offtracker 1.0.2__zip → 2.7.7__zip

offtracker-1.0.2/offtracker/X_analysis.py

@@ -1,332 +0,0 @@
-
-import pandas as pd
-import numpy as np
-import os, sys, pybedtools
-sys.path.append( os.path.abspath(os.path.dirname(__file__)) )
-from X_general import *
-
-def signal_formula1(signal, nonsignal, pseudocount):
-    # 背景均值略小于 1
-    assert pseudocount>0
-    return signal/(nonsignal+pseudocount)
-
-def signal_formula2(signal, nonsignal, pseudocount):
-    # 背景均值为 1
-    assert pseudocount>0
-    return (signal+pseudocount)/(nonsignal+pseudocount)
-
-def signal_formula3(signal, nonsignal, pseudocount):
-    # 调整背景均值为 1
-    assert pseudocount>0
-    out = (signal - nonsignal + 1)
-    out.loc[out<0] = 0
-    return out
-
-def signal_formula4(signal, nonsignal, pseudocount):
-    # 背景均值为 1
-    assert pseudocount>0
-    return signal
-
-def shape_formula1(normed_left_signal, normed_left_nonsignal, normed_right_signal, normed_right_nonsignal, bkg_noise, ratio_thresh=1.5, exp_weight = 0.3):
-    # 防止破坏性的极小值出现
-    normed_left_signal = normed_left_signal.clip(lower=1)
-    normed_left_nonsignal = normed_left_nonsignal.clip(lower=1)
-    normed_right_signal = normed_right_signal.clip(lower=1)
-    normed_right_nonsignal = normed_right_nonsignal.clip(lower=1) 
-    left_ratio = normed_left_signal/normed_left_nonsignal
-    right_ratio = normed_right_signal/normed_right_nonsignal
-    #
-    good_shape = pd.concat([left_ratio,right_ratio],axis=1).min(axis=1)>ratio_thresh
-    left_ratio.loc[~good_shape]=1
-    right_ratio.loc[~good_shape]=1
-    bonus_coef = left_ratio*right_ratio
-    bonus_coef = np.power(bonus_coef,exp_weight)
-    return bonus_coef
-
-def shape_formula2(normed_left_signal, normed_left_nonsignal, normed_right_signal, normed_right_nonsignal, bkg_noise, ratio_thresh=1, exp_weight = 0.3):
-    left_residual = normed_left_signal - normed_left_nonsignal
-    right_residual = normed_right_signal - normed_right_nonsignal
-    # 这里先取 max，也可以取 min 或者 mean
-    good_left = left_residual>ratio_thresh
-    good_right = right_residual>ratio_thresh
-    good_shape = good_left&good_right
-    left_residual.loc[~good_shape]=0
-    right_residual.loc[~good_shape]=0
-    bonus_coef = (left_residual+right_residual)/(2*ratio_thresh)
-    bonus_coef = np.power(bonus_coef,exp_weight)
-    bonus_coef = bonus_coef.clip(lower=1)
-    return bonus_coef
-
-def score_formula1(exp, ctrl, pseudocount):
-    assert pseudocount>0
-    return exp/(max(ctrl,0)+pseudocount)
-
-def score_formula2(exp, ctrl, pseudocount):
-    assert pseudocount>0
-    return (exp+pseudocount)/(max(ctrl,0)+pseudocount)
-
-def score_formula3(exp, ctrl, pseudocount):
-    assert pseudocount>0
-    return exp/max(ctrl, pseudocount)
-
-def score_formula4(exp, ctrl, pseudocount):
-    assert pseudocount>0
-    return max((exp - ctrl), 0)
-
-def score_formula5(exp, ctrl, pseudocount):
-    assert pseudocount>0
-    return exp
-
-def fdr(p_vals):
-    # Benjamini-Hochberg
-    from scipy.stats import rankdata
-    ranked_p_values = rankdata(p_vals)
-    fdr = p_vals * len(p_vals) / ranked_p_values
-    fdr[fdr > 1] = 1
-    return fdr
-
-def dedup_two( df_loc, col_ID_1='ID_1', col_ID_2='ID_2'):
-    # 会根据 df_loc 的排序保留第一个 location
-    # dedup 结束后，剩下的 ID_1 + ID_2 并集可能会小于 dedup 前的并集
-    list_nondup = []
-    set_IDs = set()
-    df_IDs = df_loc[[col_ID_1,col_ID_2]]
-    for a_row in df_IDs.iterrows():
-        temp = a_row[1]
-        if (temp[col_ID_1] in set_IDs) or (temp[col_ID_2] in set_IDs):
-            # 只要有一ID出现过，即便另一ID没出现过，也不更新 set_IDs
-            list_nondup.append(False)
-        else:
-            set_IDs.add(temp[col_ID_1])
-            set_IDs.add(temp[col_ID_2])
-            list_nondup.append(True)
-    return list_nondup
-
-def cand_count(a_pref, the_sgRNA, regions, seq_folder, dir_chrom_sizes, overwrite=False):
-    # 
-    forward_bed = f'{a_pref}.fw.bed'
-    reverse_bed = f'{a_pref}.rv.bed'
-    # put into temp_dir
-    dirname = os.path.dirname(a_pref)
-    basename = os.path.basename(a_pref)
-    temp_dir = os.path.join(dirname, 'temp')
-    if not os.path.exists( temp_dir ):
-        os.makedirs(temp_dir)
-    a_pref = os.path.join(temp_dir, basename)
-    #
-    for a_region in regions:
-        work = 1
-        if os.path.isfile(f'{a_pref}_candidate_{the_sgRNA}_right_rstrand_{a_region}.count'):
-            #print(f'Candidates for {the_sgRNA} within {a_region} of {basename} exists.\n')
-            work = 0
-        if overwrite:
-            print('overwrite mode')
-            work = 1
-        if work == 1:
-            print(f'Working for {basename} within {a_region} bp.\n')
-            # 左侧区域
-            left_region=os.path.join(seq_folder, f'{the_sgRNA}_candidate_left_{a_region}.bed')
-            a = pybedtools.BedTool(left_region)
-            b = pybedtools.BedTool(forward_bed)
-            c = a.coverage(b,sorted=True,g=dir_chrom_sizes)
-            c.saveas(f'{a_pref}_candidate_{the_sgRNA}_left_fstrand_{a_region}.count')
-            b = pybedtools.BedTool(reverse_bed)
-            c = a.coverage(b,sorted=True,g=dir_chrom_sizes)
-            c.saveas(f'{a_pref}_candidate_{the_sgRNA}_left_rstrand_{a_region}.count')
-            # 右侧区域
-            right_region=os.path.join(seq_folder, f'{the_sgRNA}_candidate_right_{a_region}.bed')
-            a = pybedtools.BedTool(right_region)
-            b = pybedtools.BedTool(forward_bed)
-            c = a.coverage(b,sorted=True,g=dir_chrom_sizes)
-            c.saveas(f'{a_pref}_candidate_{the_sgRNA}_right_fstrand_{a_region}.count')
-            b = pybedtools.BedTool(reverse_bed)
-            c = a.coverage(b,sorted=True,g=dir_chrom_sizes)
-            c.saveas(f'{a_pref}_candidate_{the_sgRNA}_right_rstrand_{a_region}.count')
-
-def bkg_count(a_pref, the_sgRNA, bkgs, seq_folder, dir_chrom_sizes, overwrite=False):
-    # no need for LF and RR
-    forward_bed = f'{a_pref}.fw.bed'
-    reverse_bed = f'{a_pref}.rv.bed'
-    # put into temp_dir
-    dirname = os.path.dirname(a_pref)
-    basename = os.path.basename(a_pref)
-    temp_dir = os.path.join(dirname, 'temp')
-    if not os.path.exists( temp_dir ):
-        os.makedirs(temp_dir)
-    a_pref = os.path.join(temp_dir, basename)
-    #
-    work = 1
-    for a_region in bkgs:
-        if os.path.isfile(f'{a_pref}_candidate_{the_sgRNA}_right_fstrand_{a_region}.count'):
-            #print(f'Candidates for {the_sgRNA} within {a_region} of {basename} exists.\n')
-            work = 0
-        if overwrite:
-            print('overwrite mode')
-            work = 1
-        if work == 1:
-            print(f'Working for {basename} within {a_region} bp.\n')
-            # 左侧区域
-            left_region=os.path.join(seq_folder, f'{the_sgRNA}_candidate_left_{a_region}.bed')
-            a = pybedtools.BedTool(left_region)
-            b = pybedtools.BedTool(reverse_bed)
-            c = a.coverage(b,sorted=True,g=dir_chrom_sizes)
-            c.saveas(f'{a_pref}_candidate_{the_sgRNA}_left_rstrand_{a_region}.count')
-            # 右侧区域
-            right_region=os.path.join(seq_folder, f'{the_sgRNA}_candidate_right_{a_region}.bed')
-            a = pybedtools.BedTool(right_region)
-            b = pybedtools.BedTool(forward_bed)
-            c = a.coverage(b,sorted=True,g=dir_chrom_sizes)
-            c.saveas(f'{a_pref}_candidate_{the_sgRNA}_right_fstrand_{a_region}.count')
-
-
-def load_count(    a_sample, regions, bkgs, sgRNA_name, signal_formula, noise_length, 
-    ratio_thresh, exp_weight, shape_formula=None,
-    operator='p', region_op='mean', dirname='./',  pseudo_count=1
-    ):
-    list_noise = []
-    for a_bkg in bkgs:
-        left_count_rstrand = os.path.join(dirname, f'{a_sample}_candidate_{sgRNA_name}_left_rstrand_{a_bkg}.count')
-        left_count_rstrand = readbed(left_count_rstrand)
-        right_count_fstrand= os.path.join(dirname, f'{a_sample}_candidate_{sgRNA_name}_right_fstrand_{a_bkg}.count')
-        right_count_fstrand = readbed(right_count_fstrand)
-        list_noise.append(right_count_fstrand[3])
-        list_noise.append(left_count_rstrand[3])
-    df_noise = pd.concat(list_noise,axis=1, ignore_index=True)
-    df_noise['mean'] = df_noise.mean(axis=1)
-    mean_all = df_noise['mean'].mean()
-    df_noise['std'] = df_noise.std(axis=1)
-    df_noise['outlier'] = df_noise['mean']+2*df_noise['std']
-    for i in range(len(bkgs)*2):
-        df_noise.loc[df_noise[i]>df_noise['outlier'],i] = np.nan
-    df_noise['mean2'] = df_noise.iloc[:,:6].mean(axis=1, skipna = True)
-    n_0bkg = sum(df_noise.mean2==0)
-    if n_0bkg > 0:
-        print(f'{n_0bkg} region(s) with 0 count in background.')
-    # 由于有些位置可能出现无法 mapping 而产生大量空白，导致局部噪音过低，因此这里主要是防局部高噪音造成假阳性
-    df_noise.loc[df_noise['mean2']<mean_all, 'mean2'] = mean_all
-    df_noise['noise_bp'] = df_noise['mean2']/noise_length
-    noise_5kb = df_noise['noise_bp'].mean()*5000
-    print('Average noise within 5kb on a single strand: {:.2f}'.format(noise_5kb))
-    if noise_5kb < 10:
-        print('The sequencing depth might be too shallow')
-    list_df_counts = []
-    for a_region in regions:
-        left_count_fstrand= os.path.join(dirname, f'{a_sample}_candidate_{sgRNA_name}_left_fstrand_{a_region}.count')
-        left_count_fstrand = readbed(left_count_fstrand)
-        left_count_fstrand.columns=[f'chr_{a_region}',f'st_left_{a_region}',f'ed_left_{a_region}',f'counts_left_F_{a_region}',f'cover_left_F_bp_{a_region}',f'length_{a_region}',f'cover_left_F_pct_{a_region}']
-        right_count_fstrand=os.path.join(dirname, f'{a_sample}_candidate_{sgRNA_name}_right_fstrand_{a_region}.count')
-        right_count_fstrand = readbed(right_count_fstrand)
-        right_count_fstrand.columns=[f'chr_{a_region}',f'st_right_{a_region}',f'ed_right_{a_region}',f'counts_right_F_{a_region}',f'cover_right_F_bp_{a_region}',f'length_{a_region}',f'cover_right_F_pct_{a_region}']
-        left_count_rstrand= os.path.join(dirname, f'{a_sample}_candidate_{sgRNA_name}_left_rstrand_{a_region}.count')
-        left_count_rstrand = readbed(left_count_rstrand)
-        left_count_rstrand.columns=[f'chr_{a_region}',f'st_left_{a_region}',f'ed_left_{a_region}',f'counts_left_R_{a_region}',f'cover_left_R_bp_{a_region}',f'length_{a_region}',f'cover_left_R_pct_{a_region}']
-        right_count_rstrand=os.path.join(dirname, f'{a_sample}_candidate_{sgRNA_name}_right_rstrand_{a_region}.count')
-        right_count_rstrand = readbed(right_count_rstrand)
-        right_count_rstrand.columns=[f'chr_{a_region}',f'st_right_{a_region}',f'ed_right_{a_region}',f'counts_right_R_{a_region}',f'cover_right_R_bp_{a_region}',f'length_{a_region}',f'cover_right_R_pct_{a_region}']
-        
-        df_counts = pd.concat([left_count_fstrand[[f'chr_{a_region}',f'st_left_{a_region}', f'ed_left_{a_region}',
-                                                f'counts_left_F_{a_region}',f'cover_left_F_bp_{a_region}',f'cover_left_F_pct_{a_region}']],
-                            left_count_rstrand[[f'counts_left_R_{a_region}',f'cover_left_R_bp_{a_region}',f'cover_left_R_pct_{a_region}']],
-                            right_count_fstrand[[f'ed_right_{a_region}',f'counts_right_F_{a_region}',f'cover_right_F_bp_{a_region}',f'cover_right_F_pct_{a_region}']],
-                            right_count_rstrand[[f'counts_right_R_{a_region}',f'cover_right_R_bp_{a_region}',f'cover_right_R_pct_{a_region}']]],axis=1)
-        
-        df_counts = df_counts.reindex(columns=[f'chr_{a_region}', f'st_left_{a_region}', f'ed_right_{a_region}', f'ed_left_{a_region}',
-                                            f'counts_left_F_{a_region}',f'cover_left_F_bp_{a_region}',f'cover_left_F_pct_{a_region}',
-                                            f'counts_left_R_{a_region}',f'cover_left_R_bp_{a_region}',f'cover_left_R_pct_{a_region}',
-                                            f'counts_right_F_{a_region}',f'cover_right_F_bp_{a_region}',f'cover_right_F_pct_{a_region}',
-                                            f'counts_right_R_{a_region}',f'cover_right_R_bp_{a_region}',f'cover_right_R_pct_{a_region}'])
-        df_counts.columns = [f'chr_{a_region}', f'st_{a_region}', f'ed_{a_region}',  f'midpoint_{a_region}',
-                            f'counts_left_F_{a_region}',f'cover_left_F_bp_{a_region}',f'cover_left_F_pct_{a_region}',
-                            f'counts_left_R_{a_region}',f'cover_left_R_bp_{a_region}',f'cover_left_R_pct_{a_region}',
-                            f'counts_right_F_{a_region}',f'cover_right_F_bp_{a_region}',f'cover_right_F_pct_{a_region}',
-                            f'counts_right_R_{a_region}',f'cover_right_R_bp_{a_region}',f'cover_right_R_pct_{a_region}']
-    
-        # signal enrichment = Cs/(Cn+B)
-        bkg_noise = df_noise['noise_bp']*a_region
-        normed_left_signal = df_counts[f'counts_left_F_{a_region}']/bkg_noise
-        normed_left_nonsignal = df_counts[f'counts_left_R_{a_region}']/bkg_noise
-        normed_right_signal = df_counts[f'counts_right_R_{a_region}']/bkg_noise
-        normed_right_nonsignal = df_counts[f'counts_right_F_{a_region}']/bkg_noise
-        df_counts[f'N_LF_{a_region}'] = normed_left_signal
-        df_counts[f'N_LR_{a_region}'] = normed_left_nonsignal
-        df_counts[f'N_RR_{a_region}'] = normed_right_signal
-        df_counts[f'N_RF_{a_region}'] = normed_right_nonsignal
-        # 可变公式区
-        df_counts[f'left_signal_{a_region}'] = signal_formula(normed_left_signal, normed_left_nonsignal, pseudo_count)
-        df_counts[f'right_signal_{a_region}'] = signal_formula(normed_right_signal, normed_right_nonsignal, pseudo_count)
-        if shape_formula:
-            df_counts[f'shape_bonus_{a_region}'] = shape_formula(normed_left_signal, normed_left_nonsignal,
-                                                                 normed_right_signal, normed_right_nonsignal, 
-                                                                 bkg_noise, ratio_thresh, exp_weight)
-        else:
-            df_counts[f'shape_bonus_{a_region}'] = 1
-        list_df_counts.append(df_counts)
-    df_counts = pd.concat(list_df_counts,axis=1)
-    left_signal_cols = df_counts.columns[ df_counts.columns.str.contains('left_signal_') ]
-    right_signal_cols = df_counts.columns[ df_counts.columns.str.contains('right_signal_') ]
-    
-    print('region_op',region_op)
-    if region_op == 'mean':
-        df_counts['left_signal'] = df_counts[left_signal_cols].mean(axis=1)
-        df_counts['right_signal'] = df_counts[right_signal_cols].mean(axis=1)        
-    elif region_op == 'max':
-        df_counts['left_signal'] = df_counts[left_signal_cols].max(axis=1)
-        df_counts['right_signal'] = df_counts[right_signal_cols].max(axis=1)
-    elif region_op == 'min':
-        df_counts['left_signal'] = df_counts[left_signal_cols].min(axis=1)
-        df_counts['right_signal'] = df_counts[right_signal_cols].min(axis=1)    
-    else:
-        raise Exception('region_op should be "mean", "max", or "min" ')
-    
-    max_region = max(regions)
-    df_counts['chr'] = df_counts[f'chr_{max_region}']
-    df_counts['st'] = df_counts[f'st_{max_region}']
-    df_counts['ed'] = df_counts[f'ed_{max_region}']
-    df_counts['midpoint'] = df_counts[f'midpoint_{max_region}']
-    df_counts = df_counts.reindex( columns= ['chr','st','ed','midpoint'] + list(df_counts.columns) )
-    df_counts = df_counts.loc[:,~df_counts.columns.duplicated()].copy()
-    print('Raw regions:', len(df_counts))
-    
-    # operator 选择
-    if operator == 'p':
-        df_counts['score'] = (df_counts['left_signal']+df_counts['right_signal'])/2
-    elif operator == 'm':
-        df_counts['score'] = np.power(df_counts['left_signal']*df_counts['right_signal'],0.5)
-    
-    #
-    min_region = min(regions)
-    
-    if shape_formula:
-        # 
-        shape_bonus_cols = df_counts.columns[ df_counts.columns.str.contains('shape_bonus_') ]
-        df_counts['shape_bonus'] = df_counts[shape_bonus_cols].mean(axis=1)
-
-        
-    df_counts = df_counts.sort_values(by='score',ascending=False).reset_index(drop=True)
-    
-    ### 一些其他特征
-    
-    # 左右最小范围信号绝对强度比值与差值
-    max_adjacent_ratio = df_counts[[f'left_signal_{min_region}',f'right_signal_{min_region}']].max(axis=1)
-    min_adjacent_ratio = df_counts[[f'left_signal_{min_region}',f'right_signal_{min_region}']].min(axis=1)
-    df_counts['signal_FC'] = max_adjacent_ratio/(min_adjacent_ratio+0.001)
-
-    # 左右500bp小信号边若为负数，可能是假的
-    df_counts['left_signal_residual'] = df_counts[f'N_LF_{min_region}'] - df_counts[f'N_LR_{min_region}']
-    df_counts['right_signal_residual'] = df_counts[f'N_RR_{min_region}'] - df_counts[f'N_RF_{min_region}']
-    min_adjacent_signal = df_counts[['left_signal_residual','right_signal_residual']].min(axis=1)
-    df_counts['signal_min'] = min_adjacent_signal
-
-    # 具体位置去重
-    df_counts['location'] = igvfmt(df_counts)
-    df_counts = df_counts.drop_duplicates(subset='location').reset_index(drop=True).copy()
-    
-    # 第二版 unique_ID 
-    point_head = (df_counts['midpoint']/1000).astype(int)
-    df_counts['ID_1'] = df_counts['chr'] + ':' + point_head.astype(str)
-    point_tail = df_counts['midpoint'] % 1000
-    df_counts.loc[point_tail<500,'ID_2'] = df_counts['chr'] + ':' + (point_head-1).astype(str)
-    df_counts.loc[point_tail>=500,'ID_2'] = df_counts['chr'] + ':' + (point_head+1).astype(str)
-    
-    return df_counts, df_noise
-

offtracker-1.0.2/offtracker/_version.py

@@ -1 +0,0 @@
-__version__ = "1.0.2"

offtracker-1.0.2/offtracker/mapping/Snakefile_Trackseq

@@ -1,175 +0,0 @@
-
-configfile: "config.yaml"
-
-_threads = config["thread"]
-BinSize = str(config["binsize"])
-output_dir = config["output_dir"]
-nametype = config["nametype"]
-suffix = config["suffix"]
-name1 = nametype.replace('2','1') + '.' + suffix
-name2 = nametype + '.' + suffix
-
-import os
-
-
-rule all:
-    input:
-        expand( os.path.join(output_dir,"{sample}.fw.bed"), sample=config["sample"] ),
-        expand( os.path.join(output_dir,"{sample}.rv.bed"), sample=config["sample"] ),
-        expand( os.path.join(output_dir,"{sample}.fw.scaled.bw"), sample=config["sample"] ),
-        expand( os.path.join(output_dir,"{sample}.rv.scaled.bw"), sample=config["sample"] ),
-
-
-rule chromap:
-    input:
-        R1= lambda w: config["sample"][w.sample] + name1,
-        R2= lambda w: config["sample"][w.sample] + name2
-    threads:
-        _threads
-    params:
-        index=config["index"],
-        fasta=config["fasta"]
-    output:
-        temp(os.path.join(output_dir,"{sample}.chromapx.bed"))
-    shell:
-        """
-        chromap -l 2000 --low-mem --BED --remove-pcr-duplicates \
-        --min-read-length 10 --allocate-multi-mappings \
-        -x {params.index} -r {params.fasta} -t {threads} -1 {input.R1} -2 {input.R2} -o {output}
-        """
-
-if config["blacklist"] != 'none':
-    rule remove_blacklist:
-        input:
-            os.path.join(output_dir,"{sample}.chromapx.bed")
-        threads:
-            _threads
-        params:
-            blacklist=config["blacklist"]
-        output:
-            temp(os.path.join(output_dir,"{sample}.filtered.bed"))
-        shell:
-            "bedtools intersect -a {input} -b {params.blacklist} -v > {output}"
-
-    rule bed2fr:
-        input:
-            os.path.join(output_dir,"{sample}.filtered.bed")
-        threads:
-            _threads
-        params:
-            dir_script=config["script_folder"]
-        output:
-            fw=os.path.join(output_dir,"{sample}.fw.bed"),
-            rv=os.path.join(output_dir,"{sample}.rv.bed")
-        shell:
-            "python {params.dir_script}/1.1_bed2fr_v4.5.py -b {input}"
-else:
-    rule bed2fr:
-        input:
-            os.path.join(output_dir,"{sample}.chromapx.bed")
-        threads:
-            _threads
-        params:
-            dir_script=config["script_folder"]
-        output:
-            fw=os.path.join(output_dir,"{sample}.fw.bed"),
-            rv=os.path.join(output_dir,"{sample}.rv.bed")
-        shell:
-            "python {params.dir_script}/1.1_bed2fr_v4.5.py -b {input}"    
-
-rule bed2bdg_fw:
-    input:
-        os.path.join(output_dir,"{sample}.fw.bed")
-    threads:
-        _threads
-    params:
-        gl=config["genomelen"]
-    output:
-        temp(os.path.join(output_dir,"{sample}.fw.bdg"))
-    shell:
-        "bedtools genomecov -bg -i {input} -g {params.gl} > {output}"
-
-rule bed2bdg_rv:
-    input:
-        os.path.join(output_dir,"{sample}.rv.bed")
-    threads:
-        _threads
-    params:
-        gl=config["genomelen"]
-    output:
-        temp(os.path.join(output_dir,"{sample}.rv.bdg"))
-    shell:
-        "bedtools genomecov -bg -i {input} -g {params.gl} > {output}"
-
-rule bdg_sort_fw:
-    input:
-        fw=os.path.join(output_dir,"{sample}.fw.bdg")
-    threads:
-        _threads
-    output:
-        temp(os.path.join(output_dir,"{sample}.fw.sorted.bdg"))
-    shell:
-        "bedtools sort -i {input.fw} > {output}"
-
-rule bdg_sort_rv:
-    input:
-        rv=os.path.join(output_dir,"{sample}.rv.bdg")
-    threads:
-        _threads
-    output:
-        temp(os.path.join(output_dir,"{sample}.rv.sorted.bdg"))
-    shell:
-        "bedtools sort -i {input.rv} > {output}"
-
-rule bdg_normalize_fw:
-    input:
-        bdg=os.path.join(output_dir,"{sample}.fw.sorted.bdg"),
-        bed=os.path.join(output_dir,"{sample}.fw.bed")
-    threads:
-        _threads
-    params:
-        dir_script=config["script_folder"]
-    output:
-        temp(os.path.join(output_dir,"{sample}.fw.scaled.bdg"))
-    shell:
-        "python {params.dir_script}/1.3_bdg_normalize_v4.0.py --bdg {input.bdg} --bed {input.bed}"
-
-rule bdg_normalize_rv:
-    input:
-        bdg=os.path.join(output_dir,"{sample}.rv.sorted.bdg"),
-        bed=os.path.join(output_dir,"{sample}.rv.bed")
-    threads:
-        _threads
-    params:
-        dir_script=config["script_folder"]
-    output:
-        temp(os.path.join(output_dir,"{sample}.rv.scaled.bdg"))
-    shell:
-        "python {params.dir_script}/1.3_bdg_normalize_v4.0.py --bdg {input.bdg} --bed {input.bed}"
-
-rule bdg2bw_fw:
-    input:
-        os.path.join(output_dir,"{sample}.fw.scaled.bdg")
-    threads:
-        _threads
-    params:
-        gl=config["genomelen"],
-        dir_script=config["script_folder"]
-    output:
-        os.path.join(output_dir,"{sample}.fw.scaled.bw")
-    shell:
-        "{params.dir_script}/bedGraphToBigWig {input} {params.gl} {output}"
-
-rule bdg2bw_rv:
-    input:
-        os.path.join(output_dir,"{sample}.rv.scaled.bdg")
-    threads:
-        _threads
-    params:
-        gl=config["genomelen"],
-        dir_script=config["script_folder"]
-    output:
-        os.path.join(output_dir,"{sample}.rv.scaled.bw")
-    shell:
-        "{params.dir_script}/bedGraphToBigWig {input} {params.gl} {output}"
-