offtracker 2.10.0__zip → 2.10.2__zip

{offtracker-2.10.0/offtracker.egg-info → offtracker-2.10.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: offtracker
-Version: 2.10.0
+Version: 2.10.2
 Summary: Tracking-seq data analysis
 Home-page: https://github.com/Lan-lab/offtracker
 Author: Runda Xu
@@ -10,9 +10,9 @@ Description-Content-Type: text/markdown
 License-File: LICENSE.txt
 
 
-# OFF-TRACKER
+# Offtracker
 
-OFF-TRACKER is an end to end pipeline of Tracking-seq data analysis for detecting off-target sites of any genome editing tools that generate double-strand breaks (DSBs) or single-strand breaks (SSBs).
+Offtracker is an end to end pipeline of Tracking-seq data analysis for detecting off-target sites of any genome editing tools that generate double-strand breaks (DSBs) or single-strand breaks (SSBs).
 
 ## System requirements
 

{offtracker-2.10.0 → offtracker-2.10.2}/offtracker/X_sequence.py

@@ -155,8 +155,8 @@ def detect_fastq(folder, n_subfolder, NGS_type='paired-end'):
         if len(files_R2) > 0:
             files_R2 = pd.Series(files_R2).sort_values().reset_index(drop=True)
             # 拆分文件名
-            suffix = files_R2.str.extract('(\.fastq.*|\.fq.*)',expand=False)
-            prefix = files_R2.str.extract('(.*)(?:.fq|.fastq)',expand=False)
+            suffix = files_R2.str.extract(r'(\.fastq.*|\.fq.*)',expand=False)
+            prefix = files_R2.str.extract(r'(.*)(?:.fq|.fastq)',expand=False)
             # 将 prefix 进一步拆分为 sample_dir （真样品名） 和 nametype （某种统一后缀），支持五种样本名后缀
             nametype = []
             sample_dir = []
@@ -194,8 +194,8 @@ def detect_fastq(folder, n_subfolder, NGS_type='paired-end'):
         #
         if len(files_R1) > 0:
             # 拆分文件名
-            suffix = files_R1.str.extract('(\.fastq.*|\.fq.*)',expand=False)
-            prefix = files_R1.str.extract('(.*)(?:.fq|.fastq)',expand=False)
+            suffix = files_R1.str.extract(r'(\.fastq.*|\.fq.*)',expand=False)
+            prefix = files_R1.str.extract(r'(.*)(?:.fq|.fastq)',expand=False)
             # 单端模式下，所有前缀都视为样品名
             sample_names = prefix.apply(os.path.basename)
         else:

{offtracker-2.10.0 → offtracker-2.10.2}/offtracker/_version.py

@@ -1,4 +1,4 @@
-__version__ = "2.10.0"
+__version__ = "2.10.2"
 # 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__ = "2.10.0"
 # 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. v2.10.1   修复翻新代码结构导致的bug
+# 2025.06.17. v2.10.2   修复翻新代码结构导致的bug

{offtracker-2.10.0 → offtracker-2.10.2/offtracker.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: offtracker
-Version: 2.10.0
+Version: 2.10.2
 Summary: Tracking-seq data analysis
 Home-page: https://github.com/Lan-lab/offtracker
 Author: Runda Xu
@@ -10,9 +10,9 @@ Description-Content-Type: text/markdown
 License-File: LICENSE.txt
 
 
-# OFF-TRACKER
+# Offtracker
 
-OFF-TRACKER is an end to end pipeline of Tracking-seq data analysis for detecting off-target sites of any genome editing tools that generate double-strand breaks (DSBs) or single-strand breaks (SSBs).
+Offtracker is an end to end pipeline of Tracking-seq data analysis for detecting off-target sites of any genome editing tools that generate double-strand breaks (DSBs) or single-strand breaks (SSBs).
 
 ## System requirements
 

{offtracker-2.10.0 → offtracker-2.10.2}/scripts/offtracker_candidates.py

@@ -16,7 +16,7 @@ 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')
+script_folder= os.path.join(script_dir, 'utility')
 
 import argparse
 import pandas as pd

{offtracker-2.10.0 → offtracker-2.10.2}/scripts/offtracker_config.py

@@ -61,7 +61,7 @@ else:
     args.ignore_chr = ''
 
 # 搜索 folder 的 n级子目录下的所有 fastq/fastq.gz/fq/fq.gz 文件
-sample_names, files_R1, files_R2 = xseq.detect_fastq(args.folder, n_subfolder=args.subfolder, NGS_type=args.NGS_type)
+sample_names, files_R1, files_R2 = xseq.detect_fastq(args.folder, n_subfolder=args.subfolder)
 
 assert not isinstance(sample_names, str), 'No fastq file is detected!'
 
@@ -69,7 +69,6 @@ dict_yaml = {
     # fastq 信息
     'files_R1':dict(zip(sample_names,files_R1)),
     'files_R2':dict(zip(sample_names,files_R2)), # 单端 files_R2=[] 结果会自动为 {}
-    'NGS_type':args.NGS_type,
     # 输入输出文件夹
     'input_dir':args.folder,
     'output_dir':args.outdir,