Order of steps in decompose run

[Hilary Morrison]

Small suggestion--

When running decompose, I often have a minor error in the metadata file. Today, for example:

/bioware/python-2.7.12-201701011205/lib/python2.7/site-packages/setuptools-18.1-py2.7.egg/pkg_resources/__init__.py:1256: UserWarning: /users/morrison/.python-eggs is writable by group/others and vulnerable to attack when used with get_resource_filename. Consider a more secure location (set with .set_extraction_path or the PYTHON_EGG_CACHE environment variable).

Config Error: Not every line in the mapping file has the same number of fields (line 2 has 6 columns)

or I write 'sample' rather than 'samples',  or have numbers-only in a field. 

I don't find this out until the entire fasta has been checked out and number of datasets/reads calculated. Could you switch the order, so that the metadata file is checked before the fasta? Or add a separate utility, akin to o-get-sample-info-from-fasta?

[A. Murat Eren]

Hi Hilary,

You're right. The checks should be done before the analysis starts. I will do something about this soon.

Thank you!

--

A. Murat Eren (meren)
http://merenlab.org :: twitter :: gpg

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