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

[bugzilla-daemon at portal.open-bio.org]

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





------- Comment #7 from gcasaburi at tiscali.it  2010-06-18 13:35 EST -------
(In reply to comment #6)
> (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
> 
I will try to recopy the file on another pendrive.  I thought like you, may be
the file has a corruption at the end. I don't think is  truncated, in fact is a
.sff that represents one region of the "ptp", but the same error appers with
another file .sff2  that represents the second region of the "ptp" (diveded in
two regions for the same "run", totally 2 regions, each for one sample,  two
samples in total).  So   i don't know if there is a syntax command to modify
the error value. 
Thank you
Giorgio


-- 
Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email
------- You are receiving this mail because: -------
You are the assignee for the bug, or are watching the assignee.