[Biopython] Could Bio.SeqIO write EMBL file?

Anne Pajon ap12 at sanger.ac.uk
Wed Jan 6 12:20:30 UTC 2010


Dear,

I'm reading EMBL file with Bio.SeqIO for adding an extra feature  
qualifier to each of the annotations, and would like to write the  
modified annotated sequence back to an EMBL file.

     embl_record = SeqIO.read(open("Alistipes_shahii_WAL8301.embl"),  
"embl")
     addSystematicId(embl_record)
     print embl_record.format("genbank")

While running the above I'm getting this error:
Reading format 'embl' is supported, but not writing

Is there a way around? I know from the documentation on the wiki that  
biopython does not have a writer for EMBL format. Is there a plan of  
having one in the future? I volunteer to test it, or if it does not  
exist yet I may be able to contribute writing it... thanks to let me  
know.

Kind regards,
Anne.
--
Dr Anne Pajon - Pathogen Genomics, Team 81
Sanger Institute, Wellcome Trust Genome Campus, Hinxton
Cambridge CB10 1SA, United Kingdom
+44 (0)1223 494 798 (office) | +44 (0)7958 511 353 (mobile)



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