[Biopython-dev] sff file
Sebastian Bassi
sbassi at clubdelarazon.org
Mon Oct 26 14:09:57 EDT 2009
On Mon, Oct 26, 2009 at 3:00 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:
> Try binary mode - although on my tests it isn't essential on Unix,
> it is on Windows.
I am in Linux Ubuntu 9.04 and I followed your advice and now I did:
fh = open('/home/sbassi/E3MFGYR02_random_10_reads.sff','rb')
And now it works:
>>> for rec in SeqIO.parse(fh,'sff'):
print rec.seq
tcagGGTCTACATGTTGGTTAACCCGTACTGATTTGAATTGGCTCTTTGTCTTTCCAAAGGGAATTCATCTTCTTATGGCACACATAAAGGATAAATACAAGAATCTTCCTATTTACATCACTGAAAATGGCATGGCTGAATCAAGGAATGACTCAATACCAGTCAATGAAGCCCGCAAGGATAGTATAAGGATTAGATACCATGATGGCCATCTTAAATTCCTTCTTCAAGCGATCAAGGAAGGTGTTAATTTGAAGGGGCTTa
tcagTTTTTTTTGGAAAGGAAAACGGACGTACTCATAGATGGATCATACTGACGTTAGGAAAATAATTCATAAGACAATAAGGAAACAAAGTGTAAAAAAAAAACCTAAATGCTCAAGGAAAATACATAGCCATCTGAACAGATTTCTGCTGGAAGCCACATTTCTCGTAGAACGCCTTGTTCTCGACGCTGCAATCAAGAATCACCTTGTAGCATCCCATTGAACGCGCATGCTCCGTGAGGAACTTGATGATTCTCTTTCCCAAATGcc
(.... cut ...)
So looks that binary mode is also needed for Linux.
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