Question: Entrez progammaticly: Direct efetch or epost + efetch
0
gravatar for guedes.aureliano
3.2 years ago by
guedes.aureliano0 wrote:

Hi all,

I developed a tool in Perl to download an mount of data given entries list.

The tool are working nicely at the moment.

My script receive a large list of accession number and mount URL directly to efetch. Like above:

    my $base = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?';
    my %p = (
            'db' => $db,
            'id' => join(",", @$ids),
            'retmode' => 'text',
            'rettype' => 'fasta', #$format,
    );
    my $url = $base . join("&", map {$_ . "=" . $p{$_}} keys %p);

Each request has no more then 500 entries. 3 request followed by 1sec of sleep.

Entrez NCBI recommend use epost and history => https://www.ncbi.nlm.nih.gov/books/NBK25497/

My question is: Do I really need use EPost to send the ids for latter efetch or can I follow using direct efetch as I'm doing?

Tnks in advance

entrez efetch epost • 1.6k views
ADD COMMENTlink written 3.2 years ago by guedes.aureliano0
1

Follow NCBI's recommendation even if your solution works. You way will be noticed by NCBI sooner or later and then may get your IP banned for a period time, if you are causing problems on their end.

If you are just retrieving fasta sequences, using blastdbcmd from blast+ and local blast database indexes works much faster.

ADD REPLYlink modified 3.2 years ago • written 3.2 years ago by genomax91k
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