[Biopython-dev] sff file

[Sebastian Bassi]

On Mon, Oct 26, 2009 at 2:16 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:
> If you want a general example, that is a good choice.  It is an unmodified file
> created by the Roche tools containing just 10 random reads. The folder also
> contains FASTA and QUAL files (with and without trimming), as converted
> by the Roche tools.

Looks like there is a problem:

>>> from Bio import SeqIO
>>> fh = open('/home/sbassi/E3MFGYR02_random_10_reads.sff')
>>> for rec in SeqIO.parse(fh,'sff'):
	print rec.id

	
E3MFGYR02JWQ7T
E3MFGYR02JA6IL
(... cut ...)

>>> for rec in SeqIO.parse(fh,'sff'):
	print rec.seq

	
Traceback (most recent call last):
  File "<pyshell#6>", line 1, in <module>
    for rec in SeqIO.parse(fh,'sff'):
  File "/usr/local/lib/python2.6/dist-packages/biopython-1.52-py2.6-linux-i686.egg/Bio/SeqIO/SffIO.py",
line 354, in SffIterator
    = _sff_file_header(handle)
  File "/usr/local/lib/python2.6/dist-packages/biopython-1.52-py2.6-linux-i686.egg/Bio/SeqIO/SffIO.py",
line 56, in _sff_file_header
    raise ValueError("Wrong SFF magic number in header")
ValueError: Wrong SFF magic number in header


I have 1.52 plus SffIO.py and __init__.py from your branch.