filtering feature tables tutorial addition #39
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Conflicts: source/tutorials/import-sequence-data.rst source/tutorials/import.rst source/tutorials/index.rst
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| Both of these methods can also be applied to filter contingent on the maximum number of features or samples, using the ``--p-max-features`` and ``--p-max-samples`` parameters. | ||
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| Identifier-based filtering |
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Is it worth trying to call this Index-based filtering or is that too technical?
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Or Identity-based filtering which sounds more natural to me for some reason?
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Went with Index-based, and indicated that this refers to identifiers. In QIIME 1 we usually refer to these as identifiers, but I think we should transition to this terminology (which will important for consistency when we have real index/metadata support).
| Metadata-based filtering | ||
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| Metadata-based filtering is similar to identifier-based filtering, except that the list of identifiers to keep is determined based on metadata rather than being provided by the user directly. This is achieved using the ``--m-sample-metadata-file`` or ``--m-feature-metadata-file`` parameter (for ``filter-samples`` or ``filter-features``, respectively) and the ``--p-where`` parameter. The user provides a description of the samples that should be retained based on their metadata using ``--p-where``, where the syntax for this description is the SQLite where-clause syntax. |
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This paragraph is a little confusing. Is it possible to introduce the --p-where clause first? Reading it the first time it seemed like this was an augmentation of the identifier-filter, but then went on to redefine the same parameters in the same way (felt like a deja vu) causing me to assume that I had misread the previous section somehow.
This is achieved by providing a ``--p-where`` parameter in addition to a
``--m-sample-metadata-file``/``--m-feature-metadata-file`` (as described above).
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Also I think we should link out SQLite where-clause to something like: https://www.tutorialspoint.com/sqlite/sqlite_where_clause.htm (a more canonical resource would be nice, but the SQLite homepage was a grammar definition, which isn't user-friendly)
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How about the generic WHERE entry on wikipedia? We aren't using any SQLite-only features, and there seems to be some nice examples of predicates here.
| .. command-block:: | ||
| qiime feature-table filter-samples --i-table table.qza --m-sample-metadata-file sample-metadata.tsv --p-where "Subject='subject-1'" --o-filtered-table filtered-table | ||
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| ``--p-where`` expressions can be made more complex as follows. Here, the ``--p-where`` parameter is specifying that we want to retain only the samples whose ``Subject`` is ``subject-1`` *and* whose ``BodySite`` is ``gut`` in ``sample-metadata.tsv``. |
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I would emphasize the quotation marks as well here.
| curl -sL "https://docs.google.com/spreadsheets/d/1_3ZbqCtAYx-9BJYHoWlICkVJ4W_QGMfJRPLedt_0hws/export?gid=0&format=tsv" > sample-metadata.tsv | ||
| curl -sLO https://data.qiime2.org/2.0.6/tutorials/filtering-feature-tables/table.qza | ||
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| Frequency-based filtering |
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Should this be Total frequency-based filtering? With just frequency I didn't really intuit what it was doing. Based on this wikipedia example it looks like we are filtering the "marginal totals". Is that vocabulary useful here?
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👍 Went with Total-frequency-based.
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Addressed all of your comments, thanks @ebolyen and @thermokarst! |
Fixes #21.