that seems like overkill since they would be called for every test, not
just the sync_biom_and_mf. or are you suggesting making just a new class
for sync_biom_to_mf and its own setup?


On Tue, Dec 10, 2013 at 11:25 AM, Jai Ram Rideout
<notifications@github.com>wrote:

> In tests/test_util.py:
>
> > +        'NotInOtuTable2\tcat5\t8',
> > +        'Sample3\tcat2\t3',
> > +        'Sample5\tcat3\t5',
> > +        'Sample6\tcat3\t6',
> > +        'NotInOtuTable1\tcat5\t7']
> > +        MF_OUT_3 = ['#SampleIttest_cat\ttest_corr',
> > +        'Sample1\tcat1\t1',
> > +        'Sample2\tcat1\t2',
> > +        'Sample3\tcat2\t3',
> > +        'Sample5\tcat3\t5',
> > +        'Sample6\tcat3\t6']
> > +        BT_4 = """{"id": "None","format": "Biological Observation Matrix 1.0.0","format_url": "http://biom-format.org","type": "OTU table","generated_by": "BIOM-Format 1.1.2","date": "2013-08-16T15:23:02.872397","matrix_type": "sparse","matrix_element_type": "float","shape": [6, 8],"data": [[0,0,28.0],[0,1,52.0],[0,2,51.0],[0,3,78.0],[0,4,16.0],[0,5,77.0],[0,6,73.0],[0,7,6.0],[1,0,25.0],[1,1,14.0],[1,2,11.0],[1,3,32.0],[1,4,48.0],[1,5,63.0],[1,6,27.0],[1,7,38.0],[2,0,31.0],[2,1,2.0],[2,2,15.0],[2,3,69.0],[2,4,64.0],[2,5,27.0],[2,6,64.0],[2,7,54.0],[3,0,36.0],[3,1,68.0],[3,2,70.0],[3,3,65.0],[3,4,33.0],[3,5,62.0],[3,6,60.0],[3,7,23.0],[4,0,16.0],[4,1,41.0],[4,2,59.0],[4,3,40.0],[4,4,15.0],[4,5,3.0],[4,6,35.0],[4,7,5.0],[5,0,32.0],[5,1,8.0],[5,2,54.0],[5,3,98.0],[5,4,29.0],[5,5,50.0],[5,6
>  ,93.0],[5,7,19.0]],"rows": [{"id": "OTU1", "metadata": {"taxonomy": "k__One"}},{"id": "OTU2", "metadata": {"taxonomy": "k__Two"}},{"id": "OTU3", "metadata": {"taxonomy": "k__Three"}},{"id": "OTU4", "metadata": {"taxonomy": "k__Four"}},{"id": "OTU5", "metadata": {"taxonomy": "k__Five"}},{"id": "OTU6", "metadata": {"taxonomy": "k__Six"}}],"columns": [{"id": "Sample1", "metadata": null},{"id": "Sample2", "metadata": null},{"id": "Sample3", "metadata": null},{"id": "Sample4", "metadata": null},{"id": "Sample5", "metadata": nu
>  ll},{"id": "Sample6", "metadata": null},{"id": "Sample7", "metadata": null},{"id": "Sample8", "metadata": null}]}"""
> > +        mf_exp, _ = parse_mapping_file_to_dict(MF_OUT_1)
> > +        bt_exp = parse_biom_table(BT_IN_1) #bt doesn't change in this test
> > +        mf_obs, bt_obs, nonshared_samples = \
> > +            sync_biom_and_mf(parse_mapping_file_to_dict(MF_IN_1)[0],
>
> The parse_mapping_file_to_dict and parse_biom_table calls should happen
> in setUp.
>
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