[Bio-linux-dev] AmpliconNoise Bug in QIIME

[Tim Booth]

Hi Mike,

I was just about to release my new Qiime 1.4 package, so I added your
patch this morning and I'm just waiting for the DEB to rebuild on
Launchpad (I'm now using Launchpad for staging new packages):

https://launchpad.net/~tbooth/+archive/ppa1/+sourcepub/2282287/+listing-archive-extra

Launchpad says it should queue up the 64-bit build in about 20 minutes
(ie. by 5:30 today) so would you be able to test it for me before I put
it on the main server?

Cheers,

TIM

On Thu, 2012-03-01 at 09:22 +0000, Mike Cox wrote:
> Hi Tim,
> 
> 
> We came across a bug in all versions of AmpliconNoise in QIIME
> recently (1.3 on Biolinux, 1.4 macqiime, 1.4 virtual boxes), where
> primers were no longer being stripped from the output (inflating OTU
> estimates and affecting ID particularly with redundant primers).
> 
> 
> It has been fixed in the SVN version of QIIME 1.4 and I've fixed it
> locally on my machine by
> editing /usr/share/pyshared/qiime/workflow.py.
> Previously:
> 
> cmd = 'Parse.pl '+bc_seqs[i]+' '+truncate_len+' < '+\
> 
> so that it reads:
> 
> cmd = 'Parse.pl '+bc_seqs[i]+one_primer+' '+truncate_len+' < '+\
> 
> and confirmed this works for the install.
> 
> I don't know whether it's worth updating the package to the SVN QIIME
> 1.4 where the fix is incorporated, or waiting for version 1.5 to do
> the update (I don't know what their planned release date is for that
> one).
> 
> Cheers
> 
> 
> Mike
> 
> 
> 
> 
> 
> blog: http://palecomic.tumblr.com/
> skype: mikeyjcox
> twitter: mikeyj

-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB 

http://nebc.nerc.ac.uk
+44 1491 69 2705

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