partis-bcr 1.0.6__py3-none-any.whl → 1.0.7__py3-none-any.whl

{partis_bcr-1.0.6.dist-info → partis_bcr-1.0.7.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: partis-bcr
-Version: 1.0.6
+Version: 1.0.7
 Summary: B- and T-cell receptor sequence annotation, simulation, clonal family and germline inference
 Home-page: https://github.com/psathyrella/partis
 Author: Duncan Ralph
@@ -20,6 +20,7 @@ Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
 Requires-Python: >=3.7
 Description-Content-Type: text/markdown
 License-File: COPYING

{partis_bcr-1.0.6.dist-info → partis_bcr-1.0.7.dist-info}/RECORD

@@ -22,7 +22,6 @@ bin/makeHtml,sha256=SMMulEmYoU4ve4jlCRNaDuw9f4FS4t8g_FGE7z5Ndb4,1190
 bin/mds-run.py,sha256=rShy5b3oqvFZqhNdVxrtyZ4nw7whK-SKPAYl2thXooU,2003
 bin/parse-output.py,sha256=_vlx4ptHEoKiztm2RrCMqQZYlFriFmv4Sv17E6M6J9o,19533
 bin/partis,sha256=fm-5jD5mjvz3GsCeT5Q_gqeUCTCWalKgV5VJ012Xrdk,225118
-bin/partis-pip,sha256=STJkb_lm94kKxthpmIsMgFIhBWsoOJAtRJZbiFewaAU,5562
 bin/partis-test.py,sha256=CS0H2eckShv9TIPh-p_6jeaBuDd3zlRTDjaHmXU3Ln4,63749
 bin/partis.py,sha256=fm-5jD5mjvz3GsCeT5Q_gqeUCTCWalKgV5VJ012Xrdk,225118
 bin/plot-gl-set-trees.py,sha256=bgWPBmzzlD_YgWl9nQetGdzmgosXDKyVyfvaHs0VvVc,25695
@@ -297,18 +296,18 @@ data/substitution-profiles/GSSPs_for_VH_genes_with_at_least_300_lineages.txt,sha
 data/substitution-profiles/GSSPs_for_VK_genes_with_at_least_300_lineages.txt,sha256=dyMU1R_Izk_ciOVTNWmGL5SQBIKDCCKpxXM6eTGO4Fg,184138
 data/substitution-profiles/GSSPs_for_VL_genes_with_at_least_300_lineages.txt,sha256=CMFb1gk8MbfaMb6y0_qLLiKErrx866C2EafKRSPesB4,184979
 data/substitution-profiles/notes.txt,sha256=-DK9E31YovqOWaXR1Q-LL5KFhjVJcSLwXbriajUq1TA,389
-packages/ham/bcrham,sha256=EfXBRtZfvPosw3I56boG6FGingnLzP-PJ5tKj1H7cxM,1194352
+packages/ham/bcrham,sha256=p5PJ7gX0kvDcG3OI9uAHrLN7WuG5xcYdjC1dW2yv8iY,1194352
 packages/ig-sw/src/ig_align/ig-sw,sha256=SNFYfMlvX9s9T64t9fYIB5ugD6cZ016SZVbRhrz5Pro,293464
-partis_bcr-1.0.6.data/scripts/cf-alleles.py,sha256=AgFLoRfcwuX1InVpE3zG6-unqoCBGOeCTpEl_RZftvU,4723
-partis_bcr-1.0.6.data/scripts/cf-germlines.py,sha256=8_bq0ue3ALFQ-a7-ntnhkbCaBdQ5mlWtQgNeQP_TvcQ,3135
-partis_bcr-1.0.6.data/scripts/compare-plotdirs.py,sha256=AABVGUOwlLCijjo-wwDLfLHiq80TrFVm8mE-4Zqn5Sg,16370
-partis_bcr-1.0.6.data/scripts/extract-pairing-info.py,sha256=IGPd4jYpsW3IPgsrxTJrk9jAwUKlb45eX3lOpb8Maos,2941
-partis_bcr-1.0.6.data/scripts/gctree-run.py,sha256=BfSZCFgqdhUEqVsv2h20o6OkS6KbQgx5tfvBhySRx2U,13950
-partis_bcr-1.0.6.data/scripts/get-naive-probabilities.py,sha256=WfuglaedP3PF0wpksGiUSvfAg4wJoNlucTPa1Wl9MDo,6916
-partis_bcr-1.0.6.data/scripts/parse-output.py,sha256=8nrg0ip3XDhme02NCiI45BrSqCNvbRIbKYErD8STk8U,19519
-partis_bcr-1.0.6.data/scripts/partis-test.py,sha256=bQq_sT9v2DVQBgUGqQzdvy-q1jUrqAxV6Sl-tzENwus,63735
-partis_bcr-1.0.6.data/scripts/split-loci.py,sha256=K0WXQYtloL5rs46mwvEXUecqT3iG8bbqwNOTNwfpvzY,20704
-partis_bcr-1.0.6.dist-info/licenses/COPYING,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
+partis_bcr-1.0.7.data/scripts/cf-alleles.py,sha256=AgFLoRfcwuX1InVpE3zG6-unqoCBGOeCTpEl_RZftvU,4723
+partis_bcr-1.0.7.data/scripts/cf-germlines.py,sha256=8_bq0ue3ALFQ-a7-ntnhkbCaBdQ5mlWtQgNeQP_TvcQ,3135
+partis_bcr-1.0.7.data/scripts/compare-plotdirs.py,sha256=AABVGUOwlLCijjo-wwDLfLHiq80TrFVm8mE-4Zqn5Sg,16370
+partis_bcr-1.0.7.data/scripts/extract-pairing-info.py,sha256=IGPd4jYpsW3IPgsrxTJrk9jAwUKlb45eX3lOpb8Maos,2941
+partis_bcr-1.0.7.data/scripts/gctree-run.py,sha256=BfSZCFgqdhUEqVsv2h20o6OkS6KbQgx5tfvBhySRx2U,13950
+partis_bcr-1.0.7.data/scripts/get-naive-probabilities.py,sha256=WfuglaedP3PF0wpksGiUSvfAg4wJoNlucTPa1Wl9MDo,6916
+partis_bcr-1.0.7.data/scripts/parse-output.py,sha256=8nrg0ip3XDhme02NCiI45BrSqCNvbRIbKYErD8STk8U,19519
+partis_bcr-1.0.7.data/scripts/partis-test.py,sha256=bQq_sT9v2DVQBgUGqQzdvy-q1jUrqAxV6Sl-tzENwus,63735
+partis_bcr-1.0.7.data/scripts/split-loci.py,sha256=K0WXQYtloL5rs46mwvEXUecqT3iG8bbqwNOTNwfpvzY,20704
+partis_bcr-1.0.7.dist-info/licenses/COPYING,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
 python/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 python/alleleclusterer.py,sha256=x50E_lJMlKPc-CPkdkM1qe4AvVi-mkDJ1cBDxs5L-ms,30551
 python/allelefinder.py,sha256=SgJjopk5ivLOcmTumsWq5PZ05aPZ6zQyjTd1fxeRjaM,80402
@@ -347,7 +346,7 @@ python/scanplot.py,sha256=-ZXle3lW5C2ZRECC6r0xJokscZT0-A_VV7om6We_HbY,64864
 python/seqfileopener.py,sha256=6WZQaG-0R3KNk3ZYLP2bAJ9ViR7b9viSB-vTePaaMh0,26880
 python/treegenerator.py,sha256=aExfulBvj2CeNDcnX6AG-jeDiEmOvEzfSsDtt9psMVk,18909
 python/treeutils.py,sha256=aSKSxKZK2attLKrJv3xrDVWekgwtQVhqrnqZKs9c-uM,282309
-python/utils.py,sha256=RZr79jh3jLkYPBZW4N6210CkC-rKlrlxx2uu-ER5jdA,492652
+python/utils.py,sha256=-luzQ8iLDF2AeQZd-9IewUDdfxhVKxokxQgVLxrBgis,492651
 python/viterbicluster.py,sha256=ub8vHxJbTDUtx2QUS2rGFFRQVKyGMdaGbDtFtNcaTgc,2070
 python/vrc01.py,sha256=f3PpRV9ZOU9kxJCKdoJlP9wvKB7FEgMM8WoNpevsEOE,10813
 python/waterer.py,sha256=sPBsJchmK2EO3M5UCwZq_S5mRV3eYFuIZoite4Js62g,109955
@@ -7310,8 +7309,8 @@ test/ref-results-slow/test/parameters/simu/true/mute-freqs/IGHV4-NL1_star_01.csv
 test/ref-results-slow/test/parameters/simu/true/mute-freqs/IGHV5-10-1_star_01.csv,sha256=S075HCAZnbZpAMsXeLMmMXEGVHFs_Euk1XujtFQ46y4,41974
 test/ref-results-slow/test/parameters/simu/true/mute-freqs/IGHV5-51_star_01.csv,sha256=QJGyDRqD2JezXsuMbNNXGSCM-kjaN2h4QGpgsaqTqXQ,57817
 test/ref-results-slow/test/parameters/simu/true/mute-freqs/IGHV7-4-1_star_02.csv,sha256=k5KeCR5Qa6iEF0IEHR63DDdJStqAjcZxgZOUbKDFNaY,39977
-partis_bcr-1.0.6.dist-info/METADATA,sha256=kG5P0EfVVMZYGh7F6uYhI1uPiSlpUxukWRiJ6XRD1vA,5024
-partis_bcr-1.0.6.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-partis_bcr-1.0.6.dist-info/entry_points.txt,sha256=Q-AkAQ91YwiKNHruS32ACdY4_IQdpZhpij2EuVDmdnM,44
-partis_bcr-1.0.6.dist-info/top_level.txt,sha256=J-z0poNcsv31IHB413--iOY8LoHBKiTHeybHX3abokI,7
-partis_bcr-1.0.6.dist-info/RECORD,,
+partis_bcr-1.0.7.dist-info/METADATA,sha256=ckhldbhLch81KuEpjwt9h1VOHdP8YEAzVKAy66WguiI,5075
+partis_bcr-1.0.7.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+partis_bcr-1.0.7.dist-info/entry_points.txt,sha256=Q-AkAQ91YwiKNHruS32ACdY4_IQdpZhpij2EuVDmdnM,44
+partis_bcr-1.0.7.dist-info/top_level.txt,sha256=J-z0poNcsv31IHB413--iOY8LoHBKiTHeybHX3abokI,7
+partis_bcr-1.0.7.dist-info/RECORD,,

python/utils.py

@@ -7324,7 +7324,7 @@ def run_vsearch(action, seqdict, workdir, threshold, match_mismatch='2:-4', gap_
         if platform.system() == 'Linux':
             binstr = 'linux'
         elif platform.system() == 'Darwin':
-            binstr += 'macos'
+            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)

bin/partis-pip

@@ -1,116 +0,0 @@
-#!/usr/bin/env python3
-from __future__ import absolute_import, division, unicode_literals
-from __future__ import print_function
-import argparse
-import copy
-import time
-import random
-import sys
-import subprocess
-# import multiprocessing
-import numpy
-import scipy
-import math
-import itertools
-import collections
-import traceback
-from io import open
-import colored_traceback.always
-import os
-import json
-import csv
-import operator
-import glob
-from collections import defaultdict
-
-# Auto-detect installation type and set up imports accordingly
-def setup_partis_environment():
-    # Check if we're in a pip installation or source installation
-    current_dir = os.path.dirname(os.path.realpath(__file__))
-    
-    # Try to detect pip installation structure
-    if current_dir.endswith('/site-packages/bin'):
-        # We're in a pip installation: /site-packages/bin/partis
-        site_packages_dir = os.path.dirname(current_dir)  # /site-packages
-        partis_dir = site_packages_dir
-        
-        # Set up environment for pip installation
-        os.environ['PARTIS_DIR'] = partis_dir
-        sys.path.insert(1, site_packages_dir)
-        
-        # Import using pip package structure
-        import partis.utils as utils
-        import partis.glutils as glutils
-        import partis.treeutils as treeutils
-        import partis.processargs as processargs
-        import partis.seqfileopener as seqfileopener
-        from partis.partitiondriver import PartitionDriver
-        from partis.clusterpath import ClusterPath
-        import partis.paircluster as paircluster
-        from partis.parametercounter import ParameterCounter
-        from partis.corrcounter import CorrCounter
-        from partis.waterer import Waterer
-        
-        return utils, glutils, treeutils, processargs, seqfileopener, PartitionDriver, ClusterPath, paircluster, ParameterCounter, CorrCounter, Waterer, partis_dir
-        
-    else:
-        # We're in a source installation: assume standard partis directory structure
-        partis_dir = os.path.dirname(os.path.realpath(__file__)).replace('/bin', '')
-        if not os.path.exists(partis_dir):
-            print('%s partis dir %s doesn\'t exist, so python path may not be correctly set' % (os.path.dirname(os.path.realpath(__file__)), partis_dir))
-        sys.path.insert(1, partis_dir)
-        
-        # Set up environment for source installation  
-        os.environ['PARTIS_DIR'] = partis_dir
-        
-        # Import using source structure
-        import python.utils as utils
-        import python.glutils as glutils
-        import python.treeutils as treeutils
-        import python.processargs as processargs
-        import python.seqfileopener as seqfileopener
-        from python.partitiondriver import PartitionDriver
-        from python.clusterpath import ClusterPath
-        import python.paircluster as paircluster
-        from python.parametercounter import ParameterCounter
-        from python.corrcounter import CorrCounter
-        from python.waterer import Waterer
-        
-        return utils, glutils, treeutils, processargs, seqfileopener, PartitionDriver, ClusterPath, paircluster, ParameterCounter, CorrCounter, Waterer, partis_dir
-
-# Initialize environment and imports
-utils, glutils, treeutils, processargs, seqfileopener, PartitionDriver, ClusterPath, paircluster, ParameterCounter, CorrCounter, Waterer, partis_dir = setup_partis_environment()
-
-# ----------------------------------------------------------------------------------------
-def run_simulation(args):
-    # ----------------------------------------------------------------------------------------
-    def run_sub_cmds(working_gldir):
-        # ----------------------------------------------------------------------------------------
-        def get_sub_events(iproc):
-            n_sub_events = args.n_sim_events // args.n_procs
-            if iproc == args.n_procs - 1 and args.n_sim_events % args.n_procs > 0:  # do any extra ones in the last proc (has to match sub file writer below)
-                n_sub_events += args.n_sim_events % args.n_procs
-            n_per_proc_list.append(n_sub_events)
-            return n_sub_events
-        # ----------------------------------------------------------------------------------------
-        def get_workdir(iproc):
-            return utils.choose_random_subdir('/tmp') + '/partis-simu-' + str(random.randint(0, 999999))
-        # ----------------------------------------------------------------------------------------
-        if args.n_procs == 1:
-            sub_cmds = [get_simulation_cmd(working_gldir, n_events=args.n_sim_events, random_seed=random.randint(0, 999999), outfname=args.outfname, workdir=None)]
-        else:
-            n_per_proc_list = []
-            sub_cmds = []
-            for iproc in range(args.n_procs):
-                workdir = get_workdir(iproc)
-                outfname = workdir + '/simu-' + str(iproc) + '.yaml'
-                sub_cmds.append(get_simulation_cmd(working_gldir, n_events=get_sub_events(iproc), random_seed=random.randint(0, 999999), outfname=outfname, workdir=workdir))
-        
-        utils.run_cmds(sub_cmds, shell=True, n_max_procs=args.n_procs, sleep=False, debug=args.debug, proc_limit_str='   %d / %d ' % (len(sub_cmds), len(sub_cmds)))
-        
-        if args.n_procs > 1:
-            merge_simulation_outputs(sub_cmds)
-
-    # ... rest of the simulation code would continue here, but for brevity I'll skip to the main parts
-
-# Copy the rest of the original bin/partis file content here, but I'll jump to the main execution part