[Biopython-dev] [Bug 3102] Error converting sff into fastq

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http://bugzilla.open-bio.org/show_bug.cgi?id=3102





------- Comment #5 from gcasaburi at tiscali.it  2010-06-18 11:03 EST -------
(In reply to comment #4)
> Thanks Chris.
> Giorgio - Could you confirm which version of Biopython are you using?
> To me the error message suggests the SFF file is corrupted (damaged). Is it
> very large? Could you attach it to this bug (or email it to me personally) to
> check?
> Have you been able to process the SFF file with any other tools (e.g.
> sff_extract which should work on Windows/Linux/Mac, or the Roche tools which
> are Linux only)?
> If you copied the SFF file over your network, or over the internet from your
> sequencing center, perhaps there was an error there. Could you try
> re-downloading the SFF file?
> Regards,
> Peter
Thank u for the answer. I have the last version of Biopython, The file is 1,12
giga, so i think is difficult to attach the file. The file has been taken
directly from the usb port of the 454 with a pendrive and now is in a normal
PC. With Biopthon i'v been able to read and open this sff file, but at the end
of the reading appers the message (Value error:...). So when i try to convert
the file in fasta the same message apper to be, bloking any work. So why the
file is open reading, with all information (flow, lewnght) but impossible to
edit, convert??? Thank u hope u can help us.
Grater from ITALY


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