I'd rather not draw this out even longer since this has been in progress
since August. Can you please address the comments and then send Adam and I
the updated file by email? Notes on using Github can be found here:

https://docs.google.com/document/d/17lath3EHqNc7H2MBE_u9FTxRGDhylfIh3QhzIct0GT8/edit#heading=h.1a44we13rblz


On Mon, Dec 30, 2013 at 11:04 AM, amnona <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",
>
> Tried to do the corrections but i'm really at a loss on the whole github
> thing. when you or adam will be in, if you can explain to me the idea how
> it works i'll insert the changes.
> … <#14344ae0447f3326_>
> On Mon, Dec 30, 2013 at 10:17 AM, 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 progress
> on this Amnon? We *really* need to get this finished. — Reply to this email
> directly or view it on GitHub<
> https://github.com/qiime/American-Gut/pull/50/files#r8587790> .
>
> —
> Reply to this email directly or view it on GitHub<https://github.com/qiime/American-Gut/pull/50/files#r8588580>
> .
>