partis-bcr 1.0.0__py3-none-any.whl → 1.0.2__py3-none-any.whl

{partis_bcr-1.0.0.dist-info → partis_bcr-1.0.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: partis-bcr
-Version: 1.0.0
+Version: 1.0.2
 Summary: B- and T-cell receptor sequence annotation, simulation, clonal family and germline inference
 Home-page: https://github.com/psathyrella/partis
 Author: Duncan Ralph

{partis_bcr-1.0.0.dist-info → partis_bcr-1.0.2.dist-info}/RECORD

@@ -1,3 +1,47 @@
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+python/cache/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+python/cache/cached_uncertainties.py,sha256=GNs18AG8ROdDg0OOrcArsU73Ev1U8k5Gsnf79WndHG8,4257821
+partis_bcr-1.0.2.dist-info/METADATA,sha256=OMZO1vX1KCG3OQvWJvnVbsMl_OBJ8aoG4QwTk1CFvxI,4976
+partis_bcr-1.0.2.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+partis_bcr-1.0.2.dist-info/entry_points.txt,sha256=Q-AkAQ91YwiKNHruS32ACdY4_IQdpZhpij2EuVDmdnM,44
+partis_bcr-1.0.2.dist-info/top_level.txt,sha256=J-z0poNcsv31IHB413--iOY8LoHBKiTHeybHX3abokI,7
+partis_bcr-1.0.2.dist-info/RECORD,,

partis_bcr-1.0.2.dist-info/top_level.txt

@@ -0,0 +1 @@
+python

{partis → python}/glutils.py

@@ -46,7 +46,7 @@ def functionality_fname(species=None, gldir=None):  # _not_ generally present (b
         species = 'human'
         print('  %s using default species %s for functionality file' % (utils.color('yellow', 'warning'), species))
     if gldir is None:
-        gldir = os.path.dirname(os.path.realpath(__file__)).replace('/python', '')
+        gldir = utils.get_partis_dir()
     return '%s/data/germlines/%s/functionalities.csv' % (gldir, species)
 
 csv_headers = ['gene', 'cyst_position', 'tryp_position', 'phen_position', 'aligned_seq']

python/main.py

@@ -0,0 +1,30 @@
+#!/usr/bin/env python3
+"""
+Main entry point for partis package
+"""
+
+import os
+import sys
+
+def main():
+    """Main entry point for partis command line interface."""
+    # Set up the partis environment 
+    current_dir = os.path.dirname(os.path.realpath(__file__))
+    site_packages_dir = os.path.dirname(current_dir)  # site-packages/
+    
+    # Let the original bin/partis script auto-detect its location
+    # Don't override PARTIS_DIR - let it be set naturally
+    
+    # Execute the original bin/partis script
+    bin_partis = os.path.join(site_packages_dir, 'bin', 'partis')
+    
+    if os.path.exists(bin_partis):
+        import subprocess
+        result = subprocess.run([sys.executable, bin_partis] + sys.argv[1:])
+        sys.exit(result.returncode)
+    else:
+        print(f'Error: partis script not found at {bin_partis}')
+        sys.exit(1)
+
+if __name__ == '__main__':
+    main()

{partis → python}/plotting.py

@@ -749,7 +749,10 @@ legends = {'vollmers-0.9' : 'VJ CDR3 0.9',
            'subset-partition' : 'subset partis',
            'vsearch-subset-partition' : 'vsearch subset partis',
            'star-partition' : 'star partis',
-           'phylo-naive-iqtree' : 'IQ-TREE (masked)',
+           'phylo-naive-iqtree' : 'IQ-TREE (CDR3 N)',
+           'phylo-naive-iqtree-fuzz-0' : 'IQ-TREE (fuzz 0)',
+           'phylo-naive-iqtree-fuzz-1' : 'IQ-TREE (fuzz 1)',
+           'phylo-naive-iqtree-fuzz-2' : 'IQ-TREE (fuzz 2)',
            'single-chain-partis' : 'single chain partis',
            'annotate' : '1-seq. partis',
            'seed-partition' : 'full partis (seed)',
@@ -867,6 +870,9 @@ colors = {'true' : '#006600',
           'vsearch-subset-partition' : '#ff7f0e',  #c04000',
           'star-partition' :  '#ff7f0e',
           'phylo-naive-iqtree' :  'grey',
+          'phylo-naive-iqtree-fuzz-0' :  'grey',
+          'phylo-naive-iqtree-fuzz-1' :  'grey',
+          'phylo-naive-iqtree-fuzz-2' :  'grey',
           'single-chain-partis' : '#006600',
           'single-chain-scoper' : '#006600',
           'annotate' : '#1f77b4',
@@ -935,6 +941,9 @@ linestyles = {'naive-hamming-partition' : 'dashed',
               'changeo' : 'dashed',
               'scoper' : 'dashed',
               'mobille' : 'dashed',
+              'phylo-naive-iqtree-fuzz-0' : 'dotted',
+              'phylo-naive-iqtree-fuzz-1' : 'dashdot',
+              'phylo-naive-iqtree-fuzz-2' : 'dashed',
               'igblast' : 'dotted',
               'mixcr' : 'dotted',
               'misassign-distance-0.03' : 'dashed',

{partis → python}/treeutils.py

@@ -1043,7 +1043,7 @@ def collapse_zero_length_leaves(dtree, sequence_uids, dont_warn=False, debug=Fal
 def run_tree_inference(method, input_seqfos=None, annotation=None, naive_seq=None, naive_seq_name='XnaiveX', no_naive=False, actions='prep:run:read',
                        taxon_namespace=None, suppress_internal_node_taxa=False, persistent_workdir=None, redo=False, outfix='out', cmdfo=None,
                        glfo=None, parameter_dir=None, use_docker=False, linearham_dir=None, iclust=None, seed_id=None, only_pass_leaves=False,
-                       collapse_duplicate_seqs=False, keys_not_to_collapse=None, dont_collapse_zero_len_leaves=False, phylo_naive_inference=False, debug=False):
+                       collapse_duplicate_seqs=False, keys_not_to_collapse=None, dont_collapse_zero_len_leaves=False, phylo_naive_inference_fuzz=None, debug=False):
     # ----------------------------------------------------------------------------------------
     def lhindir(workdir):
         return '%s/input' % workdir
@@ -1053,13 +1053,14 @@ def run_tree_inference(method, input_seqfos=None, annotation=None, naive_seq=Non
             cmd = '%s/bin/FastTree -gtr -nt -out %s %s' % (utils.get_partis_dir(), ofn(workdir), ifn(workdir))
         elif method in iqt_methods:
             vsn = '1.6.12' if method=='iqtree' else method.split('-')[1]
-            cmd = '%s/packages/iqtree-%s-Linux/bin/iqtree%s -asr -s %s -pre %s/%s -o %s' % (utils.get_partis_dir(), vsn, '2' if vsn[0]=='2' else '', ifn(workdir), os.path.dirname(ifn(workdir)), outfix, naive_seq_name)
+            cmd = '%s/bin/iqtree-%s -asr -s %s -pre %s/%s -o %s' % (utils.get_partis_dir(), vsn, ifn(workdir), os.path.dirname(ifn(workdir)), outfix, naive_seq_name)
+            # cmd = '%s/packages/iqtree-%s-Linux/bin/iqtree%s -asr -s %s -pre %s/%s -o %s' % (utils.get_partis_dir(), vsn, '2' if vsn[0]=='2' else '', ifn(workdir), os.path.dirname(ifn(workdir)), outfix, naive_seq_name)
             if redo:
                 cmd += ' -redo'
         elif method == 'raxml':
             rcmds = ['#!/bin/bash']
-            rcmds += ['%s/packages/raxml/raxml-ng --model GTR+G --msa %s --msa-format FASTA' % (utils.get_partis_dir(), ifn(workdir))]
-            rcmds += ['%s/packages/raxml/raxml-ng --model GTR+G --msa %s --msa-format FASTA --ancestral --tree %s' % (utils.get_partis_dir(), ifn(workdir), ofn(workdir))]
+            rcmds += ['%s/bin/raxml-ng --model GTR+G --msa %s --msa-format FASTA' % (utils.get_partis_dir(), ifn(workdir))]
+            rcmds += ['%s/bin/raxml-ng --model GTR+G --msa %s --msa-format FASTA --ancestral --tree %s' % (utils.get_partis_dir(), ifn(workdir), ofn(workdir))]
             utils.write_cmd_file('\n'.join(rcmds) + '\n', '%s/run.sh'%workdir)
             cmd = '%s/run.sh'%workdir
         elif 'gctree' in method:
@@ -1256,17 +1257,18 @@ def run_tree_inference(method, input_seqfos=None, annotation=None, naive_seq=Non
     assert actions in ['prep:run:read', 'prep', 'read']  # other combinations could make sense, but don't need them atm
     if method == 'linearham' and glfo is None:
         raise Exception('need to pass in glfo in order to run linearham (e.g. linearham can\'t work on the fake h/l annotations')
-    if phylo_naive_inference:
+    if phylo_naive_inference_fuzz is not None:
         assert method in iqt_methods  # needs implementing for other methods
 
     is_fake_paired = annotation is not None and annotation.get('is_fake_paired', False)
     if input_seqfos is None:
         assert naive_seq is None  # can't specify it two ways
         input_seqfos = utils.seqfos_from_line(annotation, prepend_naive=True, naive_name=naive_seq_name, extra_keys=keys_not_to_collapse, add_sfos_for_multiplicity='gctree' in method)
-        if phylo_naive_inference:
+        if phylo_naive_inference_fuzz is not None:
             assert input_seqfos[0]['name'] == naive_seq_name
-            # utils.add_implicit_info(glfo, annotation)
-            input_seqfos[0]['seq'] = utils.get_cdr3_masked_naive(annotation, n_fuzz=phylo_naive_inference)
+            masked_seq = utils.get_cdr3_masked_naive(annotation, n_fuzz=phylo_naive_inference_fuzz)
+            input_seqfos[0]['seq'] = masked_seq  # replace naive seq with masked seq
+            input_seqfos.insert(0, {'name' : 'masked-%s-1'%naive_seq_name, 'seq' : masked_seq})  # add masked seq as new seqfo
     elif naive_seq is not None:
         input_seqfos = [{'name' : naive_seq_name, 'seq' : naive_seq}] + input_seqfos
     elif not no_naive:  # force calling fcn to affirmatively indicate it doesn't want the naive sequence in the tree (since at one point we forget to add it, with bad consequences)
@@ -1335,7 +1337,7 @@ def run_tree_inference(method, input_seqfos=None, annotation=None, naive_seq=Non
 
     removed_nodes = None
     # fasttree, iqtree, and gctree put all observed seqs as leaves, so we sometimes want to collapse [near-]zero-length leaves onto their internal node parent
-    if not dont_collapse_zero_len_leaves and not only_pass_leaves and not suppress_internal_node_taxa and not phylo_naive_inference:  # only_pass_leaves means we're probably caring about tree inference accuracy, so want all initial leaves to end up as final leaves to ease comparisons, while suppress_internal_node_taxa has to do with clusterpath tree method
+    if not dont_collapse_zero_len_leaves and not only_pass_leaves and not suppress_internal_node_taxa and phylo_naive_inference_fuzz is None:  # only_pass_leaves means we're probably caring about tree inference accuracy, so want all initial leaves to end up as final leaves to ease comparisons, while suppress_internal_node_taxa has to do with clusterpath tree method
         if debug:
             print('      collapsing zero length leaves')
         removed_nodes = collapse_zero_length_leaves(dtree, uid_list + [naive_seq_name], dont_warn=collapse_duplicate_seqs, debug=debug)
@@ -1346,7 +1348,7 @@ def run_tree_inference(method, input_seqfos=None, annotation=None, naive_seq=Non
         re_insert_ambig(input_seqfos, padded_seq_info_list)
     if len(inf_seqfos) > 0:
         check_lengths(input_seqfos, inf_seqfos)
-    if phylo_naive_inference:
+    if phylo_naive_inference_fuzz is not None:
         assert inf_antn is None  # just needs to be implemented for the methods that return inf_antn rather than inf_seqfos
         root_dists = [(s, dtree.find_node_with_taxon_label(s['name']).distance_from_root()) for s in inf_seqfos]  # (seqfo, distance) pairs
         nearfo, neardist = sorted(root_dists, key=operator.itemgetter(1))[0]
@@ -2337,7 +2339,7 @@ def parse_lonr(outdir, input_seqfos, naive_seq_name, reco_info=None, debug=False
 # ----------------------------------------------------------------------------------------
 def run_lonr(input_seqfos, naive_seq_name, workdir, tree_method, lonr_code_file=None, phylip_treefile=None, phylip_seqfile=None, seed=1, debug=False):
     if lonr_code_file is None:
-        lonr_code_file = os.path.dirname(os.path.realpath(__file__)).replace('/python', '/bin/lonr.r')
+        lonr_code_file = '%s/bin/lonr.r' % utils.get_partis_dir()
     if not os.path.exists(lonr_code_file):
         raise Exception('lonr code file %s d.n.e.' % lonr_code_file)
     if tree_method not in ('dnapars', 'neighbor'):
@@ -2624,7 +2626,7 @@ def get_treefos(args, antn_list, glfo=None, debug=False):  # note that <antn_lis
 # NOTE <inf_lines_to_use> should be *all* your annotations (so the subclust workdirs are correct), *not* just one cluster at a time
 def get_trees_for_annotations(inf_lines_to_use, treefname=None, cpath=None, workdir=None, cluster_indices=None, tree_inference_method=None, inf_outdir=None,
                               glfo=None, parameter_dir=None, linearham_dir=None, min_cluster_size=4, seed_id=None, only_pass_leaves=False, collapse_duplicate_seqs=False,
-                              keys_not_to_collapse=None, phylo_naive_inference=False, debug=False):
+                              keys_not_to_collapse=None, phylo_naive_inference_fuzz=None, debug=False):
     # ----------------------------------------------------------------------------------------
     def addtree(iclust, dtree, origin):
         treefos[iclust] = {'tree' : dtree, 'origin' : origin}
@@ -2697,7 +2699,7 @@ def get_trees_for_annotations(inf_lines_to_use, treefname=None, cpath=None, work
             # NOTE if you add an arg here, you probably also need to add it to the 'read' call of the same fcn below
             cmdfos[iclust] = run_tree_inference(tree_inference_method, annotation=line, actions='prep', persistent_workdir=perswdir(iclust), glfo=glfo, iclust=iclust, parameter_dir=parameter_dir,
                                                 linearham_dir=linearham_dir, seed_id=seed_id, only_pass_leaves=only_pass_leaves, collapse_duplicate_seqs=collapse_duplicate_seqs,
-                                                keys_not_to_collapse=keys_not_to_collapse, phylo_naive_inference=phylo_naive_inference, debug=debug)  # this'll still return the cmdfo if the output exists (since we need it for parsing below), but we won't actually rerun it
+                                                keys_not_to_collapse=keys_not_to_collapse, phylo_naive_inference_fuzz=phylo_naive_inference_fuzz, debug=debug)  # this'll still return the cmdfo if the output exists (since we need it for parsing below), but we won't actually rerun it
             dtree = None
             origin = tree_inference_method
         else:
@@ -2730,7 +2732,7 @@ def get_trees_for_annotations(inf_lines_to_use, treefname=None, cpath=None, work
                 continue
             dtree, inf_seqfos, inf_antn = run_tree_inference(tree_inference_method, annotation=line, actions='read', persistent_workdir=perswdir(iclust), cmdfo=cfo, glfo=glfo, seed_id=seed_id,
                                                              only_pass_leaves=only_pass_leaves, collapse_duplicate_seqs=collapse_duplicate_seqs, keys_not_to_collapse=keys_not_to_collapse,
-                                                             phylo_naive_inference=phylo_naive_inference, debug=debug)
+                                                             phylo_naive_inference_fuzz=phylo_naive_inference_fuzz, debug=debug)
             if tree_inference_method == 'linearham':  # NOTE linearham infers the whole annotation, not just ancestral seqs (also note this annotation will have all of its sampled trees in l['tree-info']['linearham']['trees'], and logprob in ['logprob']
                 for mkey in [k for k in utils.input_metafile_keys.values() if k in line]:  # have to copy over any input meta keys
                     inf_antn[mkey] = [utils.per_seq_val(line, mkey, u, use_default=True) for u in inf_antn['unique_ids']]
@@ -2805,7 +2807,7 @@ def add_smetrics(args, metrics_to_calc, annotations, lb_tau, inf_partition=None,
         if 'tree' in args.selection_metric_plot_cfg or any(m in metrics_to_calc for m in ['lbi', 'lbr', 'lbf', 'aa-lbi', 'aa-lbr', 'aa-lbf']):  # get the tree if we're making tree plots or if any of the requested metrics need a tree
             treefos = get_trees_for_annotations(inf_lines_to_use, treefname=args.treefname, workdir=workdir, cluster_indices=args.cluster_indices, tree_inference_method=args.tree_inference_method,
                                                 inf_outdir=tree_inference_outdir, glfo=glfo, parameter_dir=args.paired_outdir if args.paired_loci else args.parameter_dir, linearham_dir=args.linearham_dir,
-                                                seed_id=args.seed_unique_id, only_pass_leaves=args.infer_trees_with_only_leaves, phylo_naive_inference=args.phylo_naive_inference, debug=debug)
+                                                seed_id=args.seed_unique_id, only_pass_leaves=args.infer_trees_with_only_leaves, phylo_naive_inference_fuzz=args.phylo_naive_inference_fuzz, debug=debug)
         check_cluster_indices(args.cluster_indices, n_after, inf_lines_to_use)
         n_already_there, n_skipped_uid = 0, 0
         final_inf_lines = []
@@ -3212,7 +3214,7 @@ def run_laplacian_spectra(treestr, workdir=None, plotdir=None, plotname=None, ti
     cmdlines = [
         'library(ape, quiet=TRUE)',
         # 'library(RPANDA, quiet=TRUE)',  # old way, before I had to modify the source code because the CRAN version removes all eigenvalues <1 (for method="standard" -- with method="normal" it's <0, which is probably better, but it also seems to smoosh all the eigenvalues to be almost exactly 1)
-        'library("RPANDA", lib.loc="%s/packages/RPANDA/lib", quiet=TRUE)' % os.path.dirname(os.path.realpath(__file__)).replace('/python', ''),
+        'library("RPANDA", lib.loc="%s/packages/RPANDA/lib", quiet=TRUE)' % utils.get_partis_dir(),
         'tree <- read.tree(text = "%s")' % treestr,
         # 'print(tree)',
         'specvals <- spectR(tree, method=c("standard"))',  # compute eigenvalues (and some metrics describing the distribution, e.g. skewness, kurtosis, eigengap)

{partis → python}/utils.py

@@ -29,6 +29,7 @@ import operator
 import yaml
 import six
 import hashlib
+from pathlib import Path
 from io import open
 try:
     from yaml import CLoader as Loader, CDumper as Dumper
@@ -50,7 +51,7 @@ def csv_wmode(mode='w'):
 
 # ----------------------------------------------------------------------------------------
 def get_partis_dir():
-    return os.path.dirname(os.path.realpath(__file__)).replace('/python', '')
+    return str(Path(__file__).resolve().parent.parent)
 
 # ----------------------------------------------------------------------------------------
 def fsdir():
@@ -4570,7 +4571,7 @@ def add_naive_seq_aa(line):
 # ----------------------------------------------------------------------------------------
 # return naive sequence with uncertain bases (e.g. non-templated insertions) replace with Ns
 # n_fuzz: number of bases by which to expand non-templated insertions (set to negative value to mask entire cdr3 [excluding conserved codons])
-def get_cdr3_masked_naive(antn, n_fuzz=3, debug=True):
+def get_cdr3_masked_naive(antn, n_fuzz=1, debug=True):
     if antn.get('is_fake_paired', False):
         raise Exception('can\'t mask fake paired annotation')
     masked_seq = antn['naive_seq']
@@ -7320,13 +7321,13 @@ def run_vsearch(action, seqdict, workdir, threshold, match_mismatch='2:-4', gap_
 
     # figure out which vsearch binary to use
     if vsearch_binary is None:
-        vsearch_binary = os.path.dirname(os.path.realpath(__file__)).replace('/python', '') + '/bin'
         if platform.system() == 'Linux':
-            vsearch_binary += '/vsearch-2.4.3-linux-x86_64'
+            binstr = 'linux'
         elif platform.system() == 'Darwin':
-            vsearch_binary += '/vsearch-2.4.3-macos-x86_64'
+            binstr += 'macos'
         else:
             raise Exception('%s no vsearch binary in bin/ for platform \'%s\' (you can specify your own full vsearch path with --vsearch-binary)' % (color('red', 'error'), platform.system()))
+        vsearch_binary = '%s/bin/vsearch-2.4.3-%s-x86_64' % (get_partis_dir(), binstr)
 
     # build command
     cmd = vsearch_binary
@@ -7416,7 +7417,7 @@ def run_swarm(seqs, workdir, differences=1, n_procs=1):
         for name, seq in seqs.items():
             fastafile.write('>%s_%d\n%s\n' % (name, dummy_abundance, remove_ambiguous_ends(seq).replace('N', 'A')))
 
-    cmd = os.path.dirname(os.path.realpath(__file__)).replace('/python', '') + '/bin/swarm-2.1.13-linux-x86_64 ' + infname
+    cmd = '%s/bin/swarm-2.1.13-linux-x86_64 %s' % (get_partis_dir(), infname)
     cmd += ' --differences ' + str(differences)
     if differences == 1:
         cmd += ' --fastidious'
@@ -7531,7 +7532,13 @@ def get_chimera_max_abs_diff(line, iseq, chunk_len=75, max_ambig_frac=0.1, debug
 
 # ----------------------------------------------------------------------------------------
 def get_version_info(debug=False):
-    git_dir = os.path.dirname(os.path.realpath(__file__)).replace('/python', '/.git')
+    git_dir = '%s/.git' % get_partis_dir()
+    if not os.path.exists(git_dir):
+        try:
+            from importlib.metadata import version
+            return {'tag': version('partis-bcr'), 'commit': 'installed'}
+        except ImportError:
+            return {'tag': 'unknown', 'commit': 'installed'}
     vinfo = {}
     vinfo['commit'] = subprocess.check_output(['git', '--git-dir', git_dir, 'rev-parse', 'HEAD'], universal_newlines=True).strip()
     if debug:

partis/main.py

@@ -1,59 +0,0 @@
-#!/usr/bin/env python3
-"""
-Main entry point for partis package
-"""
-
-import os
-import sys
-
-def main():
-    """Main entry point for partis command line interface."""
-    # Find the partis installation directory
-    # If installed via pip, this will be in site-packages/partis/
-    # If in development, it should find the root directory
-    current_dir = os.path.dirname(os.path.realpath(__file__))
-    
-    # Look for the partis root directory
-    partis_dir = None
-    search_paths = [
-        os.path.dirname(current_dir),  # ../
-        os.path.dirname(os.path.dirname(current_dir)),  # ../../ (for site-packages/partis/main.py)
-    ]
-    
-    for search_path in search_paths:
-        if os.path.exists(os.path.join(search_path, 'bin', 'partis')):
-            partis_dir = search_path
-            break
-    
-    if partis_dir is None:
-        # Try to use the current directory structure assuming pip install
-        partis_dir = os.path.dirname(current_dir)
-        if not os.path.exists(os.path.join(partis_dir, 'data')):
-            print('Error: Could not locate partis installation directory')
-            sys.exit(1)
-    
-    # Set up environment for partis
-    sys.path.insert(0, partis_dir)
-    os.environ['PARTIS_DIR'] = partis_dir
-    
-    # Import and execute the partis main functionality
-    try:
-        # Try to import the original partis logic
-        original_partis = os.path.join(partis_dir, 'bin', 'partis')
-        if os.path.exists(original_partis):
-            # Read and execute the original script, but set up the environment first
-            globals_dict = {'__file__': original_partis}
-            with open(original_partis, 'r') as f:
-                partis_code = f.read()
-            exec(partis_code, globals_dict)
-        else:
-            print(f'Error: partis script not found at {original_partis}')
-            sys.exit(1)
-    except Exception as e:
-        print(f'Error running partis: {e}')
-        import traceback
-        traceback.print_exc()
-        sys.exit(1)
-
-if __name__ == '__main__':
-    main()

partis_bcr-1.0.0.dist-info/top_level.txt

@@ -1 +0,0 @@
-partis