[BioPython] biopython and dbSNP (2)

Teemu Kuulasmaa Teemu.Kuulasmaa at uku.fi
Wed Mar 29 04:07:00 EST 2006

> Peter (BioPython List) wrote:
> The blank lines shouldn't be a problem for the BioPython's FASTA parser.
> However, due to the extra lines look like "{Result Number}: {Identifier} 
> [{Species}]" this is NOT a valid FASTA format file.
> This may be an NCBI EUtils problem... following their FAQ, I tested this 
> URL:
> http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=snp&id=8192602&report=FASTA
> and this:
> http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=snp&id=8192602,8192603&report=FASTA
> And it does the same sort of thing :(
> I have emailed the NCBI...
> Peter

Thank you for your response Peter!

Like you said the NCBI EUtils result is not valid Fasta formated file. I 
hope that NCBI will fix this issue soon.

Let us know if you get any kind of feedback from NCBI!


  Teemu Kuulasmaa, M.Sc.

  University of Kuopio
  Laboratory of Internal Medicine
  P.O.Box 1627
  70211 Kuopio

  Tel	+358 1716 3498
  Fax	+358 1716 2445

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