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1.1.4

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@KatyBrown KatyBrown released this 06 Jun 18:39
v1.1.4
eefeae6

New features

  • Added two new mini alignment options - identity and similarity plots
    Identity plots show which positions in your alignment are identical to the consensus, different to the consensus or gaps. Created using the --plot_consensus_identity parameter.
    identity

Similarity plots calculate a substitution score for your alignment vs the consensus, using a substitution matrix of your choice, and colour the plot according to this score. Created using the --plot_consensus_similarity parameter.
similarity

  • Added additional statistics plots, plotted by default when --plot_stats_input or --plot_stats_output is specified.

    • The nucleotide or amino acid frequency in the alignment and, for nucleotide alignments, the A/T (U) vs C/G ratio
      resfreq_nt
    • For nucleotide alignments, the proportion of each "change" in nucleotide relative to the consensus.
      changefreq

  • Added the option to remove sequences with duplicate names from the alignment, keeping either the first or last instance of each sequence name, with the parameter --deduplicate_ids.

Testing, Packaging and Documentation

  • Updated CI workflow to cover more recent versions of Python
  • Changed all requirements in package to require a minimum rather than fixed version of software
  • Various updates to tests using images to work with latest version of pytest
  • Minor updates to readthedocs build

Debugging

  • Minor debug to crop_divergent to run remove_gap_only by default afterwards
  • Improved markup for remove_gap_only
  • Adjustment to move Q amino acids slightly higher in sequence logos
  • Removed error sometimes raised if no cleaning functions are run
  • Updated utilityFunctions.listFonts() as the matplotlib method used here was deprecated
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