Entering edit mode
9.2 years ago
parinitaujoodha ▴ 20
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?
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