offtracker 2.10.7__zip → 2.10.8__zip

{offtracker-2.10.7/offtracker.egg-info → offtracker-2.10.8}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: offtracker
-Version: 2.10.7
+Version: 2.10.8
 Summary: Tracking-seq data analysis
 Home-page: https://github.com/Lan-lab/offtracker
 Author: Runda Xu

{offtracker-2.10.7 → offtracker-2.10.8}/offtracker/_version.py

@@ -1,4 +1,4 @@
-__version__ = "2.10.7"
+__version__ = "2.10.8"
 # 2023.08.11. v1.1.0	adding a option for not normalizing the bw file
 # 2023.10.26. v1.9.0	prerelease for v2.0
 # 2023.10.27. v2.0.0	大更新，还没微调
@@ -33,4 +33,5 @@ __version__ = "2.10.7"
 # 2025.04.25. v2.8.0	修复了 offtracker candidates 会把小写序列转换成 N 的 bug
 # 2025.05.22. v2.9.0	翻新部分代码结构
 # 2025.06.05. v2.10.0	增加了QC模块。保留了负数score的记录，并在plot时显示为红字。增加了 "--ignore_chr" 用于跳过common chr过滤。
-# 2025.06.17. v2.10.7   修复翻新代码结构导致的bug
+# 2025.06.17. v2.10.7   修复翻新代码结构导致的bug
+# 2025.06.27. v2.10.8   将 chmod 放在了 setup.py 里

{offtracker-2.10.7 → offtracker-2.10.8/offtracker.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: offtracker
-Version: 2.10.7
+Version: 2.10.8
 Summary: Tracking-seq data analysis
 Home-page: https://github.com/Lan-lab/offtracker
 Author: Runda Xu

{offtracker-2.10.7 → offtracker-2.10.8}/scripts/offtracker_analysis.py

@@ -9,8 +9,7 @@ if sys.version_info < (3,0):
 
 import offtracker
 import offtracker.X_sequence as xseq
-script_dir = os.path.abspath(os.path.dirname(offtracker.__file__))
-script_folder= os.path.join(script_dir, 'mapping')
+
 
 import argparse
 import pandas as pd
@@ -40,6 +39,8 @@ def main():
     parser.add_argument('-o','--outdir'  , type=str, default='first',  help='The output folder. Default is the first folder of --folder' )
     parser.add_argument('--outname'      , type=str, default='same',   help='The suffix of output files. Default is the same --exp' )
     parser.add_argument('--signal_only'  , action='store_true', help='A developer option: stop before group analysis. ' )
+    # parser.add_argument('--individual_results', action='store_true', help='When multiple samples meet the exp pattern, only one merged result is generated.\n' \
+    #                                                                       'Set --individual_results to additionally output the individual result of each exp sample. ' )
     parser.add_argument('--overwrite'    , action='store_true', help='Whether to overwrite existed dataframes.' )
     parser.add_argument('--clean'        , action='store_true', help='Whether to remove temp files')
 

{offtracker-2.10.7 → offtracker-2.10.8}/scripts/offtracker_config.py

@@ -13,7 +13,7 @@ import offtracker
 import offtracker.X_sequence as xseq
 script_dir = os.path.abspath(os.path.dirname(offtracker.__file__))
 utility_dir = os.path.join(script_dir, 'utility')
-os.chmod( os.path.join(utility_dir, 'bedGraphToBigWig'), 0o755)
+# os.chmod( os.path.join(utility_dir, 'bedGraphToBigWig'), 0o755)
 
 ###
 parser = argparse.ArgumentParser()

{offtracker-2.10.7 → offtracker-2.10.8}/scripts/offtracker_qc.py

@@ -12,7 +12,7 @@ import offtracker.X_sequence as xseq
 
 script_dir = os.path.abspath(os.path.dirname(offtracker.__file__))
 utility_dir = os.path.join(script_dir, 'utility')
-os.chmod( os.path.join(utility_dir, 'bedGraphToBigWig'), 0o755)
+# os.chmod( os.path.join(utility_dir, 'bedGraphToBigWig'), 0o755)
 
 ###
 parser = argparse.ArgumentParser()

{offtracker-2.10.7 → offtracker-2.10.8}/setup.py

@@ -1,11 +1,15 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-import io
-import os
-import sys
-from shutil import rmtree
-from setuptools import find_packages, setup, Command
+import io, os
+# import sys
+# from shutil import rmtree
+from setuptools import setup
+
+# import pkg_resources
+from importlib_metadata import distribution
+from setuptools.command.install import install
+from setuptools.command.develop import develop
 
 #
 NAME = 'offtracker'
@@ -26,7 +30,7 @@ with open(os.path.join(here, package_folder, '_version.py'),'r',encoding='utf-8'
 
 # requirements
 REQUIRED = [
-    'biopython', 'pybedtools', 'pyyaml', 'pandas', 'numpy',
+   'pandas', 'numpy', 'biopython', 'pybedtools', 'pyyaml', 
 ]
 ## pybedtools may be not supported in Windows
 
@@ -37,6 +41,26 @@ except FileNotFoundError:
     long_description = DESCRIPTION
 
 
+
+
+class PostInstallCommand(install):
+    def run(self):
+        install.run(self)
+        # 获取文件位置
+        dist = distribution('offtracker')
+        package_path = dist.locate_file('')
+        utility_dir = os.path.join(package_path, 'offtracker/utility')
+        os.chmod( os.path.join(utility_dir, 'bedGraphToBigWig'), 0o755)
+
+class PostDevelopCommand(develop):
+    def run(self):
+        develop.run(self)
+        # 获取文件位置
+        dist = distribution('offtracker')
+        package_path = dist.locate_file('')
+        utility_dir = os.path.join(package_path, 'offtracker/utility')
+        os.chmod( os.path.join(utility_dir, 'bedGraphToBigWig'), 0o755)
+
 setup(
     name=NAME,
     version=VERSION,
@@ -49,6 +73,10 @@ setup(
     python_requires=REQUIRES_PYTHON,
     packages=['offtracker'],
     package_data={'offtracker': ['snakefile/*','utility/*']},
+    cmdclass={
+        'install': PostInstallCommand,
+        'develop': PostDevelopCommand,
+    },
     scripts = ['scripts/offtracker_qc.py',
                'scripts/offtracker_config.py',
                'scripts/offtracker_candidates.py',

{offtracker-2.10.7 → offtracker-2.10.8}/offtracker.egg-info/requires.txt

@@ -1,5 +1,5 @@
+pandas
+numpy
 biopython
 pybedtools
 pyyaml
-pandas
-numpy