offtracker 2.12.2__zip → 2.12.3__zip

{offtracker-2.12.2/offtracker.egg-info → offtracker-2.12.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: offtracker
-Version: 2.12.2
+Version: 2.12.3
 Summary: Tracking-seq data analysis
 Home-page: https://github.com/Lan-lab/offtracker
 Author: Runda Xu

{offtracker-2.12.2 → offtracker-2.12.3}/offtracker/X_sequence.py

@@ -115,7 +115,7 @@ def add_ID(df, chr_col=0, midpoint='cleavage_site'):#, midpoint='midpoint'):
 
 
 
-def detect_fastq(folder, n_subfolder, NGS_type='paired-end'):
+def detect_fastq(folder, n_subfolder, NGS_type='paired-end', skip_trimmed=False):
     """
     搜索 folder 的 n级子目录下的所有 fastq/fastq.gz/fq/fq.gz 文件
     paired-end 模式 : 识别 2.fq/2.fastq 为 paired-end 的 R2 文件，并验证对应 R1 文件
@@ -151,6 +151,9 @@ def detect_fastq(folder, n_subfolder, NGS_type='paired-end'):
             fq_files = glob.glob( os.path.join(folder, n_subfolder*'*/', fastq ) )
             print(f'{len(fq_files)} {fastq[2:]} samples detected')
             files_R2.extend( fq_files )
+
+        if skip_trimmed:
+            files_R2 = [f for f in files_R2 if '_trimmed_2.fq.gz' not in f]
         #
         if len(files_R2) > 0:
             files_R2 = pd.Series(files_R2).sort_values().reset_index(drop=True)

{offtracker-2.12.2 → offtracker-2.12.3}/offtracker/_version.py

@@ -1,4 +1,4 @@
-__version__ = "2.12.2"
+__version__ = "2.12.3"
 # 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
@@ -40,4 +40,5 @@ __version__ = "2.12.2"
 # 2025.06.28. v2.10.11  回滚到2.10.9外加修正
 # 2025.07.02. v2.11.4   基于 blast 的缺陷更新 candidates，去除 quick mode
 # 2025.07.04. v2.11.5   offtracker_analysis 提前 skip 已有结果的样本
-# 2025.07.04. v2.12.2   新增 region_index 标记区域，用于更好的去重
+# 2025.07.04. v2.12.2   新增 region_index 标记区域，用于更好的去重
+# 2025.07.18. v2.12.3   新增QC自动避免重复读取 trimmed fastq files

{offtracker-2.12.2 → offtracker-2.12.3/offtracker.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: offtracker
-Version: 2.12.2
+Version: 2.12.3
 Summary: Tracking-seq data analysis
 Home-page: https://github.com/Lan-lab/offtracker
 Author: Runda Xu

{offtracker-2.12.2 → offtracker-2.12.3}/scripts/offtracker_qc.py

@@ -29,7 +29,8 @@ def main():
     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('--include_trimmed', action='store_true',        help='Do not skip trimmed fastq files')
+    
     args = parser.parse_args()
 
     # 自动化的参数调整和报错
@@ -42,7 +43,10 @@ def main():
             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)
+    if args.include_trimmed:
+        sample_names, files_R1, files_R2 = xseq.detect_fastq(args.folder, n_subfolder=args.subfolder)
+    else:
+        sample_names, files_R1, files_R2 = xseq.detect_fastq(args.folder, n_subfolder=args.subfolder, skip_trimmed=True)
 
     assert not isinstance(sample_names, str), 'No fastq file is detected!'