bscampp 1.0.6__py3-none-any.whl → 1.0.7__py3-none-any.whl

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Files changed (10) hide show
  1. bscampp/__init__.py +1 -1
  2. bscampp/configs.py +0 -1
  3. bscampp/functions.py +18 -5
  4. bscampp/pipeline.py +0 -2
  5. {bscampp-1.0.6.dist-info → bscampp-1.0.7.dist-info}/METADATA +5 -4
  6. {bscampp-1.0.6.dist-info → bscampp-1.0.7.dist-info}/RECORD +10 -10
  7. {bscampp-1.0.6.dist-info → bscampp-1.0.7.dist-info}/WHEEL +1 -1
  8. {bscampp-1.0.6.dist-info → bscampp-1.0.7.dist-info}/entry_points.txt +0 -0
  9. {bscampp-1.0.6.dist-info → bscampp-1.0.7.dist-info/licenses}/LICENSE +0 -0
  10. {bscampp-1.0.6.dist-info → bscampp-1.0.7.dist-info}/top_level.txt +0 -0
bscampp/__init__.py CHANGED
@@ -12,7 +12,7 @@ import logging, os
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  # not really needed for BSCAMPP but safe to update here
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  os.sys.setrecursionlimit(1000000)
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- __version__ = "1.0.6"
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+ __version__ = "1.0.7"
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  _INSTALL_PATH = __path__[0]
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  # global variables to store all loggers
bscampp/configs.py CHANGED
@@ -22,7 +22,6 @@ _LOG = get_logger(__name__)
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  Configuration defined by users and by default values
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  '''
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  class Configs:
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- global _root_dir
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  # basic input paths
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  info_path = None # info file for pplacer or EPA-ng
bscampp/functions.py CHANGED
@@ -11,6 +11,10 @@ import bscampp.utils as utils
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  import concurrent.futures
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+ # suppress userwarning when doing subtree suppress_unifurcations
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+ import warnings
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+ warnings.filterwarnings("ignore", category=UserWarning)
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+
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  _LOG = get_logger(__name__)
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  ############################# helper functions ################################
@@ -405,7 +409,8 @@ def placeQueriesToSubtrees(tree, leaf_dict, new_subtree_dict, placed_query_list,
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  aln, qaln, cmdline_args, workdir, qname_map, qname_map_rev,
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  pool, lock, dry_run=False):
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  t0 = time.perf_counter()
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- _LOG.info('Performing placement on each subtree...')
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+ _LOG.info("Performing placement on each subtree with {}...".format(
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+ Configs.placement_method))
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  if dry_run:
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  return dict()
@@ -461,7 +466,7 @@ def placeQueriesToSubtrees(tree, leaf_dict, new_subtree_dict, placed_query_list,
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  job = EPAngJob(path=Configs.epang_path,
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  info_path=Configs.info_path, tree_path=tmp_tree,
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  aln_path=tmp_aln, qaln_path=tmp_qaln,
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- outdir=subtree_dir, num_cpus=Configs.num_cpus)
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+ outdir=subtree_dir, num_cpus=Configs.cpus_per_job)
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  jobs.append(job)
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  ## for EPA-ng, ensure that outpath name is changed to the one we want
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  #_outpath = job.run(logging=f'subtree_{final_subtree_count}')
@@ -481,7 +486,7 @@ def placeQueriesToSubtrees(tree, leaf_dict, new_subtree_dict, placed_query_list,
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  job = PplacerTaxtasticJob(path=Configs.pplacer_path,
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  refpkg_dir=refpkg_dir,
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  #molecule=Configs.molecule, model=Configs.model,
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- outpath=tmp_output, num_cpus=Configs.num_cpus,
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+ outpath=tmp_output, num_cpus=Configs.cpus_per_job,
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  qaln_path=tmp_qaln)
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  #tmp_output = job.run(logging=f'subtree_{final_subtree_count}')
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  jobs.append(job)
@@ -521,8 +526,16 @@ def placeQueriesToSubtrees(tree, leaf_dict, new_subtree_dict, placed_query_list,
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  for tmp_place in place_json["placements"]:
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  # convert qname back using qname_map_rev
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- qname = qname_map_rev[tmp_place[tgt][0]]
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- tmp_place[tgt][0] = qname
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+ tmp_name = tmp_place[tgt][0]
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+
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+ # >EPA-ng: tgt=="n" --> qname is string
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+ if isinstance(tmp_name, str):
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+ qname = qname_map_rev[tmp_name]
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+ tmp_place[tgt][0] = qname
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+ # >pplacer: tgt=="nm" --> qname is a list of two fields
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+ elif isinstance(tmp_name, list):
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+ qname = qname_map_rev[tmp_name[0]]
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+ tmp_place[tgt][0][0] = qname
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  placed_query_list.append(qname)
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  #placed_query_list.append(tmp_place[tgt][0])
bscampp/pipeline.py CHANGED
@@ -180,8 +180,6 @@ def clean_temp_files():
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  _LOG.info(f'- Removed {temp}')
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  def parseArguments(dry_run=False, method="BSCAMPP"):
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- global _root_dir, main_config_path
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-
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  default_outdir = f"{method.lower()}_output"
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  default_outname = f"{method.lower()}_result"
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{bscampp-1.0.6.dist-info → bscampp-1.0.7.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
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- Metadata-Version: 2.2
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+ Metadata-Version: 2.4
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  Name: bscampp
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- Version: 1.0.6
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+ Version: 1.0.7
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  Summary: BSCAMPP and SCAMPP - Scalable Phylogenetic Placement Tools
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  Author-email: Eleanor Wedell <ewedell2@illinois.edu>, Chengze Shen <chengze5@illinois.edu>
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  License: MIT License
@@ -49,12 +49,13 @@ Requires-Dist: ConfigParser>=5.0.0
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  Requires-Dist: numpy>=1.21.6
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  Requires-Dist: treeswift>=1.1.45
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  Requires-Dist: taxtastic>=0.9.3
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+ Dynamic: license-file
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  # BSCAMPP and SCAMPP - Two Scalable Phylogenetic Placement Methods and Frameworks
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+ [![PyPI - Version](https://img.shields.io/pypi/v/bscampp)](https://pypi.org/project/bscampp/#history)
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  [![PyPI - Python Version](https://img.shields.io/pypi/pyversions/bscampp)](https://pypi.org/project/bscampp/)
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- [![PyPI - Version](https://img.shields.io/pypi/v/bscampp?color=blue)](https://pypi.org/project/bscampp/#history)
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  [![Build Status](https://img.shields.io/github/actions/workflow/status/ewedell/BSCAMPP/python-package.yml?branch=main&label=build)](https://github.com/ewedell/BSCAMPP/)
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- [![PyPI - License](https://img.shields.io/pypi/l/bscampp?color=blue)](https://github.com/ewedell/BSCAMPP/blob/main/LICENSE)
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+ [![PyPI - License](https://img.shields.io/pypi/l/bscampp)](https://github.com/ewedell/BSCAMPP/blob/main/LICENSE)
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  [![Changelog](https://img.shields.io/badge/CHANGELOG-grey)](https://github.com/ewedell/BSCAMPP/blob/main/CHANGELOG.md)
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  **Table of Contents**
{bscampp-1.0.6.dist-info → bscampp-1.0.7.dist-info}/RECORD RENAMED
@@ -1,10 +1,10 @@
1
- bscampp/__init__.py,sha256=eDIMYifzKrFdtA3Ac7OvPTyIHUO1ZLgVaM0pKFxxEHE,2289
2
- bscampp/configs.py,sha256=perl6u5hto6J3JV1JMbsTQ6tqr2uGOk-Z9jfzflid0s,6122
1
+ bscampp/__init__.py,sha256=iWcT9i33I9mkOxFgfa7aRxjn_tRPYY7yW6zcuhbjTWk,2289
2
+ bscampp/configs.py,sha256=M53nndokxi3WczhpKGWpxOcI2nXIkgpQKhj5gYpee8w,6101
3
3
  bscampp/default.config,sha256=CEfsUHBy--vwJhEcUuJ0btfuGQWb_lKMVWUIP9f5YGw,112
4
- bscampp/functions.py,sha256=DGHQJLLzXSghDKbha0LW0YPip_45M6MI4t3zdDpzULI,22448
4
+ bscampp/functions.py,sha256=ywv3-h1l81YayioSTmNiciBZnbi56zyIGc-5Ni-jXG4,23016
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  bscampp/init_configs.py,sha256=EA9sMN5jWj6zj2b-7tN19LhX2Ef61ByQLxQRLHAqLDM,3600
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  bscampp/jobs.py,sha256=v7buZJs1AnNoXiILwu-W8fo3QjxAh3i9Mp7xfmlJvAY,7569
7
- bscampp/pipeline.py,sha256=IPZnXZmVxGGfbVUuGCQh5X9oBq48-6pA9QkuvMGPTag,14000
7
+ bscampp/pipeline.py,sha256=J-RQH54R27m6fhzIpGX0MJuE3ZFk5rcnsROpwC_n5CE,13960
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  bscampp/utils.py,sha256=-wns6FaWMKD2wVqjxdBQvjTdagTjywBIaGfqb2mupe4,30039
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  bscampp/tools/epa-ng,sha256=f3EVoZAAOXLN6l521qp-TrWDl5J2nqL3tGgjPaQE9WQ,3772096
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  bscampp/tools/pplacer,sha256=p0H4eo9uuiYoWS_kJbPfauOV99i7BXJdZSiwXIuLxTw,7834576
@@ -17,9 +17,9 @@ bscampp/tools/hamming_distance/src/fragment_tree_hamming.cpp,sha256=xCmyAT-OZJOD
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  bscampp/tools/hamming_distance/src/fragment_tree_hamming_new.cpp,sha256=eKxgODRlpf0hU84QjNhigvRhWCT9tiJZjA5oQFQ1bUk,7404
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  bscampp/tools/hamming_distance/src/homology.cpp,sha256=ZE0uXZWQ-cN4U1Wk5kUr_KKHgzsgA6Sno-IViRa4tmI,6053
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  bscampp/tools/hamming_distance/src/new_hamming.cpp,sha256=fBRm99RquBZgZjaLOn9xDI3cH9NchhrxKbL-11j8fmk,5342
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- bscampp-1.0.6.dist-info/LICENSE,sha256=HEa4YQdOR0e2Gz-NiOwr9X6aJcZtY0AGmlJQDmfN0Iw,1064
21
- bscampp-1.0.6.dist-info/METADATA,sha256=0sWAKK30wlps8i0d1BdFqyv5MZVgefRnTn_-yMmO8lQ,12602
22
- bscampp-1.0.6.dist-info/WHEEL,sha256=52BFRY2Up02UkjOa29eZOS2VxUrpPORXg1pkohGGUS8,91
23
- bscampp-1.0.6.dist-info/entry_points.txt,sha256=4Ft83qHc39tNNpMLgSgFXDHM-vuAB99JtmczCQj5pq8,204
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- bscampp-1.0.6.dist-info/top_level.txt,sha256=1loGRUAft6Tcdq0f3lHbVwWN7W_SW1srfhAVSpg9DWE,8
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- bscampp-1.0.6.dist-info/RECORD,,
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+ bscampp-1.0.7.dist-info/licenses/LICENSE,sha256=HEa4YQdOR0e2Gz-NiOwr9X6aJcZtY0AGmlJQDmfN0Iw,1064
21
+ bscampp-1.0.7.dist-info/METADATA,sha256=2Tk1eF72pNPIttqSsfwiNclB8H0bShbMhca0aAr8wKo,12602
22
+ bscampp-1.0.7.dist-info/WHEEL,sha256=CmyFI0kx5cdEMTLiONQRbGQwjIoR1aIYB7eCAQ4KPJ0,91
23
+ bscampp-1.0.7.dist-info/entry_points.txt,sha256=4Ft83qHc39tNNpMLgSgFXDHM-vuAB99JtmczCQj5pq8,204
24
+ bscampp-1.0.7.dist-info/top_level.txt,sha256=1loGRUAft6Tcdq0f3lHbVwWN7W_SW1srfhAVSpg9DWE,8
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+ bscampp-1.0.7.dist-info/RECORD,,
{bscampp-1.0.6.dist-info → bscampp-1.0.7.dist-info}/WHEEL RENAMED
@@ -1,5 +1,5 @@
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  Wheel-Version: 1.0
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- Generator: setuptools (76.0.0)
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+ Generator: setuptools (78.1.0)
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  Root-Is-Purelib: true
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  Tag: py3-none-any
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