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Forum: Bioinformatics 05-07-2013, 06:05 PM
Replies: 21
Views: 9,120
Posted By pfh
You need to make sure you run the setup.py script...

You need to make sure you run the setup.py script with python 2.7. First work out how to run python 2.7, eg rather than typing "python" you might need to type "python2.7". Then to install nesoni from...
Forum: Bioinformatics 05-03-2013, 10:48 PM
Replies: 21
Views: 9,120
Posted By pfh
Hi Mona, Looks like OrderedDict was added in...

Hi Mona,

Looks like OrderedDict was added in Python 2.7. I need to update the requirements in the README!

Ok, two options:

1. Install Python 2.7. I don't know enough about package management...
Forum: Bioinformatics 11-24-2010, 03:44 PM
Replies: 21
Views: 9,120
Posted By pfh
The relevant program from SHRiMP 2 will be...

The relevant program from SHRiMP 2 will be "gmapper-ls".

It looks like this is failing to run, and then samtools is discombobulated by receiving empty input.
Forum: Bioinformatics 08-15-2010, 07:01 PM
Replies: 21
Views: 9,120
Posted By pfh
This might be a minor difference between Cython...

This might be a minor difference between Cython versions, which version are you using? I have 0.12.1.

Anyway, this might fix it:

http://bioinformatics.net.au/nesoni-0.36.tar.gz
Forum: Bioinformatics 08-12-2010, 10:54 PM
Replies: 21
Views: 9,120
Posted By pfh
Ah. Oops. distutils didn't automatically update...

Ah. Oops. distutils didn't automatically update the MANIFEST for some reason.

Try this: http://bioinformatics.net.au/nesoni-0.35.tar.gz


Note that "nesoni shrimp" and "nesoni consensus" use...
Forum: Bioinformatics 11-08-2009, 02:13 PM
Replies: 2
Views: 4,048
Posted By pfh
I've written some software that can do this for...

I've written some software that can do this for bacteria. Doesn't work with eukaryotes though, various scalability issues yet to be overcome. http://www.vicbioinformatics.com/software.nesoni.shtml
...
Forum: Bioinformatics 05-05-2008, 09:24 PM
Replies: 9
Views: 4,488
Posted By pfh
Sequence alignment is vectorizable, and there are...

Sequence alignment is vectorizable, and there are various SIMD implementations. There is a brute force sequence aligner in the FASTA package that uses SIMD, for example.

If you want to align...
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