jbloomlab / dms_tools2

software for the analysis and visualization of deep mutational scanning data
GNU General Public License v3.0
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adding syn_selection_by_codon module #34

Closed fwelsh closed 4 years ago

fwelsh commented 4 years ago

Added a new module which identifies sites with selection on synonymous codons, using Fisher's Exact test to calculate codon enrichment at each site.

jbloom commented 4 years ago

@fwelsh: Can you make and then push a few additional changes before I merge this:

  1. Change function name to something syn_selection_by_codon in the new syn_synonymous module. The reason is that we are currently doing a different test for each module; in a future version we might test by amino acid (using 2 X N table), and that would by syn_selection_by_aminoacid.

  2. Add spaces after the initial - here, otherwise the docs won't render correctly as a space is required after list items.

  3. Update the CHANGELOG.rst file to indicate that in the new version 2.6.2 you have added the syn_selection module.

  4. Update the version number here to 2.6.2.