I'll try to have a look next week :-)
 On Dec 22, 2013 10:14 PM, "adamrp" <notifications@github.com> wrote:

> In ipynb/contaminant_filtering.ipynb:
>
> > +     "collapsed": false,
> > +     "input": [
> > +      "!filter_fasta.py -f $merged_sequences_fp -o $merged_sequences_fecal_only_fp --mapping_fp=$merged_mapping_file_fp --valid_states=\"BODY_SITE:UBERON:feces\""
> > +     ],
> > +     "language": "python",
> > +     "metadata": {},
> > +     "outputs": []
> > +    },
> > +    {
> > +     "cell_type": "markdown",
> > +     "metadata": {},
> > +     "source": [
> > +      "The filtering will proceed according to the following steps:\n",
> > +      "\n",
> > +      "1. Identify the most abundant Gammaproteobactia and select the representative sequences from the most abundant, such that the cumulative abundance of remaining Gammaproteobacteria is no greater than 3%\n",
> > +      "2. Find all sequences in the American Gut sequences that map to these OTUs at 97PI\n",
>
> Nothing yet; @amnona <https://github.com/amnona>? Adam
> … <#1431da9b567116b3_>
> On Sun, Dec 22, 2013 at 6:39 PM, Daniel McDonald <notifications@github.com>wrote:
> > In ipynb/contaminant_filtering.ipynb: > > > + "collapsed": false, > > +
> "input": [ > > + "!filter_fasta.py -f $merged_sequences_fp -o
> $merged_sequences_fecal_only_fp --mapping_fp=$merged_mapping_file_fp
> --valid_states=\"BODY_SITE:UBERON:feces\"" > > + ], > > + "language":
> "python", > > + "metadata": {}, > > + "outputs": [] > > + }, > > + { > > +
> "cell_type": "markdown", > > + "metadata": {}, > > + "source": [ > > + "The
> filtering will proceed according to the following steps:\n", > > + "\n", >
> > + "1. Identify the most abundant Gammaproteobactia and select the
> representative sequences from the most abundant, such that the cumulative
> abundance of remaining Gammaproteobacteria is no greater than 3%\n", > > +
> "2. Find all sequences in the American Gut sequences that map to these OTUs
> at 97PI\n", > > Any word from Amnon on this? > … <#1431d1b732c72155_> > On
> Mon, Dec 16, 2013 at 5:51 PM, adamrp <notifications@github.com> wrote: In
> ipynb/contaminant_filtering.ipynb: > + "collapsed": false, > + "input": [ >
> + "!filter_fasta.py -f $merged_sequences_fp -o
> $merged_sequences_fecal_only_fp --mapping_fp=$merged_mapping_file_fp
> --valid_states=\"BODY_SITE:UBERON:feces\"" > + ], > + "language": "python",
> > + "metadata": {}, > + "outputs": [] > + }, > + { > + "cell_type":
> "markdown", > + "metadata": {}, > + "source": [ > + "The filtering will
> proceed according to the following steps:\n", > + "\n", > + "1. Identify
> the most abundant Gammaproteobactia and select the representative sequences
> from the most abundant, such that the cumulative abundance of remaining
> Gammaproteobacteria is no greater than 3%\n", > + "2. Find all sequences in
> the American Gut sequences that map to these OTUs at 97PI\n", I'll change
> it once Amnon has the opportunity to see the rest of these comments. —
> Reply to this email directly or view it on GitHub<
> https://github.com/qiime/American-Gut/pull/50/files#r8389025> . — Reply
> to this email directly or view it on GitHub<
> https://github.com/qiime/American-Gut/pull/50/files#r8521874> .
>
> —
> Reply to this email directly or view it on GitHub<https://github.com/qiime/American-Gut/pull/50/files#r8522448>
> .
>