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Filter mapping file issue #2062
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Changes the code for the qiime.filter.filter_mapping_file to work as intended. Pep8 has been checked for the lines modified, other failures in those files are unrelated to this commit.
This commit updates the script filter_samples_from_otu_table.py so that it has a script usage test for the --output_mapping_fp option as well as modifying how that option works.
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Build results will soon be (or already are) available at: http://ci.qiime.org/job/qiime-github-pr/1663/ |
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retest this please |
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Build results will soon be (or already are) available at: http://ci.qiime.org/job/qiime-github-pr/1719/ |
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This PR does 3 things:
qiime.filter.filter_mapping_filebehaves to match the documentation.--output_mapping_fpinfilter_samples_from_otu_table.py: now writes a subsetted mapping file that retains all the metadata columns of the original passed mapping file regardless of their uniqueness status.filter_samples_from_otu_table.pyfor the--output_mapping_fpI believe change 2 is good because: we are not exposing the control of whether or not unique metadata columns are written in the script (we don't mention it in the documentation either) and so it is very startling to see that data disappear when you use the
--output_mapping_fpoption. In addition, its easy to remove columns in e.g. excel, whereas its annoying to have to add columns back in if you have output a reduced mapping file. Also, its useful to retain non-unique and totally unique columns with a reduced mapping file if you are e.g. trying to work with a new dataset and see what the values for a particular set of samples are.