sumt 3.8.2__tar.gz → 3.8.4__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- {sumt-3.8.2 → sumt-3.8.4}/PKG-INFO +2 -2
- {sumt-3.8.2 → sumt-3.8.4}/README.md +1 -1
- {sumt-3.8.2 → sumt-3.8.4}/setup.cfg +1 -1
- {sumt-3.8.2 → sumt-3.8.4}/sumt.egg-info/PKG-INFO +2 -2
- {sumt-3.8.2 → sumt-3.8.4}/sumt.py +7 -5
- {sumt-3.8.2 → sumt-3.8.4}/LICENSE +0 -0
- {sumt-3.8.2 → sumt-3.8.4}/pyproject.toml +0 -0
- {sumt-3.8.2 → sumt-3.8.4}/sumt.egg-info/SOURCES.txt +0 -0
- {sumt-3.8.2 → sumt-3.8.4}/sumt.egg-info/dependency_links.txt +0 -0
- {sumt-3.8.2 → sumt-3.8.4}/sumt.egg-info/entry_points.txt +0 -0
- {sumt-3.8.2 → sumt-3.8.4}/sumt.egg-info/requires.txt +0 -0
- {sumt-3.8.2 → sumt-3.8.4}/sumt.egg-info/top_level.txt +0 -0
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Metadata-Version: 2.1
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Name: sumt
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Version: 3.8.
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Version: 3.8.4
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Summary: Computes consensus trees and other phylogenetic tree summaries
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Home-page: https://github.com/agormp/sumt
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Author: Anders Gorm Pedersen
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@@ -16,7 +16,7 @@ Requires-Dist: psutil
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# sumt
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[](https://pepy.tech/project/sumt)
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[](https://zenodo.org/doi/10.5281/zenodo.10148693)
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# sumt
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[](https://pepy.tech/project/sumt)
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[](https://zenodo.org/doi/10.5281/zenodo.10148693)
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@@ -1,6 +1,6 @@
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Metadata-Version: 2.1
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Name: sumt
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Version: 3.8.
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Version: 3.8.4
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Summary: Computes consensus trees and other phylogenetic tree summaries
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Home-page: https://github.com/agormp/sumt
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Author: Anders Gorm Pedersen
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@@ -16,7 +16,7 @@ Requires-Dist: psutil
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# sumt
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[](https://pepy.tech/project/sumt)
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[](https://zenodo.org/doi/10.5281/zenodo.10148693)
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@@ -203,9 +203,11 @@ def parse_commandline(commandlist):
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if args.burninfrac is None:
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args.burninfrac = [0.0] * len(args.infilelist)
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elif len(args.burninfrac) == 1:
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burnin_value = args.burninfrac[0]
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args.burninfrac = [burnin_value] * len(args.infilelist)
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elif len(args.burninfrac) != len(args.infilelist):
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raise parser.error(msg)
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parser.error("either provide one burnin value, or one value per input file")
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if any(x < 0 or x > 1 for x in args.burninfrac):
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parser.error("option -b: NUM must be between 0.0 and 1.0")
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bayes_grp = parser.add_argument_group("Bayesian phylogeny options")
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bayes_grp.add_argument("-b", dest="burninfrac", metavar="NUM", type=float, default=None, nargs='
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bayes_grp.add_argument("-b", dest="burninfrac", metavar="NUM", type=float, default=None, nargs='+',
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help="burnin: fraction of trees to discard [0 - 1; default: %(default)s]. "
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+ "Either one value (used on all input files), or one value per input file.")
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elif args.rootminvar:
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contree.rootminvar()
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elif args.rootmaxfreq:
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treesummary.root_maxfreq(contree)
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contree = treesummary.root_maxfreq(contree)
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# If MCC tree was re-rooted, then we need to recompute log clade credibility
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if args.mcc and args.actively_rooted:
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sys.stdout.flush()
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contree = treesummary.set_ca_node_depths(contree, wt_count_burnin_filename_list)
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sys.stdout.write("done.\n")
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elif args.biplen and
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elif args.biplen and args.mcc:
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contree = treesummary.set_mean_biplen(contree)
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# If root is bifurcation and one child is leaf: Remove branchID (=leafname) and label from other child-branch
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