How To Download Genbank Files For Some Organism Using Biojava Utilities

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10.1 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

genbank • 3.7k views

ADD COMMENT • link updated 13 months ago by Ram 43k • written 10.1 years ago by parinitaujoodha ▴ 20

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why Biojava ? java alone + NCBI-E-Utils would be ok isn't it ?

ADD REPLY • link 10.1 years ago by Pierre Lindenbaum 161k

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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.

ADD REPLY • link 10.1 years ago by parinitaujoodha ▴ 20

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There's no magic: any java api would use E-Utils.

ADD REPLY • link 10.1 years ago by Pierre Lindenbaum 161k

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The E-utils package does not solve my problem since the search returns too many queries.

ADD REPLY • link 10.1 years ago by parinitaujoodha ▴ 20

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get your IDs and use Batch Entrez: http://www.ncbi.nlm.nih.gov/sites/batchentrez