patel]

For those familiar with entrez direct commands, I'm wondering how I can use commands like efetch, esearch, elink to get the necessary information from local databases. For example, here is a piece of code that I would like to do locally:

system("esearch -db protein -query $inputGI | elink -target nuccore | efetch | xtract);

the databases are downloaded locally, and I am aware of the SearchIO on Bioperl but I am very unsure how I can use that to extract the information I need.

[Giovanni M Dall'Olio]

you would have to set up a local mirror of all NCBI resources, then go through the documentation of the direct utils to see if there is an option to specify a custom mirror.

Answer 1

[Pierre Lindenbaum]

Download entrez direct, find & open the file edirect.pl

change:

$base = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/";

to a custom URL