Question: Esearch results not matching up with online results
0
gravatar for cha27cha
15 months ago by
cha27cha0
cha27cha0 wrote:

I am using the code below to perform an esearch, but the id's that I get from IdList are not matching up with the ID's on the online search.

 handle = Entrez.esearch(db = "nucleotide", term = "chordata[orgn] AND chromosome", retmax = 200, idtype = "acc")
 genome_ids = Entrez.read(handle)['IdList']

Does anyone know why? And does anyone know how I can download the chromosomal and mitochondrial genome of all the organisms from the chordata phylum? I want to do it using BioPython through the E-utilities.

entrez biopython esearch • 445 views
ADD COMMENTlink modified 10 months ago by RamRS24k • written 15 months ago by cha27cha0

If your code doesn't retrieve the same thing as the online tool, it means it's doing something different. The most common source of discrepancies is the use of different parameters, in particular default parameters can be different between the web site and the code.

For downloading large data sets from NCBI, I would recommend using their FTP site. E-utilities are slow and if you hammer the NCBI web site with queries, you'll get banned.

ADD REPLYlink written 15 months ago by Jean-Karim Heriche20k
2
gravatar for vkkodali
10 months ago by
vkkodali1.2k
United States
vkkodali1.2k wrote:

You cannot call IdList directly like that. Try the following:

handle = Entrez.esearch(db = "nucleotide", term = "chordata[orgn] AND chromosome", retmax = 200, idtype = "acc")
genome_ids = Entrez.read(handle)
genome_ids = genome_ids['IdList']
ADD COMMENTlink written 10 months ago by vkkodali1.2k
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: 1990 users visited in the last hour