offtracker 2.13.0__zip → 2.13.2__zip

{offtracker-2.13.0/offtracker.egg-info → offtracker-2.13.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: offtracker
-Version: 2.13.0
+Version: 2.13.2
 Summary: Tracking-seq data analysis
 Home-page: https://github.com/Lan-lab/offtracker
 Author: Runda Xu

{offtracker-2.13.0 → offtracker-2.13.2}/offtracker/X_offtracker.py

@@ -608,6 +608,12 @@ def left_realign(dp_bdg_chr, loc_shift_left, ref_fasta, sgRNA_seq, PAM, PAM_loc,
     flank_regions = [500]
     signals = target_signal(dp_bdg_chr.to_pandas(), chrom, cleavage_site, flank_regions=flank_regions)
     L_neg_1000 = signals[2]
+    R_neg_1000 = signals[5]
+    # 如果右侧范围变负数了，说明过头了
+    if R_neg_1000 < 0:
+        sr_candidate.loc['realign'] = 'fail'
+        return sr_candidate
+
     # 计算左移后的 L_neg_1000，如果还是负数则迭代，最多迭代 10 次
     if L_neg_1000 < 0:
         st = sr_candidate['st']
@@ -632,7 +638,13 @@ def right_realign(dp_bdg_chr, loc_shift_right, ref_fasta, sgRNA_seq, PAM, PAM_lo
     cleavage_site = sr_candidate['cleavage_site']
     flank_regions = [500]
     signals = target_signal(dp_bdg_chr.to_pandas(), chrom, cleavage_site, flank_regions=flank_regions)
+    L_neg_1000 = signals[2]
     R_neg_1000 = signals[5]
+    # 如果左侧范围变负数了，说明过头了
+    if L_neg_1000 < 0:
+        sr_candidate.loc['realign'] = 'fail'
+        return sr_candidate
+
     # 计算右移后的 R_neg_1000，如果还是负数则迭代，最多迭代 10 次
     if R_neg_1000 < 0:
         st = sr_candidate['st']

{offtracker-2.13.0 → offtracker-2.13.2}/offtracker/_version.py

@@ -1,4 +1,4 @@
-__version__ = "2.13.0"
+__version__ = "2.13.2"
 # 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
@@ -43,3 +43,5 @@ __version__ = "2.13.0"
 # 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
 # 2025.08.08. v2.13.0	测试 local realign 功能
+# 2025.08.09. v2.13.1	测试 correction 功能
+# 2025.08.09. v2.13.2	chromap + trim 参数

{offtracker-2.13.0 → offtracker-2.13.2}/offtracker/snakefile/Snakefile_offtracker.smk

@@ -48,7 +48,7 @@ rule chromap:
         temp(os.path.join(_output_dir,"{sample}.chromapx.bed"))
     shell:
         """
-        chromap -l 3000 --low-mem --BED --remove-pcr-duplicates \
+        chromap -l 3000 --low-mem --BED --remove-pcr-duplicates --trim-adapters \
         --min-read-length 10 --allocate-multi-mappings \
         -x {params.index} -r {params.fasta} -t {threads} -1 {input.R1} -2 {input.R2} -o {output}
         """

{offtracker-2.13.0 → offtracker-2.13.2/offtracker.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: offtracker
-Version: 2.13.0
+Version: 2.13.2
 Summary: Tracking-seq data analysis
 Home-page: https://github.com/Lan-lab/offtracker
 Author: Runda Xu

{offtracker-2.13.0 → offtracker-2.13.2}/offtracker.egg-info/SOURCES.txt

@@ -24,6 +24,7 @@ offtracker/utility/offtracker_blacklist_mm10.merged.bed
 scripts/offtracker_analysis.py
 scripts/offtracker_candidates.py
 scripts/offtracker_config.py
+scripts/offtracker_correction.py
 scripts/offtracker_init.py
 scripts/offtracker_plot.py
 scripts/offtracker_qc.py

{offtracker-2.13.0 → offtracker-2.13.2}/scripts/offtracker_analysis.py

@@ -22,24 +22,29 @@ def main():
     parser = argparse.ArgumentParser()
     parser.description='Analyze the Tracking-seq data.'
     parser.add_argument('-f','--folder'  , type=str, required=True,    nargs='+', help='Directory of the data folder.' )
-    parser.add_argument('--seqfolder'    , type=str, required=True,    help='folder containing df_candidate created by offtracker_cadidates.py.')
+    parser.add_argument('--seqfolder'    , type=str, default ='none',  help='folder containing df_candidate created by offtracker_cadidates.py.')
     parser.add_argument('--name'         , type=str, required=True,    help='custom name of the sgRNA' )
     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=float, default=0.05,     help='FDR threshold for the final result. Default is 0.05.')
-    parser.add_argument('--score'        , type=float, default=1.9,        help='Track score threshold for the final result. Default is 1.9.')
+    parser.add_argument('--fdr'          , type=float, default=0.05,   help='FDR threshold for the final result. Default is 0.05.')
+    parser.add_argument('--score'        , type=float, 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.')
     parser.add_argument('--flank_max'    , type=int, default=100000,   help='Maximun flanking distance from the candidate site.')
     parser.add_argument('--flank_regions', type=int, default=[1000,2000,3000,5000], nargs='+',help='flanking regions for calculating signal.')
     parser.add_argument('--SeqScorePower', type=float, default=4,      help='The seq score power' )
-    parser.add_argument('--CtrClip'      , type=float, default=-0.5,     help='The lower clip for control samples' )
+    parser.add_argument('--CtrClip'      , type=float, default=-0.5,   help='The lower clip for control samples' )
     parser.add_argument('-t','--thread'  , type=int, default=4,        help='Number of threads for parallel computing')
     parser.add_argument('-g','--genome'  , type=str, default='hg38',   help='File of chromosome sizes, or "hg38", "mm10" ')
     parser.add_argument('-o','--outdir'  , type=str, default='first',  help='The output folder. Default is the first folder of --folder' )
     parser.add_argument('--outname'      , type=str, default='same',   help='The suffix of output files. Default is the same --exp' )
     parser.add_argument('--signal_only'  , action='store_true', help='A developer option: stop before group analysis. ' )
+    # for offtracker_correction
+    parser.add_argument('--check_loc'    , action='store_true', help='New in v2.13, for other scripts. Do not use this option. ' )
+    parser.add_argument('--seqfile'      , type=str, default='none',   help='Assign a specific df_candidate file.')
+
+    # other parameters
     # parser.add_argument('--individual_results', action='store_true', help='When multiple samples meet the exp pattern, only one merged result is generated.\n' \
     #                                                                       'Set --individual_results to additionally output the individual result of each exp sample. ' )
     parser.add_argument('--overwrite'    , action='store_true', help='Whether to overwrite existed dataframes.' )
@@ -79,7 +84,12 @@ def main():
     
     # load df_candidate
     try:
-        df_candidate = pl.read_csv(os.path.join(args.seqfolder,f'df_candidate_{sgRNA_name}.csv')).to_pandas()
+        if args.seqfile != 'none':
+            df_candidate = pl.read_csv(args.seqfile).to_pandas()
+        elif args.seqfolder != 'none':
+            df_candidate = pl.read_csv(os.path.join(args.seqfolder,f'df_candidate_{sgRNA_name}.csv')).to_pandas()
+        else:
+            raise ValueError('Please provide --seqfolder or --seqfile')
         df_candidate.index = df_candidate['target_location']
         df_candidate_brief = df_candidate[['chr','st','ed','best_strand','best_target','best_seq_score',
                                  'deletion', 'insertion','mismatch', 'GG', 
@@ -160,8 +170,11 @@ def main():
         if (os.path.isfile(output))&(not args.overwrite):
             print(output, 'exists, skipped')
             continue
-        df_bdg = xseq.read_bed(a_file)
-        df_bdg.columns = ['chr','start','end','residual']
+        # 2025.08.09. 改用 pl 读取加速
+        df_bdg = pl.read_csv(a_file, separator='\t', has_header=False,
+                             schema_overrides={'chr':pl.String,'start':pl.Int32,
+                                               'end':pl.Int32,'residual':pl.Float32}).to_pandas() # xseq.read_bed(a_file)
+        # df_bdg.columns = ['chr','start','end','residual']
         # 将 df_bdg 按照染色体分组
         sample_groups = df_bdg.groupby('chr')
         # 2024.06.03. fix a bug that df_bdg has less chr than df_candidate
@@ -308,7 +321,7 @@ def main():
         # 2025.07.06 更新去重方式
         df_result = df_score.drop_duplicates(subset=['region_index'], keep='first').copy()
 
-        # 标准化分布      
+        # 标准化分布，2025.08.09
         target_std=0.15
         n_outliers = int(np.ceil(len(df_result)*0.01))
         score_bkg = df_result['raw_score'][n_outliers:-n_outliers]
@@ -317,7 +330,7 @@ def main():
         df_result['track_score'] = (df_result['raw_score'] - mean_score_bkg) / std_score_bkg
         df_result['track_score'] = df_result['track_score']*target_std + 1
         df_result = df_result.sort_values(by='track_score', ascending=False)
-        df_result['log2_track_score'] = np.log2(df_result['track_score'].clip(lower=0.5))   
+        df_result['log2_track_score'] = np.log2(df_result['track_score'].clip(lower=0.5))
 
         # 单边信号周围有更高分的，去掉
         # v2.1 后 cols_L, cols_R 要手动
@@ -362,35 +375,30 @@ def main():
         df_result['rank'] = range(1,len(df_result)+1)
         df_result.to_csv(output)
 
-    output = f'Offtracker_result_{outname}.csv'
-    # 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，但是很少见，如果 control 用的是别的 sgRNA 的样本，对应脱靶位置附近一般就是负数
-    # bool_neg_score = df_result['track_score']< -1
-    df_output = df_result[bool_fdr|bool_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']]
-        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']
-    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']]
-        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']
-    
-
-    # 2025.08.08. 增加对阳性位点的 target_location 重比对功能，避免 blast 比对后的 realign 在更大范围内的存在不准确的情况
-
-
-
+    if not args.check_loc:
+        output = f'Offtracker_result_{outname}.csv'
+        # 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，但是很少见，如果 control 用的是别的 sgRNA 的样本，对应脱靶位置附近一般就是负数
+        # bool_neg_score = df_result['track_score']< -1
+        df_output = df_result[bool_fdr|bool_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']]
+            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']
+        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']]
+            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']
     
-    df_output.to_csv(f'Offtracker_result_{outname}.csv', index=False)
+        df_output.to_csv(f'Offtracker_result_{outname}.csv', index=False)
 
     if args.clean:
         shutil.rmtree('./temp')

offtracker-2.13.2/scripts/offtracker_correction.py

@@ -0,0 +1,324 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import polars as pl
+import pandas as pd
+import numpy as np
+import offtracker
+import argparse
+import os, glob
+import shlex, subprocess
+from scipy.stats import norm
+
+def main():
+    parser = argparse.ArgumentParser()
+    parser.description='New function in 2026. Check and correct potential incorrect target locations.'
+    parser.add_argument('-f','--folder'  , type=str, required=True,    nargs='+', help='Directory of the data folder.' )
+    parser.add_argument('--name'         , type=str, required=True,    help='custom name of the sgRNA' )
+    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=float, default=0.05,   help='FDR threshold for the final result. Default is 0.05.')
+    parser.add_argument('--score'        , type=float, 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.')
+    parser.add_argument('--flank_max'    , type=int, default=100000,   help='Maximun flanking distance from the candidate site.')
+    parser.add_argument('--flank_regions', type=int, default=[1000,2000,3000,5000], nargs='+',help='flanking regions for calculating signal.')
+    parser.add_argument('--SeqScorePower', type=float, default=4,      help='The seq score power' )
+    parser.add_argument('--CtrClip'      , type=float, default=-0.5,   help='The lower clip for control samples' )
+    parser.add_argument('-t','--thread'  , type=int, default=4,        help='Number of threads for parallel computing')
+    parser.add_argument('-g','--genome'  , type=str, default='hg38',   help='File of chromosome sizes, or "hg38", "mm10" ')
+    parser.add_argument('-o','--outdir'  , type=str, default='first',  help='The output folder. Default is the first folder of --folder' )
+    parser.add_argument('--outname'      , type=str, default='same',   help='The suffix of output files. Default is the same --exp' )
+    # new argument
+    parser.add_argument('-r','--ref'     , type=str, required=True,    help='The fasta file of reference genome')
+    parser.add_argument('--sgrna' ,        type=str, required=True,    help='One sgRNA sequence without PAM' )
+    parser.add_argument('--pam'   ,        type=str, required=True,    help='The protospacer adjacent motif' )
+    parser.add_argument('--pam_location',  type=str, default='downstream', help='Upstream or downstream, default is downstream (Cas9)' )
+    # not used
+    parser.add_argument('--seqfolder'    , type=str, default='none',    help='Actually not used in this script.Only in case you forget to remove this argument.')
+
+    args = parser.parse_args()
+    # 2025.08.08. 增加对阳性位点的 target_location 重比对功能，避免 blast 比对后的 realign 在更大范围内的存在不准确的情况
+    # 实验性功能，如果 exp 有多个样本的话目前只取第一个 bdg 来分析
+
+    ##########################
+    ## parameter initiation ##
+    ##########################
+
+    folders = args.folder
+    sgRNA_name = args.name + '_loc_correction'
+    pattern_exp = args.exp
+    pattern_ctr = args.control
+    fdr_thresh = args.fdr
+    score_thresh = args.score
+    binsize = args.binsize
+    flank_max = args.flank_max
+    flank_regions = args.flank_regions # 如果 analysis 时修改了这个参数没有写 1000 的话会出bug，暂时懒得改了
+    smooth_times = args.smooth
+    window_size = args.window
+    seq_score_power = args.SeqScorePower
+    ctr_clip = args.CtrClip
+
+
+    if args.outname == 'same':
+        if isinstance(pattern_exp, list):
+            outname = '_'.join(pattern_exp)
+        else:
+            outname = pattern_exp
+    else:
+        outname = args.outname
+
+    outdir = args.outdir
+    if outdir == 'first':
+        outdir = folders[0]
+    os.chdir(outdir)
+    # out temp folder
+    if not os.path.exists( os.path.join(outdir,'temp') ):
+        os.makedirs(os.path.join(outdir,'temp'))
+    # data temp folder
+    for a_folder in folders:
+        temp_dir = os.path.join(a_folder, 'temp')
+        if not os.path.exists( temp_dir ):
+            os.makedirs(temp_dir)
+
+    ##################
+    ## glob samples ##
+    ##################
+    all_sample_names = []
+    all_sample_files = []
+    for a_folder in folders:    
+        bdg_files = pd.Series(glob.glob(os.path.join( a_folder, '*.add.bdg' ))).sort_values().reset_index(drop=True)
+        sample_names = bdg_files.apply(os.path.basename).str.extract(r'(.*)\.\d+\.add\.bdg',expand=False)
+        all_sample_names.extend( sample_names )
+        all_sample_files.extend( bdg_files )
+    all_sample_files = pd.Series(all_sample_files)
+    all_sample_names = pd.Series(all_sample_names)
+    print('all sample names in the folders:')
+    print(all_sample_names)
+    print('your string pattern for experimental groups: ', pattern_exp)
+    ctr_samples = []
+    if pattern_ctr == 'none':
+        if pattern_exp == 'all':
+            exp_samples = list( all_sample_names )
+        else:
+            exp_samples = []
+            for a_mark in pattern_exp:
+                exp_samples.extend( list( all_sample_names[all_sample_names.str.contains(a_mark)] ) )
+    elif pattern_ctr == 'others':
+        if pattern_exp == 'all':
+            exp_samples = list( all_sample_names )
+        else:
+            exp_samples = []
+            for a_mark in pattern_exp:
+                exp_samples.extend( list( all_sample_names[all_sample_names.str.contains(a_mark)] ) )
+            ctr_samples = list( all_sample_names[~all_sample_names.isin(exp_samples)] )
+    else:
+        for a_mark in pattern_ctr:
+            ctr_samples.extend( list( all_sample_names[all_sample_names.str.contains(a_mark)] ) )
+        if pattern_exp == 'all':
+            exp_samples = list( all_sample_names[~all_sample_names.isin(ctr_samples)] )
+        else:
+            exp_samples = []
+            for a_mark in pattern_exp:
+                exp_samples.extend( list( all_sample_names[all_sample_names.str.contains(a_mark)] ) )
+    n_exp = len(exp_samples)
+    n_ctr = len(ctr_samples)
+    print(f'Experimental group has {n_exp} samples:\n{exp_samples}')
+    print(f'Control group has {n_ctr} samples:\n{ctr_samples}')
+
+    # mark 错误时
+    assert n_exp > 0, 'No experimental sample is found. Please check the name pattern.'
+    if (n_ctr==0)&(pattern_ctr != 'none'):
+        print('Name pattern for control sample(s) was given, but no file meet the pattern.')
+        return 'Program terminated'
+
+    # summarize samples
+    bool_exp = all_sample_names.isin(exp_samples)
+    bool_ctr = all_sample_names.isin(ctr_samples)
+    exp_sample_files = all_sample_files[bool_exp]
+    ctr_sample_files = all_sample_files[bool_ctr]
+    exp_sample_names = all_sample_names[bool_exp]
+    ctr_sample_names = all_sample_names[bool_ctr]
+    # selected_sample_files = pd.concat([exp_sample_files,ctr_sample_files])
+    # selected_sample_names = pd.concat([exp_sample_names,ctr_sample_names]) # no use
+
+
+
+    ####################
+    ## run correction ##
+    ####################
+
+    # new parameters
+    ref_fasta = args.ref
+    sgRNA_seq = args.sgrna
+    PAM = args.pam
+    PAM_loc = args.pam_location
+    # read result
+    dp_result = pl.read_csv(f'./temp/df_result_{outname}.csv')
+    # negative for next section
+    bool_fdr_bkg = dp_result['fdr']>fdr_thresh
+    bool_score_bkg = dp_result['track_score']<score_thresh
+    dp_result_bkg = dp_result.filter(bool_fdr_bkg & bool_score_bkg)
+    # positive
+    bool_fdr = pl.col('fdr')<=fdr_thresh
+    bool_score = pl.col('track_score')>=score_thresh
+    dp_result = dp_result.filter(bool_fdr & bool_score)
+    # bdg
+    dp_bdg = pl.read_csv(exp_sample_files.iloc[0], separator='\t', has_header=False,
+                             schema_overrides={'chr':pl.String,'start':pl.Int32,'end':pl.Int32,'residual':pl.Float32})
+    # check and realign
+    bool_left_neg=(dp_result['exp_L_neg_1000']<-5)&(dp_result['exp_R_neg_1000']==0)
+    bool_right_neg=(dp_result['exp_R_neg_1000']<-5)&(dp_result['exp_L_neg_1000']==0)
+    list_good_result = []
+    list_bad_left = []
+    list_bad_right = []
+    n_left_for_correct = 0
+    n_right_for_correct = 0
+    for a_left_bool, a_right_bool, a_row in zip(bool_left_neg, bool_right_neg, dp_result.iter_rows(named=True)):
+        if a_left_bool & a_right_bool:
+            raise ValueError('abnormal on both left and right')
+        if a_left_bool:
+            n_left_for_correct += 1
+            loc_shift_left = a_row['chr'] + ':' + str(a_row['st']-1000) + '-' + str(a_row['ed']-20)
+            region_index = a_row['region_index']
+            dp_bdg_chr = dp_bdg.filter(pl.col('chr') == a_row['chr'])
+            sr_candidate = offtracker.left_realign(dp_bdg_chr, loc_shift_left, ref_fasta, sgRNA_seq, PAM, PAM_loc, n_iter=0)
+            sr_candidate.loc['region_index'] = region_index
+            list_bad_left.append(sr_candidate)
+        elif a_right_bool:
+            n_right_for_correct += 1
+            loc_shift_right = a_row['chr'] + ':' + str(a_row['st']+20) + '-' + str(a_row['ed']+1000)
+            region_index = a_row['region_index']
+            dp_bdg_chr = dp_bdg.filter(pl.col('chr') == a_row['chr'])
+            sr_candidate = offtracker.right_realign(dp_bdg_chr, loc_shift_right, ref_fasta, sgRNA_seq, PAM, PAM_loc, n_iter=0)
+            sr_candidate.loc['region_index'] = region_index
+            list_bad_right.append(sr_candidate)
+        else:
+            list_good_result.append(a_row)
+    dp_result_good = pl.DataFrame(list_good_result)
+    df_cand_left = pd.DataFrame(list_bad_left)
+    df_cand_right = pd.DataFrame(list_bad_right)
+    df_cand_realign = pd.concat([df_cand_left, df_cand_right])
+    if len(df_cand_realign) == 0:
+        print('No candidate is found for realignment.')
+        return 'finished'
+
+    # 情况判断
+    n_success_realign = sum(df_cand_realign['realign']=='success')
+    n_fail_realign = sum(df_cand_realign['realign']!='success')
+    if (n_success_realign == 0) and (n_fail_realign > 0):
+        print(f'{n_fail_realign} candidates are found for realignment, but all failed.')
+        return 'finished'
+    elif (n_success_realign > 0) and (n_fail_realign > 0):
+        print(f'{n_success_realign} candidates succeeded, and {n_fail_realign} candidates failed.')
+    else:
+        print(f'{n_success_realign} candidates succeeded.')
+
+    df_cand_realign = df_cand_realign[df_cand_realign['realign']=='success']
+    seqfile = rf'correction_df_candidate_{outname}_realign.csv'
+    df_cand_realign.to_csv(seqfile)
+    
+    # run offtracker_analysis with check_loc mode
+    running_log = rf'correction_analysis_{outname}.log'
+    # list 转空格分割参数
+    if isinstance(pattern_exp, list):
+        param_pattern_exp = ' '.join(pattern_exp)
+    else:
+        param_pattern_exp = pattern_exp
+    if isinstance(pattern_ctr, list):
+        param_pattern_ctr = ' '.join(pattern_ctr)
+    else:
+        param_pattern_ctr = pattern_ctr
+    if isinstance(flank_regions, list):
+        param_flank_regions = ' '.join([str(x) for x in flank_regions])
+    else:
+        param_flank_regions = flank_regions
+    if isinstance(folders, list):
+        param_folders = ' '.join([str(x) for x in folders])
+    else:
+        param_folders = folders
+
+    with open(running_log, "w+") as running_log:
+        command   = f'offtracker_analysis.py -t {args.thread} -g {args.genome} --seqfile {seqfile} --name {sgRNA_name} \
+        --exp {param_pattern_exp} --control {param_pattern_ctr} --outname {outname}_loc_correction -f {param_folders} -o {outdir} \
+        --fdr {fdr_thresh} --window {window_size} --smooth {smooth_times} --SeqScorePower {seq_score_power} \
+        --score {score_thresh} --binsize {binsize} --flank_max {flank_max} --flank_regions {param_flank_regions} --CtrClip {ctr_clip} \
+        --check_loc'
+        command2  = shlex.split('bash -c "{}"'.format(command))
+        process_1 = subprocess.Popen(command2, stdout=running_log, stderr=subprocess.STDOUT )
+        process_1.wait(timeout=100000)
+        retc  = process_1.returncode
+        if retc==0:
+            print((f'correction_analysis {outname} is done!'))
+        else:
+            print((f'correction_analysis {outname} is failed!'))
+
+
+    #######################
+    ## recalculate score ##
+    #######################
+
+    dp_result_realign = pl.read_csv(f'./temp/df_result_{outname}_loc_correction.csv')
+
+    # 兼容旧版输出列名
+    list_col = dp_result_realign.columns[:-5]
+    dp_result_new = pl.concat([dp_result_realign[list_col], dp_result_good[list_col], dp_result_bkg[list_col]])
+
+    # 标准化分布, polars 版   
+    target_std=0.15
+    n_outliers = int(np.ceil(len(dp_result_new)*0.01))
+    score_bkg = dp_result_new['raw_score'][n_outliers:-n_outliers]
+    mean_score_bkg = score_bkg.mean()
+    std_score_bkg = score_bkg.std()
+    dp_result_new = dp_result_new.with_columns(
+        (pl.col('raw_score').sub(mean_score_bkg)/std_score_bkg).alias('track_score')
+    )
+    dp_result_new = dp_result_new.with_columns(
+        pl.col('track_score').mul(target_std).add(1).alias('track_score')
+    )
+    dp_result_new = dp_result_new.with_columns(
+        pl.col('track_score').clip(lower_bound=0.5).log(base=2).alias('log2_track_score')
+    )
+    dp_result_new = dp_result_new.sort('track_score', descending=True)
+
+    # pv and fdr
+    score_for_fitting = dp_result_new['log2_track_score'][n_outliers:-n_outliers]
+    mu, std = norm.fit(score_for_fitting) 
+    print('mean_score:{:.3f};std:{:.3f}'.format(mu,std))
+    dp_result_new = dp_result_new.with_columns(
+        pl.col('log2_track_score').map_elements( lambda x: norm.sf(x,loc=mu,scale=std), return_dtype=pl.Float64 ).clip(lower_bound=1e-320).alias('pv')
+    )
+    dp_result_new = dp_result_new.with_columns(
+        fdr=offtracker.fdr(dp_result_new['pv']).alias('fdr'),
+        rank=pl.Series(range(1,len(dp_result_new)+1))
+    ) #.with_row_index(name='rank',offset=1)
+    dp_result_new.write_csv(f'./temp/df_result_{outname}.csv') # 覆盖原结果
+
+    # ouput Offtracker result
+    bool_fdr = pl.col('fdr')<=fdr_thresh
+    bool_score = pl.col('track_score')>=score_thresh
+    dp_output = dp_result_new.filter(bool_fdr|bool_score)
+    if pattern_ctr != 'none':
+        dp_output = dp_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']]
+        dp_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']
+    else:
+        dp_output = dp_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']]
+        dp_output.columns = ['target_location', 'strand', 'target', 'deletion', 'insertion', 'mismatch',
+                            'L_length', 'R_length','signal_length',
+                            'seq_score', 'track_score', 'log2_track_score','FDR', 'rank']
+    dp_output.write_csv(f'Offtracker_result_{outname}.csv')
+
+    return 'correction finished'
+
+if __name__ == '__main__' :
+    result = main()
+    print(result)
+
+

{offtracker-2.13.0 → offtracker-2.13.2}/setup.py

@@ -54,6 +54,7 @@ setup(
                 'scripts/offtracker_config.py',
                 'scripts/offtracker_candidates.py',
                 'scripts/offtracker_analysis.py',
+                'scripts/offtracker_correction.py',
                 'scripts/offtracker_plot.py'],
     install_requires=REQUIRED,
     include_package_data=True