partis-bcr 1.0.11.post1.dev1__cp312-cp312-manylinux1_x86_64.whl → 1.0.11.post1.dev3__cp312-cp312-manylinux1_x86_64.whl

bin/partis

@@ -1639,7 +1639,7 @@ parent_args.append({'name' : '--plot-and-fit-absolutely-everything', 'kwargs' :
 parent_args.append({'name' : '--get-selection-metrics', 'kwargs' : {'action' : 'store_true', 'help' : 'calculate selection metrics for each cluster (can also be run on existing output with \'get-selection-metrics\' action). By default it calculates fast, but very approximate, trees (see manual for details).'}})
 parent_args.append({'name' : '--min-selection-metric-cluster-size', 'kwargs' : {'type' : int, 'default' : treeutils.default_min_selection_metric_cluster_size, 'help' : 'When calculating selection metrics, ignore clusters smaller than this. See also --min-paired-cluster-size-to-read, which is similar but applies earlier, when reading clusters from files.'}})
 parent_args.append({'name' : '--min-paired-cluster-size-to-read', 'kwargs' : {'type' : int, 'default' : treeutils.default_min_selection_metric_cluster_size, 'help' : 'When reading paired annotations when getting selection metrics or plotting partitions, ignore clusters with either N h or l ids smaller than this. See also --min-selection-metric-cluster-size, which is similar but only skips selection metric calculation.'}})
-parent_args.append({'name' : '--treefname', 'kwargs' : {'help' : 'newick-formatted file with a tree corresponding to the sequences either in --infname (if making new output, i.e. action is annotate or partition) or --outfname (if reading existing output, i.e. action is get-selection-metrics) (unrelated to --input-simulation-treefname).'}})
+parent_args.append({'name' : '--treefname', 'kwargs' : {'help' : 'newick-formatted file with a tree corresponding to the sequences either in --infname (if making new output, i.e. action is annotate or partition) or --outfname (if reading existing output, i.e. action is get-selection-metrics). Used for instance if getting selection metrics using trees inferred by an external program (unrelated to --input-simulation-treefname).'}})
 parent_args.append({'name' : '--tree-inference-method', 'kwargs' : {'choices' : ['fasttree', 'iqtree', 'iqtree-1.6.beta3', 'iqtree-2.3.1', 'raxml', 'gctree', 'gctree-base', 'gctree-mut-mult', 'gctree-no-dag', 'linearham', 'igphyml', 'cpath'], 'help' : 'Method to use when inferring trees (default: fasttree)'}})
 parent_args.append({'name' : '--tree-inference-subdir', 'kwargs' : {'help' : 'Subdirectory of the (automatically-set) tree inference workdir to which to write tree inference output files. By default, these are written to a subdir of --outfname/--paired-outdir with the name of the inference method, but this argument allows multiple versions, as with --sub-plotdir.'}})
 parent_args.append({'name' : '--infer-trees-with-only-leaves', 'kwargs' : {'action' : 'store_true', 'help' : 'Discard internal nodes in true trees when inferring phylogenetic trees.'}})

bin/partis-test.py

@@ -299,6 +299,10 @@ class Tester(object):
 
         if ptest == 'simulate':
             argfo['parameter-dir'] = self.paramdir(input_stype, 'data')
+            # if args.no_tree_gen:
+            #     argfo['extras'] += ['--input-simulation-treefname', '%s/test/trees.nwk'%utils.get_partis_dir()]
+            if args.no_per_base_mutation:
+                argfo['extras'] += ['--no-per-base-mutation']
         else:
             argfo['inpath'] = self.inpath('new' if args.bust_cache else 'ref', input_dtype)
             if ptest.find('subset-') != 0:
@@ -932,6 +936,8 @@ parser.add_argument('--only-bust-current', action='store_true', help='only bust
 parser.add_argument('--paired', action='store_true', help='run paired tests, i.e. with --paired-loci. Note that this doesn\'t test all the things (e.g. seed partitioning) that non-paired does.')
 parser.add_argument('--run-all', action='store_true', help='run all four combinations of tests: paired/non-paired and slow/non-slow (by default only runs one). *Not* for use with --bust-cache, which runs all of them by default.')
 parser.add_argument('--no-simu', action='store_true', help='don\'t run simulation, e.g. if using a minimal install')
+# parser.add_argument('--no-tree-gen', action='store_true', help='if set, use the pre-generated newick file instead of generating trees with R/TreeSim (to avoid R installation)')
+parser.add_argument('--no-per-base-mutation', action='store_true', help='use simpler, non-per-base mutation model (to avoid bpp-newlik compilation)')
 parser.add_argument('--ig-or-tr', default='ig')
 parser.add_argument('--print-width', type=int, default=300, help='set to 0 for infinite')
 

bin/partis.py

@@ -1639,7 +1639,7 @@ parent_args.append({'name' : '--plot-and-fit-absolutely-everything', 'kwargs' :
 parent_args.append({'name' : '--get-selection-metrics', 'kwargs' : {'action' : 'store_true', 'help' : 'calculate selection metrics for each cluster (can also be run on existing output with \'get-selection-metrics\' action). By default it calculates fast, but very approximate, trees (see manual for details).'}})
 parent_args.append({'name' : '--min-selection-metric-cluster-size', 'kwargs' : {'type' : int, 'default' : treeutils.default_min_selection_metric_cluster_size, 'help' : 'When calculating selection metrics, ignore clusters smaller than this. See also --min-paired-cluster-size-to-read, which is similar but applies earlier, when reading clusters from files.'}})
 parent_args.append({'name' : '--min-paired-cluster-size-to-read', 'kwargs' : {'type' : int, 'default' : treeutils.default_min_selection_metric_cluster_size, 'help' : 'When reading paired annotations when getting selection metrics or plotting partitions, ignore clusters with either N h or l ids smaller than this. See also --min-selection-metric-cluster-size, which is similar but only skips selection metric calculation.'}})
-parent_args.append({'name' : '--treefname', 'kwargs' : {'help' : 'newick-formatted file with a tree corresponding to the sequences either in --infname (if making new output, i.e. action is annotate or partition) or --outfname (if reading existing output, i.e. action is get-selection-metrics) (unrelated to --input-simulation-treefname).'}})
+parent_args.append({'name' : '--treefname', 'kwargs' : {'help' : 'newick-formatted file with a tree corresponding to the sequences either in --infname (if making new output, i.e. action is annotate or partition) or --outfname (if reading existing output, i.e. action is get-selection-metrics). Used for instance if getting selection metrics using trees inferred by an external program (unrelated to --input-simulation-treefname).'}})
 parent_args.append({'name' : '--tree-inference-method', 'kwargs' : {'choices' : ['fasttree', 'iqtree', 'iqtree-1.6.beta3', 'iqtree-2.3.1', 'raxml', 'gctree', 'gctree-base', 'gctree-mut-mult', 'gctree-no-dag', 'linearham', 'igphyml', 'cpath'], 'help' : 'Method to use when inferring trees (default: fasttree)'}})
 parent_args.append({'name' : '--tree-inference-subdir', 'kwargs' : {'help' : 'Subdirectory of the (automatically-set) tree inference workdir to which to write tree inference output files. By default, these are written to a subdir of --outfname/--paired-outdir with the name of the inference method, but this argument allows multiple versions, as with --sub-plotdir.'}})
 parent_args.append({'name' : '--infer-trees-with-only-leaves', 'kwargs' : {'action' : 'store_true', 'help' : 'Discard internal nodes in true trees when inferring phylogenetic trees.'}})

{partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/partis-test.py

@@ -299,6 +299,10 @@ class Tester(object):
 
         if ptest == 'simulate':
             argfo['parameter-dir'] = self.paramdir(input_stype, 'data')
+            # if args.no_tree_gen:
+            #     argfo['extras'] += ['--input-simulation-treefname', '%s/test/trees.nwk'%utils.get_partis_dir()]
+            if args.no_per_base_mutation:
+                argfo['extras'] += ['--no-per-base-mutation']
         else:
             argfo['inpath'] = self.inpath('new' if args.bust_cache else 'ref', input_dtype)
             if ptest.find('subset-') != 0:
@@ -932,6 +936,8 @@ parser.add_argument('--only-bust-current', action='store_true', help='only bust
 parser.add_argument('--paired', action='store_true', help='run paired tests, i.e. with --paired-loci. Note that this doesn\'t test all the things (e.g. seed partitioning) that non-paired does.')
 parser.add_argument('--run-all', action='store_true', help='run all four combinations of tests: paired/non-paired and slow/non-slow (by default only runs one). *Not* for use with --bust-cache, which runs all of them by default.')
 parser.add_argument('--no-simu', action='store_true', help='don\'t run simulation, e.g. if using a minimal install')
+# parser.add_argument('--no-tree-gen', action='store_true', help='if set, use the pre-generated newick file instead of generating trees with R/TreeSim (to avoid R installation)')
+parser.add_argument('--no-per-base-mutation', action='store_true', help='use simpler, non-per-base mutation model (to avoid bpp-newlik compilation)')
 parser.add_argument('--ig-or-tr', default='ig')
 parser.add_argument('--print-width', type=int, default=300, help='set to 0 for infinite')
 

{partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.11.post1.dev3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: partis-bcr
-Version: 1.0.11.post1.dev1
+Version: 1.0.11.post1.dev3
 Summary: B- and T-cell receptor sequence annotation, simulation, clonal family and germline inference
 Home-page: https://github.com/psathyrella/partis
 Author: Duncan Ralph