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

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





------- Comment #6 from biopython-bugzilla at maubp.freeserve.co.uk  2010-06-18 11:28 EST -------
(In reply to comment #5)
> Thank u for the answer. I have the last version of Biopython,

Good.

> The file is 1,12 giga, so i think is difficult to attach the file.

Yes, too big to attach or email :(

> The file has been taken directly from the usb port of the 454 with a
> pendrive and now is in a normal PC.

I would try copying it again using a different USB memory stick / pen drive.

> 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

It sounds like there is an error is near the end of the file. You can open the
file and read lots of reads up until the error. If you use Bio.SeqIO.parse()
or Bio.SeqIO.convert() these will fail once you get to the bad read. Perhaps
the file is truncated (only partly copied)?

Peter


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