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mpwt 0.5

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@ArnaudBelcour ArnaudBelcour released this 02 Jul 11:36
v0.5
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Learn about vigilant mode.

Warning:
In this version, the behaviours of some arguments have been changed.

  • the -r/size_reduction argument will delete PGDB inside ptools-local and compressed the results in zip (issue #26).
  • the --clean argument (when used with -f/input_folder argument) will delete only PGDBs corresponding to species in the input_folder (issue #23).

Add:

  • support for Pathologic Format (PF) file (issue #19).
  • taxon_id.tsv file to manage taxon_id for species. With the argument --taxon-id/taxon_file argument, you can force mpwt to use taxon from taxon_id.tsv for all type of files (Genbank, GFF or PF).
  • a new argument --ignore-error/ignore_error to ignore PathoLogic failed builds (issue #21). With this argument, mpwt will continue to run even if PathoLogic have crashed for some species. It will perform the rest of the workflow for the successful build.
  • time measure of each steps of mpwt. They will be printed if you use -v/verbose or they can be accessed at the end of the log_error.txt file (created with --log).

Fix:

  • interaction between --clean and the other arguments.
  • error if -r/size_reduction is used without output_folder argument.
  • a typo error with the name of a function (remove_pgdbs).

Modification:

  • split multipwt.py in multiple modules to ease reading (issue #25).
  • --clean behaviour when used with -f/input_folder (issue #23) to delete only input species PGDB.
  • -r/size_reduction behaviour: it will delete the PGDB from ptools-local and it will move the results into a compressed zip file.
  • add table and list in Readme.
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