[Bio-linux-dev] AmpliconNoise Bug in QIIME

[Mike Cox]

Thanks Tim,

installed and the ampliconnoise patch works,

Cheers

Mike


On Thu, Mar 1, 2012 at 16:51, Tim Booth <tbooth at ceh.ac.uk> wrote:

> 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
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> Wallingford, England
> OX10 8BB
>
> http://nebc.nerc.ac.uk
> +44 1491 69 2705
>
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