offtracker 2.10.4__zip → 2.10.6__zip

{offtracker-2.10.4/offtracker.egg-info → offtracker-2.10.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: offtracker
-Version: 2.10.4
+Version: 2.10.6
 Summary: Tracking-seq data analysis
 Home-page: https://github.com/Lan-lab/offtracker
 Author: Runda Xu

{offtracker-2.10.4 → offtracker-2.10.6}/offtracker/_version.py

@@ -1,4 +1,4 @@
-__version__ = "2.10.4"
+__version__ = "2.10.6"
 # 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 +33,4 @@ __version__ = "2.10.4"
 # 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. v2.10.4   修复翻新代码结构导致的bug
+# 2025.06.17. v2.10.6   修复翻新代码结构导致的bug

{offtracker-2.10.4 → offtracker-2.10.6/offtracker.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: offtracker
-Version: 2.10.4
+Version: 2.10.6
 Summary: Tracking-seq data analysis
 Home-page: https://github.com/Lan-lab/offtracker
 Author: Runda Xu

{offtracker-2.10.4 → offtracker-2.10.6}/scripts/offtracker_analysis.py

@@ -27,7 +27,7 @@ def main():
     parser.add_argument('--exp'          , type=str, default='all',    nargs='+', help='A substring mark in the name of experimental samples. The default is to use all samples other than control' )
     parser.add_argument('--control'      , type=str, default='none',   nargs='+', help='A substring mark in the name of control samples. The default is no control. "others" for all samples other than --exp.' )
     parser.add_argument('--fdr'          , type=int, default=0.01,     help='FDR threshold for the final result. Default is 0.01.')
-    parser.add_argument('--score'        , type=int, default=2,        help='Track score threshold for the final result. Default is 2.')
+    parser.add_argument('--score'        , type=int, default=1.9,        help='Track score threshold for the final result. Default is 1.9.')
     parser.add_argument('--smooth'       , type=int, default=1,        help='Smooth strength for the signal.')
     parser.add_argument('--window'       , type=int, default=3,        help='Window size for smoothing the signal.')
     parser.add_argument('--binsize'      , type=int, default=100,      help='Window size for smoothing the signal.')
@@ -253,7 +253,7 @@ def main():
     ##########################
     output = f'./temp/df_result_{outname}.csv'
     if (os.path.isfile(output))&(not args.overwrite):
-        print(f'skip {outname} as the result exists')
+        print(f'skip {output} as the result exists')
         df_result =  pd.read_csv(output, index_col=0)
     else:
         if pattern_ctr != 'none':
@@ -349,27 +349,32 @@ def main():
         df_result['pv'] = df_result['pv'].clip(lower=1e-320)
         df_result['fdr'] = offtracker.fdr(df_result['pv'])
         df_result['rank'] = range(1,len(df_result)+1)
-        df_result.to_csv(output)        
+        df_result.to_csv(output)
+
+    output = f'Offtracker_result_{outname}.csv'
+    if (os.path.isfile(output))&(not args.overwrite):
+        print(f'skip {output} as the result exists')
+    else:
         # 2024.06.03. 以防 fdr<=fdr_thresh 滤掉了 track_score>=2 的位点
         bool_fdr = df_result['fdr']<=fdr_thresh
         bool_score = df_result['track_score']>=score_thresh
         # 2025.06.05. BE可能会形成单边信号，导致 track_score 为负数，也保留
-        bool_neg_score = df_result['track_score']<-0.5
+        bool_neg_score = df_result['track_score']< -1
         df_output = df_result[bool_fdr|bool_score|bool_neg_score].copy()
         if pattern_ctr != 'none':
             df_output = df_output[['target_location', 'best_strand','best_target','deletion','insertion','mismatch',
-                                   'exp_L_length', 'exp_R_length','ctr_L_length','ctr_R_length','L_length','R_length','signal_length',
-                                  'norm_best_seq_score','track_score', 'log2_track_score','fdr','rank']]
+                                'exp_L_length', 'exp_R_length','ctr_L_length','ctr_R_length','L_length','R_length','signal_length',
+                                'norm_best_seq_score','track_score', 'log2_track_score','fdr','rank']]
             df_output.columns = ['target_location', 'strand', 'target', 'deletion', 'insertion', 'mismatch', 
-                                 'exp_L_length', 'exp_R_length','ctr_L_length','ctr_R_length','L_length','R_length','signal_length',
-                                 'seq_score', 'track_score', 'log2_track_score','FDR', 'rank']
+                                'exp_L_length', 'exp_R_length','ctr_L_length','ctr_R_length','L_length','R_length','signal_length',
+                                'seq_score', 'track_score', 'log2_track_score','FDR', 'rank']
         else:
             df_output = df_output[['target_location', 'best_strand','best_target','deletion','insertion','mismatch',
-                                   'L_length', 'R_length','signal_length',
-                                  'norm_best_seq_score','track_score', 'log2_track_score','fdr','rank']]
+                                'L_length', 'R_length','signal_length',
+                                'norm_best_seq_score','track_score', 'log2_track_score','fdr','rank']]
             df_output.columns = ['target_location', 'strand', 'target', 'deletion', 'insertion', 'mismatch', 
-                                 'L_length', 'R_length','signal_length',
-                                 'seq_score', 'track_score', 'log2_track_score','FDR', 'rank']
+                                'L_length', 'R_length','signal_length',
+                                'seq_score', 'track_score', 'log2_track_score','FDR', 'rank']
         df_output.to_csv(f'Offtracker_result_{outname}.csv', index=False)
 
         if args.clean:

{offtracker-2.10.4 → offtracker-2.10.6}/scripts/offtracker_plot.py

@@ -26,10 +26,10 @@ def main():
     full_seq = gRNA + PAM
     
     df_result = pd.read_csv(args.result)
-    n_pos = len(df_result)
+    # n_pos = len(df_result)
 
     xoffplot.offtable(df_result, full_seq, length_pam = len(PAM), col_seq='target', threshold=2,
-                      title=f'{outname} ({n_pos} sites)',
+                      title=f'{outname}',
                       savefig=dir_savefig)
     
     return f'The plot is saved as {dir_savefig}'