Entering edit mode
9.2 years ago
parinitaujoodha
▴
20
Hello,
I am trying to write some codes to download certain gbk files for certain species e.g I want to download all the mycobacterium avium gbk files (only chromosome) for all the strains available. Can anyone tell me how to do this using BioJava utilities?
Thank you
why Biojava ? java alone + NCBI-E-Utils would be ok isn't it ?
I wanted to know whether there is already module that caters for this in Biojava instead of implementing it from scratch. The search function of NCBI E-utils does not correctly return the amount of species that is stored in their database. For e.g searching the number of species in mycobacterium_avium returns 5000 records instead of only 3. Do you have any idea about how to cater for this? Thank you.
There's no magic: any java api would use E-Utils.
The E-utils package does not solve my problem since the search returns too many queries.
get your IDs and use Batch Entrez: http://www.ncbi.nlm.nih.gov/sites/batchentrez
cross posted on http://stackoverflow.com/questions/22403950