sff 454 files into fasta

[Peruano]

Dear users, I have question:

I am trying to convert a .sff 454 file into fasta, using sff_extract in python2.3.4 that includes Biophyton-1.49. I have used the following command:

$ python sff_extract my_file.sff

and this results in a syntax error:


File "sff_extract", line 405

qual_line = ' '.join((str(q) for q in qual))

^

SyntaxError: invalid syntax


Does anyone could suggest what's wrong?

Thank you in advance

P.R.

[maubp]

That looks to me like some Python syntax requiring Python 2.4 or later. You could change this:

qual_line = ' '.join((str(q) for q in qual))

to:

qual_line = ' '.join([str(q) for q in qual])

but there are probably going to be more issues. I would urge you to update to Python 2.6, Python 2.5 or Python 2.4 (in that order of preference assuming you have no other constraints).

You mentioned Biopython 1.49. You should update (e.g. for FASTQ support). However, the more recent releases also required Python 2.4 or later.

Also, although there is SFF in the pipeline for Biopython is isn't included as yet (i.e. it is not even in the brand new Biopython 1.53 released yesterday). Its on a branch on github, but if you (or anyone else) would like to help test it I am confident we can have this in the next release of Biopython.

[maubp]

You mentioned Biopython 1.49. You should update (e.g. for FASTQ support). However, the more recent releases also required Python 2.4 or later.

Also, although there is SFF in the pipeline for Biopython is isn't included as yet (i.e. it is not even in the brand new Biopython 1.53 released yesterday). Its on a branch on github, but if you (or anyone else) would like to help test it I am confident we can have this in the next release of Biopython.

In case anyone is interested, the SFF support has been merged into the Biopython main branch, and should be included with our next release (Biopython 1.54). Anyone interested in testing it before then can grab the code from our repository.

http://www.biopython.org/wiki/SourceCode

[Baseless]

I know it wont help if you are setting up something very customized, but for just extracting the sequences sffinfo -s should do the trick.

And its included in the recent 2.3 software.

[maubp]

Yeah, if you have the Roche Linux only tools, sffinfo does offer SFF to FASTA (or QUAL, with or without trimming). It was there in v2.0 as well, and I expect in v1 too. See also this thread for getting the tools:

http://seqanswers.com/forums/showthread.php?t=114