[Biopython] get back raw records with SeqIO?

Cedar McKay cmckay at u.washington.edu
Thu Sep 24 21:51:31 UTC 2009


Hello all. Congratulations on the release of 1.52. I'm very pleased to  
see the large file index feature included. And even more thrilled to  
have more full featured support for writing genbank files with SeqIO.  
Thanks!

Are there plans to preserve more information in the in_genbank -->  
SeqIO --> out_genbank pipeline? For instance, at the moment, AUTHORS,  
COMMENT, etc are lost.



I have a use question about SeqIO. If I want to get back the raw  
records from a file, can I do that with SeqIO? For example, to parse a  
genbank file with many records, I do:

genbank_records = GenBank.Iterator(in_file_handle)

Can I use SeqIO similarly somehow? Can I tell it not to parse records?
My way works fine, but I presume that Bio.GenBank is going to be fazed  
out sometime.


Thanks!

Cedar





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