offtracker 2.10.8__zip → 2.10.10__zip

{offtracker-2.10.8/offtracker.egg-info → offtracker-2.10.10}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: offtracker
-Version: 2.10.8
+Version: 2.10.10
 Summary: Tracking-seq data analysis
 Home-page: https://github.com/Lan-lab/offtracker
 Author: Runda Xu
@@ -78,6 +78,9 @@ offtracker_candidates.py -t 8 -g hg38 \
 --name 'VEGFA2' --sgrna 'GACCCCCTCCACCCCGCCTC' --pam 'NGG' \
 -o /Your_Path_To_Candidates_Folder
 
+# if analyzing Cas12a, whose pam is upstream of the sgRNA, add this:
+--pam_location 'upstream'
+
 ```
 
 

{offtracker-2.10.8 → offtracker-2.10.10}/README.md

@@ -66,6 +66,9 @@ offtracker_candidates.py -t 8 -g hg38 \
 --name 'VEGFA2' --sgrna 'GACCCCCTCCACCCCGCCTC' --pam 'NGG' \
 -o /Your_Path_To_Candidates_Folder
 
+# if analyzing Cas12a, whose pam is upstream of the sgRNA, add this:
+--pam_location 'upstream'
+
 ```
 
 

{offtracker-2.10.8 → offtracker-2.10.10}/offtracker/_version.py

@@ -1,4 +1,4 @@
-__version__ = "2.10.8"
+__version__ = "2.10.10"
 # 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
@@ -34,4 +34,6 @@ __version__ = "2.10.8"
 # 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
-# 2025.06.27. v2.10.8   将 chmod 放在了 setup.py 里
+# 2025.06.27. v2.10.8   将 chmod 放在了 setup.py 里
+# 2025.06.28. v2.10.9   现在 pip 都是从 wheel 安装，不再运行 setup.py，所以增加一个 offtracker_init.py
+# 2025.06.28. v2.10.10  直接塞 script 里试试

{offtracker-2.10.8 → offtracker-2.10.10/offtracker.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: offtracker
-Version: 2.10.8
+Version: 2.10.10
 Summary: Tracking-seq data analysis
 Home-page: https://github.com/Lan-lab/offtracker
 Author: Runda Xu
@@ -78,6 +78,9 @@ offtracker_candidates.py -t 8 -g hg38 \
 --name 'VEGFA2' --sgrna 'GACCCCCTCCACCCCGCCTC' --pam 'NGG' \
 -o /Your_Path_To_Candidates_Folder
 
+# if analyzing Cas12a, whose pam is upstream of the sgRNA, add this:
+--pam_location 'upstream'
+
 ```
 
 

{offtracker-2.10.8 → offtracker-2.10.10}/offtracker.egg-info/SOURCES.txt

@@ -12,6 +12,7 @@ offtracker.egg-info/SOURCES.txt
 offtracker.egg-info/dependency_links.txt
 offtracker.egg-info/requires.txt
 offtracker.egg-info/top_level.txt
+offtracker/utility/bedGraphToBigWig
 offtracker/snakefile/Snakefile_QC.smk
 offtracker/snakefile/Snakefile_offtracker.smk
 offtracker/utility/1.1_bed2fr.py
@@ -24,5 +25,6 @@ offtracker/utility/offtracker_blacklist_mm10.merged.bed
 scripts/offtracker_analysis.py
 scripts/offtracker_candidates.py
 scripts/offtracker_config.py
+scripts/offtracker_init.py
 scripts/offtracker_plot.py
 scripts/offtracker_qc.py

{offtracker-2.10.8 → offtracker-2.10.10}/offtracker.egg-info/requires.txt

@@ -1,5 +1,5 @@
 pandas
 numpy
-biopython
+biopython<=1.85
 pybedtools
 pyyaml

{offtracker-2.10.8 → offtracker-2.10.10}/scripts/offtracker_config.py

@@ -13,7 +13,10 @@ 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)
+# try:
+#     os.chmod( os.path.join(utility_dir, 'bedGraphToBigWig'), 0o755)
+# except:
+#     print('offtracker may be installed in root but not initialized. Please run "offtracker_init.py" with root permission first.')
 
 ###
 parser = argparse.ArgumentParser()

offtracker-2.10.10/scripts/offtracker_init.py

@@ -0,0 +1,11 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import os
+from importlib_metadata import distribution
+
+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)
+print('offtracker is initialized.')

{offtracker-2.10.8 → offtracker-2.10.10}/scripts/offtracker_qc.py

@@ -12,7 +12,10 @@ 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)
+# try:
+#     os.chmod( os.path.join(utility_dir, 'bedGraphToBigWig'), 0o755)
+# except:
+#     print('offtracker may be installed in root but not initialized. Please run "offtracker_init.py" with root permission first.')
 
 ###
 parser = argparse.ArgumentParser()

{offtracker-2.10.8 → offtracker-2.10.10}/setup.py

@@ -6,10 +6,6 @@ import io, os
 # 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'
@@ -30,7 +26,7 @@ with open(os.path.join(here, package_folder, '_version.py'),'r',encoding='utf-8'
 
 # requirements
 REQUIRED = [
-   'pandas', 'numpy', 'biopython', 'pybedtools', 'pyyaml', 
+   'pandas', 'numpy', 'biopython<=1.85', 'pybedtools', 'pyyaml', 
 ]
 ## pybedtools may be not supported in Windows
 
@@ -41,26 +37,6 @@ 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,
@@ -73,15 +49,13 @@ 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',
-               'scripts/offtracker_analysis.py',
-               'scripts/offtracker_plot.py'],
+    scripts = [ 'offtracker/utility/bedGraphToBigWig',
+                'scripts/offtracker_init.py',
+                'scripts/offtracker_qc.py',
+                'scripts/offtracker_config.py',
+                'scripts/offtracker_candidates.py',
+                'scripts/offtracker_analysis.py',
+                'scripts/offtracker_plot.py'],
     install_requires=REQUIRED,
     include_package_data=True
 )