[Biopython] sff inot fasta and qual then trim

[Kiss, Csaba]

>That sounds a bit slow, can you compare this to the Biopython SFF conversion time (or any of the other tools)?
I used 
SeqIO.convert("sd6.sff", "sff-trim", "sd6_p.fasta", "fasta")
SeqIO.convert("sd6.sff", "sff-trim", "sd6_p.qual", "qual")

and it finished in 8 minutes. That's much better than 3 hours. The problem is that if I use the mothur fasta/qual files and the python fasta/qual files and trim the sequences exactly the same way in mothur, I get slightly different trimmed sequence dataset.
I am investigating further, if it would matter.
Thanks for your helps, it is much appreciated
Csaba