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1.1.3 19th July, 2024

  • Bugfix: correct a file and folder name issue that resulted in missing output files when using the option --use-clustal.

1.1.2 15th July, 2024

  • Bugfix: correct an error when running paragone full_pipeline due to mis-specified output folders.

1.1.1 28th June, 2024

  • Bugfix: raise the correct error if TAPER doesn't run successfully.
  • Removed logging of stdout/stderr for successful commands (only affects osx, due to the default use of spawn for multiprocessing).
  • Improved logging of error messages and control flow for unsuccessful commands.

1.1.0 20th June, 2024

  • Add new dependency: Julia
  • Replaced HmmCleaner with TAPER for sequence-specific cleaning/QC.
  • Remove use of Bio.Align.Applications.MafftCommandline and Bio.Align.Applications.ClustalOmegaCommandline due to deprecation.
  • Ensure an internal outgroup sequence is always selected for each taxon when multiple sequences are present (issue#5).
  • Add check that internal outgroup sequences are found in the folder provided to command align_selected_and_tree (issue#6).
  • Update error handling and logging for the steps of the pipeline that use multiprocessing.
  • Update commands in run_paragone_test_dataset.sh to match output directory names.

1.0.0 25th August, 2023

  • Bugfix: change type from int to float for --trimal_resoverlap in all relevant subparsers.
  • Add check that --trimal_resoverlap is provided if --trimal_seqoverlap is used, and vice-versa.
  • Add module version.py for a single location of ParaGone version number.

0.0.14 7th July, 2023

  • Change the parameter new_mo_algorithm to mo_algorithm_paragone for subparsers parser_full_pipeline and parser_prune_paralogs

0.0.13 6th July, 2023

  • Remove the positional parameter selected_alignment_directory from subparser add_align_selected_and_tree_parser, as align_selected_and_tree.py now hardcodes this path as 09_sequences_from_qc_trees

0.0.12 3rd July, 2023

  • Add full trimal options to steps that use trimal: check_and_align, align_selected_and_tree, and final_alignments, as well as full_pipeline.
  • Bugfix in prune_paralogs_mo.py: correct error when parsing outgroup tip labels in function prune_paralogs_from_rerooted_homotree_cjj().

0.0.11 1st May, 2023

  • Following QC but before paralog pruning, trees are now parsed to produce two additional reports in *.tsv format: per_locus_paralogy_report_post_tree_qc.tsv and per_taxon_paralogy_report_post_tree_qc.tsv.
  • Change optional flag --original_mo_algorithm to --new_mo_algorithm for subcommand prune_paralogs and full_pipeline; if used, apply a re-implementation of the MO algorithm rather than the original Yang and Smith MO algorithm. Default is to apply the original Yang and Smith MO algorithm.

0.0.10 31st March, 2023

  • Fix bug in prune_paralogs_mo.py: update outgroup trimming regex in new MO implementation to allow for optional bootstrap support values, and/or tree lengths in scientific notation (e.g. 2.079e-06)

0.0.9 23rd March, 2023

  • Add the flag --debug to the prune_paralogs subcommand. When supplied, additional details will be written to the log file. This can increase the size of the log file substantially.
  • Fix bug in prune_paralogs_mo.py where the default implementation of the MO algorithm incorrectly parsed trees rooted with a single outgroup taxon.

0.0.8 17th March, 2023

  • Fix bug in prune_paralogs_rt.py where ingroups with fewer than the minimum required taxa caused an endless loop.
  • Add optional flag --original_mo_algorithm to subcommand prune_paralogs and full_pipeline; if used, apply the original Yang and Smith MO algorithm. Default is to apply a re-implementation of the MO algorithm.
  • Prevent full MAFFT alignments from being written to log files on Linux.

0.0.7 9th March, 2023

  • Make the MAFFT option --adjustdirection (https://mafft.cbrc.jp/alignment/software/adjustdirection.html) optional for the first alignment step of the pipeline; default is not to use this flag.
  • Fix bug in MO pruning step when outgroups not monophyletic.
  • Rename flag --no_stitched_contigs to --use_clustal. Only run MAFFT first if flag --mafft_adjustdirection is also supplied.
  • For the tree QC step involving removal of long tip-branches, replace the original Yang and Smith 2014 script trim_tips.py with a wrapper around TreeShrink.
  • Remove the trim tips step from the MI pruning stage; seqs are extracted from the MI pruned trees, so long branches are not a concern at this point.
  • HmmCleaner now runs in parallel using multiprocessing.
  • Added subcommand delete_intermediate_files.