[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 #8 from biopython-bugzilla at maubp.freeserve.co.uk  2010-06-23 09:21 EST -------
Hi Giorgio,

Did coping the file again help?

In addition to trying to read the SFF files with other tools (like sff_extract
or the Roche ssfinfo) as suggested, I have some additional things you could
try.

Firstly try this private function to see how many reads there should be:

filename = r"C:\Users\Giorgio Casaburi\Desktop\sff\GIK1EHM01.sff"
from Bio import SeqIO
print SeqIO.SffIO._sff_file_header(open(filename, "rb"))[3]

Then compare this to the number of reads you could extract up until the error.

Secondly, see if the index can be loaded or not:

filename = r"C:\Users\Giorgio Casaburi\Desktop\sff\GIK1EHM01.sff"
from Bio import SeqIO
d = SeqIO.index(filename, "sff")
print len(d)

If it is just one or two bad reads, this may allow you to jump to specific
records (and so avoid getting stuck on the bad ones).

Peter


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