offtracker 2.10.1__zip → 2.10.3__zip

{offtracker-2.10.1/offtracker.egg-info → offtracker-2.10.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: offtracker
-Version: 2.10.1
+Version: 2.10.3
 Summary: Tracking-seq data analysis
 Home-page: https://github.com/Lan-lab/offtracker
 Author: Runda Xu

{offtracker-2.10.1 → offtracker-2.10.3}/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-2.10.1 → offtracker-2.10.3}/offtracker/_version.py

@@ -1,4 +1,4 @@
-__version__ = "2.10.1"
+__version__ = "2.10.3"
 # 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
@@ -33,5 +33,4 @@ __version__ = "2.10.1"
 # 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. v2.10.3   修复翻新代码结构导致的bug

{offtracker-2.10.1 → offtracker-2.10.3}/offtracker/snakefile/Snakefile_offtracker.smk

@@ -40,7 +40,7 @@ rule chromap:
         R1=lambda w: _files_R1[w.sample],
         R2=lambda w: _files_R2[w.sample]
     threads:
-        _threads
+        _thread
     params:
         index=config["index"],
         fasta=config["fasta"]
@@ -58,7 +58,7 @@ if config["blacklist"] != 'none':
         input:
             os.path.join(_output_dir,"{sample}.chromapx.bed")
         threads:
-            _threads
+            _thread
         params:
             blacklist=config["blacklist"]
         output:
@@ -70,7 +70,7 @@ if config["blacklist"] != 'none':
         input:
             os.path.join(_output_dir,"{sample}.filtered.bed")
         threads:
-            _threads
+            _thread
         params:
             dir_script=config["utility_dir"],
             ignore_chr=config["ignore_chr"],
@@ -84,7 +84,7 @@ else:
         input:
             os.path.join(_output_dir,"{sample}.chromapx.bed")
         threads:
-            _threads
+            _thread
         params:
             dir_script=config["utility_dir"],
             ignore_chr=config["ignore_chr"],
@@ -98,7 +98,7 @@ rule bed2bdg_fw:
     input:
         os.path.join(_output_dir,"{sample}.fw.bed")
     threads:
-        _threads
+        _thread
     params:
         gl=config["genomelen"]
     output:
@@ -110,7 +110,7 @@ rule bed2bdg_rv:
     input:
         os.path.join(_output_dir,"{sample}.rv.bed")
     threads:
-        _threads
+        _thread
     params:
         gl=config["genomelen"]
     output:
@@ -122,7 +122,7 @@ rule bdg_sort_fw:
     input:
         fw=os.path.join(_output_dir,"{sample}.fw.bdg")
     threads:
-        _threads
+        _thread
     output:
         temp(os.path.join(_output_dir,"{sample}.fw.sorted.bdg"))
     shell:
@@ -132,7 +132,7 @@ rule bdg_sort_rv:
     input:
         rv=os.path.join(_output_dir,"{sample}.rv.bdg")
     threads:
-        _threads
+        _thread
     output:
         temp(os.path.join(_output_dir,"{sample}.rv.sorted.bdg"))
     shell:
@@ -144,7 +144,7 @@ if _normalize == "True":
             bdg=os.path.join(_output_dir,"{sample}.fw.sorted.bdg"),
             bed=os.path.join(_output_dir,"{sample}.fw.bed")
         threads:
-            _threads
+            _thread
         params:
             dir_script=config["utility_dir"]
         output:
@@ -157,7 +157,7 @@ if _normalize == "True":
             bdg=os.path.join(_output_dir,"{sample}.rv.sorted.bdg"),
             bed=os.path.join(_output_dir,"{sample}.rv.bed")
         threads:
-            _threads
+            _thread
         params:
             dir_script=config["utility_dir"]
         output:
@@ -169,7 +169,7 @@ if _normalize == "True":
         input:
             os.path.join(_output_dir,"{sample}.fw.scaled.bdg")
         threads:
-            _threads
+            _thread
         params:
             gl=config["genomelen"],
             dir_script=config["utility_dir"]
@@ -182,7 +182,7 @@ if _normalize == "True":
         input:
             os.path.join(_output_dir,"{sample}.rv.scaled.bdg")
         threads:
-            _threads
+            _thread
         params:
             gl=config["genomelen"],
             dir_script=config["utility_dir"]
@@ -196,7 +196,7 @@ if _normalize == "True":
             fw=os.path.join(_output_dir,"{sample}.fw.scaled.bw"),
             rv=os.path.join(_output_dir,"{sample}.rv.scaled.bw")
         threads:
-            _threads
+            _thread
         output:
             os.path.join(_output_dir,"{sample}." + _BinSize + ".add.bdg")
         shell:
@@ -212,7 +212,7 @@ else:
         input:
             os.path.join(_output_dir,"{sample}.rv.sorted.bdg")
         threads:
-            _threads
+            _thread
         output:
             temp(os.path.join(_output_dir,"{sample}.rv.sorted_r.bdg"))
         shell:
@@ -222,7 +222,7 @@ else:
         input:
             os.path.join(_output_dir,"{sample}.fw.sorted.bdg")
         threads:
-            _threads
+            _thread
         params:
             gl=config["genomelen"],
             dir_script=config["utility_dir"]
@@ -235,7 +235,7 @@ else:
         input:
             os.path.join(_output_dir,"{sample}.rv.sorted_r.bdg")
         threads:
-            _threads
+            _thread
         params:
             gl=config["genomelen"],
             dir_script=config["utility_dir"]

{offtracker-2.10.1 → offtracker-2.10.3/offtracker.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: offtracker
-Version: 2.10.1
+Version: 2.10.3
 Summary: Tracking-seq data analysis
 Home-page: https://github.com/Lan-lab/offtracker
 Author: Runda Xu

{offtracker-2.10.1 → offtracker-2.10.3}/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,

{offtracker-2.10.1 → offtracker-2.10.3}/scripts/offtracker_qc.py

@@ -21,7 +21,6 @@ parser.add_argument('-f','--folder', type=str, required=True,        help='Direc
 parser.add_argument('-o','--outdir', type=str, default='same',       help='The output folder')
 parser.add_argument('--subfolder'  , type=int, default=0,            help='subfolder level')
 parser.add_argument('-t','--thread', type=int, default=8,            help='Number of threads to be used')
-parser.add_argument('--NGS_type'   , type=str, default='paired-end', help='paired-end or single-end')
 
 args = parser.parse_args()
 
@@ -35,7 +34,7 @@ else:
         os.makedirs(args.outdir)
 
 # 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!'
 
@@ -43,7 +42,6 @@ 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,