[Biopython] sff inot fasta and qual then trim

Kiss, Csaba csaba.kiss at lanl.gov
Tue Oct 23 16:04:21 UTC 2012


I am new to bio-python. I am trying to replace mothur with BioPython.
I hope that biopython is faster than mothur. All I want to do is this:

sffinfo(sff=sd11.fasta)
trim.seqs(fasta=sd11.fasta, qfile=sd11.qual, minlength = 50, maxhomop=8, qwindowsize=50, qwindowaverage =22)

Can someone help me to translate the two mothur statements above to biopython, please?
It would be greatly appreciated.
thanks


--
Best Regards:
Csaba Kiss PhD, MSc, BSc
TA-43, HRL-1, MS888
Los Alamos National Laboratory
Work:    1-505-667-9898
Cell:   1-505-920-5774





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