gwaslab 3.4.47__py3-none-any.whl → 3.4.48__py3-none-any.whl

gwaslab/g_Sumstats.py

@@ -76,6 +76,8 @@ from gwaslab.util_ex_ldsc import _estimate_rg_by_ldsc
 from gwaslab.util_ex_ldsc import _estimate_h2_cts_by_ldsc
 from gwaslab.util_ex_ldsc import _estimate_partitioned_h2_by_ldsc 
 from gwaslab.bd_get_hapmap3 import gethapmap3
+from gwaslab.util_abf_finemapping import abf_finemapping
+from gwaslab.util_abf_finemapping import make_cs
 import gc
 
 #20220309
@@ -135,6 +137,7 @@ class Sumstats():
         self.data = pd.DataFrame()
         self.log = Log()
         self.ldsc_h2 = None
+        self.ldsc_h2_results = None
         self.ldsc_rg = None
         self.ldsc_h2_cts = None
         self.ldsc_partitioned_h2_summary = None
@@ -756,13 +759,20 @@ class Sumstats():
         else:
             output = lambdaGC(self.data[["CHR",mode]],mode=mode,**kwargs)
             self.meta["Genomic inflation factor"] = output
-            return output 
+            return output
+        
+    def abf_finemapping(self, region=None, chrpos=None, snpid=None,**kwargs):        
+        region_data = abf_finemapping(self.data.copy(),region=region,chrpos=chrpos,snpid=snpid,log=self.log, **kwargs)
+        credible_sets = make_cs(region_data,threshold=0.95,log=self.log)
+        return region_data, credible_sets
+    
+    
 ## LDSC ##############################################################################################
     def estimate_h2_by_ldsc(self, build=None, verbose=True, match_allele=True, **kwargs):
         if build is None:
             build = self.meta["gwaslab"]["genome_build"]
         insumstats = gethapmap3(self.data.copy(), build=build, verbose=verbose , match_allele=True, how="right" )
-        self.ldsc_h2 = _estimate_h2_by_ldsc(insumstats=insumstats, log=self.log, verbose=verbose, **kwargs)
+        self.ldsc_h2, self.ldsc_h2_results = _estimate_h2_by_ldsc(insumstats=insumstats, log=self.log, verbose=verbose, **kwargs)
     
     def estimate_rg_by_ldsc(self, build=None, verbose=True, match_allele=True, **kwargs):
         if build is None:

gwaslab/g_version.py

@@ -15,8 +15,8 @@ def _get_version():
 def gwaslab_info():
     # version meta information
     dic={
-   "version":"3.4.47",
-   "release_date":"20240703"
+   "version":"3.4.48",
+   "release_date":"20240822"
     }
     return dic   
 

gwaslab/io_read_ldsc.py

@@ -198,16 +198,29 @@ def read_greml(filelist=[]):
     return summary
 
 def parse_ldsc_summary(ldsc_summary):
-    summary = pd.DataFrame(columns = ['h2_obs', 'h2_se','Lambda_gc','Mean_chi2','Intercept','Intercept_se',"Ratio","Ratio_se"])
+    
     lines = ldsc_summary.split("\n")
+    
+    columns = ['h2_obs', 'h2_se','Lambda_gc','Mean_chi2','Intercept','Intercept_se',"Ratio","Ratio_se","Catagories"]
+    
+    summary = pd.DataFrame(columns = columns)
+    
     row={}
+    
     try:
         objects = re.compile('[a-zA-Z\s\d]+:|[-0-9.]+[e]?[-0-9.]+|NA').findall(lines[0])
         row["h2_obs"]=objects[1]
         row["h2_se"]=objects[2]
 
-        ##next line lambda gc
+        ##check categories
+        if len(lines) == 6:
+            objects = re.compile('  -Categories:(.+)').findall(lines[1])
+            row["Catagories"] = objects[0].strip()
+            lines.pop(1)
+        else:
+            row["Catagories"] = "NA"
 
+        ##next line lambda gc
         objects = re.compile('[a-zA-Z\s\d]+:|[-0-9.]+[e]?[-0-9.]+|NA').findall(lines[1])
         row["Lambda_gc"] = objects[1]
         ##next line Mean_chi2
@@ -240,6 +253,7 @@ def parse_ldsc_summary(ldsc_summary):
         row["Intercept_se"]="NA"
         row["Ratio"]="NA"
         row["Ratio_se"]="NA"
+        row["Catagories"] = "NA"
 
     #summary = summary.append(row,ignore_index=True)
     row = pd.DataFrame([row], columns = summary.columns)

gwaslab/qc_fix_sumstats.py

@@ -1497,7 +1497,11 @@ def liftover_variant(sumstats,
              status="STATUS",
              from_build="19", 
              to_build="38"):
-    converter = get_lifter("hg"+from_build,"hg"+to_build)
+    try:
+        converter = get_lifter("hg"+from_build,"hg"+to_build,one_based=True)
+    except:
+        converter = get_lifter("hg"+from_build,"hg"+to_build)
+
     dic= get_number_to_chr(in_chr=False,xymt=["X","Y","M"])
     dic2= get_chr_to_number(out_chr=False)
     for i in sumstats[chrom].unique():
@@ -1549,7 +1553,6 @@ def parallelizeliftovervariant(sumstats,n_cores=1,chrom="CHR", pos="POS", from_b
         pool.close()
         pool.join()
     ############################################################################
-   
     unmap_num = len(sumstats.loc[sumstats[pos].isna(),:])    
     
     if remove is True:

gwaslab/util_abf_finemapping.py

@@ -0,0 +1,67 @@
+import pandas as pd
+import numpy as np
+from gwaslab.g_Log import Log
+from gwaslab.util_in_filter_value import _get_flanking_by_chrpos
+from gwaslab.util_in_filter_value import _get_flanking_by_id
+
+# Calculate PIP based on approximate Bayesian factor (ABF)
+# Wakefield, J. A bayesian measure of the probability of false discovery in genetic epidemiology studies. Am J Hum Genet 81, 208–227 (2007).
+
+
+def calc_abf(insumstats,w=0.2,log=Log(),verbose=True,**kwargs):
+
+
+
+    log.write("Start to calculate approximate Bayesian factor for {} variants".format(len(insumstats)),verbose=verbose)
+    log.write(" - Reference: akefield, J. A bayesian measure of the probability of false discovery in genetic epidemiology studies. Am J Hum Genet 81, 208–227 (2007).",verbose=verbose)
+    log.write(" - Priors for the standard deviation W of the effect size parameter β : {} ".format(w),verbose=verbose)
+    # binary -> w=0.2
+    # quant  -> w=0.15
+    omega = w**2
+    se = insumstats["SE"]
+    v = se**2
+    r = omega / (omega+v)
+    beta = insumstats["BETA"]
+    z = beta/se
+    insumstats = insumstats.copy()
+
+    # (6) ABF -> reciprocal
+    insumstats.loc[:, "log_ABF"] = 1/2* (np.log(1-r) + (r * z**2))
+    
+    return insumstats
+
+def calc_PIP(insumstats,log=Log(),verbose=True,**kwargs):
+    # Calculate the logarithmic sum of each ABF to find the logarithm of total_abf
+    log_total_abf = np.log(np.sum(np.exp(insumstats["log_ABF"] - np.max(insumstats["log_ABF"])))) + np.max(insumstats["log_ABF"])
+    insumstats = insumstats.copy()
+    log.write("Start to calculate PIP for {} variants".format(len(insumstats)),verbose=verbose)
+    # Calculate PIP on a logarithmic scale by subtracting log_total_abf from each log_abf
+    insumstats.loc[:, "log_PIP"] = insumstats['log_ABF'] - log_total_abf
+    # Convert PIP on logarithmic scale to exponential and back to normal scale
+    insumstats.loc[:, "PIP"] = np.exp(insumstats['log_PIP'])
+    return insumstats
+
+def abf_finemapping(insumstats,region=None,chrpos=None,snpid=None, log=Log(),**kwargs):
+
+    if region is not None:
+        region_data = insumstats[(insumstats["CHR"] == region[0]) & (insumstats["POS"] >= region[1]) & (insumstats["POS"] <= region[2])]
+    elif chrpos is not None:
+        region_data = _get_flanking_by_chrpos(insumstats, chrpos=chrpos,**kwargs)
+    elif snpid is not None:
+        region_data = _get_flanking_by_id(insumstats, snpid=snpid,**kwargs)
+
+    region_data = calc_abf(region_data,log=log,**kwargs)
+    region_data = calc_PIP(region_data,log=log,**kwargs)
+    return region_data
+
+def make_cs(insumstats,threshold=0.95,log=Log(),verbose=True):
+    insumstats = insumstats.sort_values(by="PIP",ascending=False)
+    pip_sum = 0
+    cs = pd.DataFrame()
+    for index, row in insumstats.iterrows():
+        cs = pd.concat([cs,pd.DataFrame(row).T])
+        pip_sum += row["PIP"]
+        if pip_sum > threshold:
+            break
+    log.write("Finished constructing a {}% credible set with {} variant(s)".format(str(threshold * 100),str(len(cs))),verbose=verbose)
+    return cs

gwaslab/util_ex_ldsc.py

@@ -304,9 +304,16 @@ def _estimate_h2_by_ldsc(insumstats, log, verbose=True, munge=False, munge_args=
     log.write(" -LDSC log:", verbose=verbose)
     summary = estimate_h2(sumstats, default_args, log)
     
+    results_table = None
+    if type(summary) is tuple:
+        results_table = summary[1]
+        summary = summary[0]
+        log.write(" -Coefficient results have been stored in .ldsc_h2_results", verbose=verbose)
+        
+
     log.write(" -Results have been stored in .ldsc_h2", verbose=verbose)
     finished(log=log,verbose=verbose,end_line=_end_line)
-    return parse_ldsc_summary(summary)
+    return parse_ldsc_summary(summary), results_table
 
 
 ####################################################################################################################

gwaslab/util_ex_run_clumping.py

@@ -11,7 +11,7 @@ from gwaslab.g_version import _checking_plink_version
 def _clump(insumstats, vcf=None, scaled=False, out="clumping_plink2", 
            p="P",mlog10p="MLOG10P", overwrite=False, study=None, bfile=None, 
            n_cores=1, memory=None, chrom=None, clump_p1=5e-8, clump_p2=5e-8, clump_r2=0.01, clump_kb=250,
-           log=Log(),verbose=True):
+           log=Log(),verbose=True,plink="plink",plink2="plink2"):
     ##start function with col checking##########################################################
     _start_line = "perfrom clumping"
     _end_line = "clumping"
@@ -111,7 +111,7 @@ def _clump(insumstats, vcf=None, scaled=False, out="clumping_plink2",
             bfile_to_use = bfile
 
         log.write(" -Performing clumping for CHR {}...".format(i),verbose=verbose)
-        log = _checking_plink_version(v=2, log=log)
+        log = _checking_plink_version(plink2=plink2, log=log)
         if memory is not None:
             memory_flag = "--memory {}".format(memory)
         
@@ -123,7 +123,7 @@ def _clump(insumstats, vcf=None, scaled=False, out="clumping_plink2",
         if scaled == True:
             # clumping using LOG10P
             script = """
-            plink2 \
+            {} \
                 {}\
                 --chr {} \
                 --clump {} \
@@ -136,11 +136,11 @@ def _clump(insumstats, vcf=None, scaled=False, out="clumping_plink2",
                 --clump-kb {} \
                 --threads {} {}\
                 --out {}
-            """.format(file_flag, chrom, clump, mlog10p,clump_log10_p1, clump_log10_p2, clump_r2, clump_kb, n_cores, memory_flag if memory is not None else "", out_single_chr)    
+            """.format(plink2, file_flag, chrom, clump, mlog10p,clump_log10_p1, clump_log10_p2, clump_r2, clump_kb, n_cores, memory_flag if memory is not None else "", out_single_chr)    
         else:
             # clumping using P
             script = """
-            plink2 \
+            {} \
                 {}\
                 --chr {} \
                 --clump {} \
@@ -152,7 +152,7 @@ def _clump(insumstats, vcf=None, scaled=False, out="clumping_plink2",
                 --clump-kb {} \
                 --threads {} {}\
                 --out {}
-            """.format(file_flag, chrom, clump, p, clump_p1, clump_p2, clump_r2, clump_kb, n_cores,memory_flag if memory is not None else "", out_single_chr)
+            """.format(plink2,file_flag, chrom, clump, p, clump_p1, clump_p2, clump_r2, clump_kb, n_cores,memory_flag if memory is not None else "", out_single_chr)
         
         try:
             output = subprocess.check_output(script, stderr=subprocess.STDOUT, shell=True,text=True)

gwaslab/viz_aux_annotate_plot.py

@@ -38,6 +38,7 @@ def annotate_single(
     region,
     region_anno_bbox_args,
     skip,
+    anno_height=1,
     amode="int",
     snpid="SNPID",
     chrom="CHR",
@@ -131,7 +132,7 @@ def annotate_single(
             
             #xy=(row["i"],row["scaled_P"]+0.2)
             xy=(row["i"],row["scaled_P"]+0.01*maxy)
-            xytext=(last_pos,1.15*maxy*arm_scale)
+            xytext=(last_pos,1.15*maxy*arm_scale*anno_height)
             
             if anno_fixed_arm_length is not None:
                 armB_length_in_point = anno_fixed_arm_length

gwaslab/viz_aux_quickfix.py

@@ -286,8 +286,9 @@ def _cut(series, mode,cutfactor,cut,skip, ylabels, cut_log, verbose, lines_to_pl
     log.write(" -Converting data above cut line...",verbose=verbose)
     if ylabels is not None:
         ylabels = pd.Series(ylabels)
-    maxy = series.max()
     series = series.copy()
+    
+    maxy = series.max()
     if "b" not in mode:
         log.write(" -Maximum -log10(P) value is "+str(maxy) +" .", verbose=verbose)
     elif "b" in mode:

gwaslab/viz_plot_compare_effect.py

@@ -77,8 +77,10 @@ def compare_effect(path1,
         scaled2 = True
     if is_q_mc=="fdr" or is_q_mc=="bon":
         is_q = True
-    else:
-        raise ValueError("Please select either fdr or bon for is_q_mc.")
+    
+    if is_q == True:
+        if is_q_mc not in [False,"fdr","bon","non"]:
+            raise ValueError("Please select either fdr or bon or non for is_q_mc.")
     if save_args is None:
         save_args = {"dpi":300,"facecolor":"white"}
     if reg_box is None:

gwaslab/viz_plot_miamiplot2.py

@@ -247,7 +247,10 @@ def plot_miami2(
         plt.subplots_adjust(hspace=region_hspace)    
     else:
         fig, ax1, ax5 = figax
-    
+
+    #if same_ylim==True:
+        #maxy = merged_sumstats[["scaled_P_1","scaled_P_2"]].max().max()
+
     log.write("Start to create Manhattan plot for sumstats1...", verbose=verbose)
     fig,log = mqqplot(merged_sumstats,
                       chrom="CHR",
@@ -284,14 +287,8 @@ def plot_miami2(
                       _if_quick_qc=False,
                      **mqq_args2)
     log.write("Finished creating Manhattan plot for sumstats2".format(_get_version()), verbose=verbose)
+    
 
-    if same_ylim==True:
-        ylim1_converted = ax1.get_ylim()
-        ylim2_converted = ax5.get_ylim()
-        if ylim1_converted > ylim2_converted:
-            ax5.set_ylim(ylim1_converted)
-        else:
-            ax1.set_ylim(ylim2_converted)
     #####################################################################################################################    
     
     ax5.set_xlabel("")

gwaslab/viz_plot_mqqplot.py

@@ -141,6 +141,7 @@ def mqqplot(insumstats,
           anno_max_iter=100,
           arm_offset=50,
           arm_scale=1,
+          anno_height=1,
           arm_scale_d=None,
           cut=0,
           skip=0,
@@ -180,6 +181,7 @@ def mqqplot(insumstats,
           xpad=None,
           xpadl=None,
           xpadr=None,
+          xtight=False,
           chrpad=0.03, 
           drop_chr_start=False,
           title =None,
@@ -552,7 +554,8 @@ def mqqplot(insumstats,
                                                                         cut_log = cut_log,
                                                                         verbose =verbose, 
                                                                         lines_to_plot=lines_to_plot,
-                                                                        log = log)
+                                                                        log = log
+                                                                        )
     except:
         log.warning("No valid data! Please check the input.")
         return None
@@ -596,19 +599,23 @@ def mqqplot(insumstats,
             sumstats.loc[sumstats["scaled_P"]>-np.log10(sig_level_plot),"s"]=4
         sumstats["chr_hue"]=sumstats[chrom].astype("string")
 
-        if vcf_path is not None:
+        if "r" in mode:
+            if vcf_path is None:
+                sumstats["LD"]=100
+                sumstats["SHAPE"]=1
             sumstats["chr_hue"]=sumstats["LD"]
+                
         ## default seetings
         
         palette = sns.color_palette(colors,n_colors=sumstats[chrom].nunique())  
-        
 
         legend = None
         style=None
         linewidth=0
         edgecolor="black"
         # if regional plot assign colors
-        if vcf_path is not None:
+        if "r" in mode:
+            #if vcf_path is not None: 
             legend=None
             linewidth=1
             if len(region_ref) == 1:
@@ -631,10 +638,9 @@ def mqqplot(insumstats,
                         palette[(i+1)*100 + j ] = hex_color
 
                 edgecolor="none"
-                scatter_args["markers"]= region_marker_shapes[:len(region_ref)]
+                scatter_args["markers"]= {(i+1):m for i,m in enumerate(region_marker_shapes[:len(region_ref)])}
                 style="SHAPE"
-                
-            
+
             
         ## if highlight 
         highlight_i = pd.DataFrame()
@@ -977,6 +983,7 @@ def mqqplot(insumstats,
                                 region=region,
                                 region_anno_bbox_args=region_anno_bbox_args,
                                 skip=skip,
+                                anno_height=anno_height,
                                 snpid=snpid,
                                 chrom=chrom,
                                 pos=pos,
@@ -1040,7 +1047,7 @@ def mqqplot(insumstats,
         if "qq" in mode:
             ax2.set_ylim(ylim)
     
-    ax1 = _add_pad_to_x_axis(ax1, xpad, xpadl, xpadr, sumstats)
+    ax1 = _add_pad_to_x_axis(ax1, xpad, xpadl, xpadr, sumstats, pos, chrpad, xtight, log = log, verbose=verbose)
 
     # Titles 
     if title and anno and len(to_annotate)>0:
@@ -1065,20 +1072,34 @@ def mqqplot(insumstats,
 
 
 
-def _add_pad_to_x_axis(ax1, xpad, xpadl, xpadr, sumstats):
+def _add_pad_to_x_axis(ax1, xpad, xpadl, xpadr, sumstats, pos, chrpad, xtight, log, verbose):
     
-    if ax1 is not None:
-        xmin, xmax = ax1.get_xlim() 
-        
-        if xpad is not None:
-            pad = xpad* sumstats["i"].max()
-            ax1.set_xlim([xmin - pad, xmin + pad])
-        if xpadl is not None:
-            pad = xpadl* sumstats["i"].max()
-            ax1.set_xlim([xmin - pad,xmax])
-        if xpadr is not None:
-            pad = xpadr* sumstats["i"].max()
-            ax1.set_xlim([xmin, xmax + pad])
+    if xtight==True:
+        log.write(" -Adjusting X padding on both side : tight mode", verbose=verbose)
+        xmax = sumstats["i"].max()
+        xmin=  sumstats["i"].min()
+        ax1.set_xlim([xmin, xmax])
+    
+    else:
+        chrpad_to_remove = sumstats[pos].max()*chrpad
+        if ax1 is not None:
+            xmin, xmax = ax1.get_xlim() 
+            length = xmax - xmin
+            
+            if xpad is not None:
+                log.write(" -Adjusting X padding on both side: {}".format(xpad), verbose=verbose)
+                pad = xpad* length #sumstats["i"].max()
+                ax1.set_xlim([xmin - pad + chrpad_to_remove, xmax + pad - chrpad_to_remove])
+            if xpad is None and xpadl is not None:
+                log.write(" -Adjusting X padding on left side: {}".format(xpadl), verbose=verbose)
+                xmin, xmax = ax1.get_xlim() 
+                pad = xpadl*length # sumstats["i"].max()
+                ax1.set_xlim([xmin - pad + chrpad_to_remove ,xmax])
+            if xpad is None and xpadr is not None:
+                log.write(" -Adjusting X padding on right side: {}".format(xpadr), verbose=verbose)
+                xmin, xmax = ax1.get_xlim() 
+                pad = xpadr*length # sumstats["i"].max()
+                ax1.set_xlim([xmin, xmax + pad - chrpad_to_remove])
 
     return ax1
 

gwaslab/viz_plot_regional2.py

@@ -5,6 +5,7 @@ import matplotlib.patches as patches
 import seaborn as sns
 import numpy as np
 import copy
+import re
 import scipy as sp
 from pyensembl import EnsemblRelease
 from allel import GenotypeArray
@@ -96,19 +97,20 @@ def _plot_regional(
                                         marker_size= marker_size,
                                         region_marker_shapes=region_marker_shapes,
                                         log=log,verbose=verbose)
-            if lead_id_single is not None:
-                lead_ids.append(lead_id_single)       
+            #if lead_id_single is not None:
+            lead_ids.append(lead_id_single)       
         
         # update region_ref to variant rsID or variantID / skip NAs
         new_region_ref = []
         for i in range(len(lead_ids)):
             if lead_ids[i] is None:
+                new_region_ref.append(region_ref[i])
                 continue
             if region_ref[i] is None:
-                if "rsID" in sumstats.columns:
-                    new_name = sumstats.loc[lead_ids[i],"rsID"]
-                elif "SNPID" in sumstats.columns:
+                if "SNPID" in sumstats.columns:
                     new_name = sumstats.loc[lead_ids[i],"SNPID"]
+                elif "rsID" in sumstats.columns:
+                    new_name = sumstats.loc[lead_ids[i],"rsID"]
                 else:
                     new_name = "chr{}:{}".format(sumstats.loc[lead_ids[i],"CHR"] , sumstats.loc[lead_ids[i],"POS"])
                 new_region_ref.append(new_name)
@@ -162,7 +164,6 @@ def _plot_regional(
         lead_snp_ys = []
         lead_snp_is = []
         lead_snp_is_colors = []
-        
         for i,lead_id_single in enumerate(lead_ids):
             if lead_id_single is not None:
                 lead_snp_ys.append(sumstats.loc[lead_id_single,"scaled_P"] )
@@ -258,11 +259,35 @@ def _get_lead_id(sumstats=None, region_ref=None, log=None, verbose=True):
     if type(lead_id) is list:
         if len(lead_id)>0:
             lead_id = int(lead_id[0])
-    
+
     if region_ref_to_check is not None:
         if type(lead_id) is list:
             if len(lead_id)==0 :
-                log.warning("{} not found.. Skipping..".format(region_ref_to_check))
+                #try:
+                matched_snpid = re.match("(chr)?[0-9]+:[0-9]+:[ATCG]+:[ATCG]+", region_ref_to_check,  re.IGNORECASE)    
+                if matched_snpid is None:
+                    pass
+                else:
+                    lead_snpid = matched_snpid.group(0).split(":")
+                    if len(lead_snpid)==4:
+                        lead_chr= int(lead_snpid[0])
+                        lead_pos= int(lead_snpid[1])
+                        lead_ea= lead_snpid[2]
+                        lead_nea= lead_snpid[3]
+                        chrpos_match = (sumstats["CHR"] == lead_chr) & (sumstats["POS"] == lead_pos)
+                        eanea_match = ((sumstats["EA"] == lead_ea) & (sumstats["NEA"] == lead_nea)) | ((sumstats["EA"] == lead_nea) & (sumstats["NEA"] == lead_ea)) 
+                        if "rsID" in sumstats.columns:
+                            lead_id = sumstats.index[chrpos_match&eanea_match].to_list()
+                        if "SNPID" in sumstats.columns:
+                            lead_id = sumstats.index[chrpos_match&eanea_match].to_list()     
+                if type(lead_id) is list:
+                    if len(lead_id)>0:
+                        lead_id = int(lead_id[0])   
+                        log.warning("Trying matching variant {} using CHR:POS:EA:NEA to {}... ".format(region_ref_to_check,lead_id))
+
+        if type(lead_id) is list:
+            if len(lead_id)==0 :
+                log.warning("Extracting variant: {} not found in sumstats.. Skipping..".format(region_ref_to_check))
                 #lead_id = sumstats["scaled_P"].idxmax()
                 lead_id = None
                 return lead_id
@@ -275,7 +300,7 @@ def _get_lead_id(sumstats=None, region_ref=None, log=None, verbose=True):
 
     return lead_id
 
-def _pinpoint_lead(sumstats,ax1,region_ref, lead_color, marker_size, log, verbose,region_marker_shapes):
+def _pinpoint_lead(sumstats,ax1,region_ref, lead_color, marker_size, log, verbose, region_marker_shapes):
     
     if region_ref is None:
         log.write(" -Extracting lead variant..." , verbose=verbose)
@@ -416,6 +441,11 @@ def _plot_gene_track(
     texts_to_adjust_left = []
     texts_to_adjust_middle = []
     texts_to_adjust_right = []
+
+    
+    sig_gene_names=[]
+    sig_gene_lefts=[]
+    sig_gene_rights=[]
     for index,row in uniq_gene_region.iterrows():
 
         gene_color="#020080"
@@ -426,21 +456,18 @@ def _plot_gene_track(
             gene_anno = "<-" + row["name"] 
         
 
-        sig_gene_names=[]
-        sig_gene_lefts=[]
-        sig_gene_rights=[]
+
         for lead_snp_i in lead_snp_is:
             if region_lead_grid is True and lead_snp_i > gene_track_start_i+row["start"] and lead_snp_i < gene_track_start_i+row["end"] :
-                    gene_color=region_lead_grid_line["color"]
-                    sig_gene_names.append(row["name"])
-                    sig_gene_lefts.append(gene_track_start_i+row["start"])
-                    sig_gene_rights.append(gene_track_start_i+row["end"])
+                gene_color=region_lead_grid_line["color"]
+                sig_gene_names.append(row["name"])
+                sig_gene_lefts.append(gene_track_start_i+row["start"])
+                sig_gene_rights.append(gene_track_start_i+row["end"])
 
             # plot gene line
             ax3.plot((gene_track_start_i+row["start"],gene_track_start_i+row["end"]),
                         (row["stack"]*2,row["stack"]*2),color=gene_color,linewidth=linewidth_in_points/10)
         
-        
         # plot gene name
         if row["end"] >= region[2]:
             #right side
@@ -459,6 +486,7 @@ def _plot_gene_track(
     for index,row in exons.iterrows():
         exon_color="#020080" 
         for sig_gene_name, sig_gene_left, sig_gene_right in zip(sig_gene_names,sig_gene_lefts,sig_gene_rights):
+            
             if not pd.isnull(row["name"]):
                 if (region_lead_grid is True) and row["name"]==sig_gene_name:
                     exon_color = region_lead_grid_line["color"]  
@@ -468,7 +496,7 @@ def _plot_gene_track(
                 exon_color = region_lead_grid_line["color"]  
             else:
                 exon_color="#020080"
-
+        
         ax3.plot((gene_track_start_i+row["start"],gene_track_start_i+row["end"]),
                     (row["stack"]*2,row["stack"]*2),linewidth=linewidth_in_points*taf[3],color=exon_color,solid_capstyle="butt")
 
@@ -550,24 +578,42 @@ def process_vcf(sumstats,
             # figure out lead variant
             lead_id = _get_lead_id(sumstats, region_ref_single, log, verbose)
         
-        if lead_id is None:
-            sumstats[rsq] = None
-            sumstats[rsq] = sumstats[rsq].astype("float")
-            sumstats[ld_single] = 0             
-            continue
 
-        lead_pos = sumstats.loc[lead_id,pos]
+        lead_series = None
+        if lead_id is None:
+            
+            matched_snpid = re.match("(chr)?[0-9]+:[0-9]+:[ATCG]+:[ATCG]+",region_ref_single,  re.IGNORECASE)
+            
+            if matched_snpid is None:
+                sumstats[rsq] = None
+                sumstats[rsq] = sumstats[rsq].astype("float")
+                sumstats[ld_single] = 0    
+                continue    
+            else:
+                
+                lead_snpid = matched_snpid.group(0).split(":")[1:]
+                lead_pos = int(lead_snpid[0])
+                lead_snpid[0]= int(lead_snpid[0])
+                lead_series = pd.Series(lead_snpid)
+        else:
+            lead_pos = sumstats.loc[lead_id,pos]
 
+        
         # if lead pos is available: 
         if lead_pos in ref_genotype["variants/POS"]:
             
             # get ref index for lead snp
-            lead_snp_ref_index = match_varaint(sumstats.loc[lead_id,[pos,nea,ea]])
-            #lead_snp_ref_index = np.where(ref_genotype["variants/POS"] == lead_pos)[0][0]
+            if lead_series is None:
+                lead_snp_ref_index = match_varaint(sumstats.loc[lead_id,[pos,nea,ea]])
+                #lead_snp_ref_index = np.where(ref_genotype["variants/POS"] == lead_pos)[0][0]
+            else:
+                log.warning("Computing LD: {} not found in sumstats but found in reference...Still Computing...".format(region_ref_single))
+                lead_snp_ref_index = match_varaint(lead_series)
 
             # non-na other snp index
             other_snps_ref_index = sumstats["REFINDEX"].dropna().astype("int").values
             # get genotype 
+            
             lead_snp_genotype = GenotypeArray([ref_genotype["calldata/GT"][lead_snp_ref_index]]).to_n_alt()
             try:
                 if len(set(lead_snp_genotype[0]))==1:
@@ -604,10 +650,10 @@ def process_vcf(sumstats,
                 sumstats.loc[to_change_color,ld_single] = 1
             to_change_color = sumstats[rsq]>ld_threshold
             sumstats.loc[to_change_color,ld_single] = index+2
-
-        sumstats.loc[lead_id,ld_single] = len(region_ld_threshold)+2
         
-        sumstats.loc[lead_id,lead] = 1
+        if lead_series is None:
+            sumstats.loc[lead_id,ld_single] = len(region_ld_threshold)+2
+            sumstats.loc[lead_id,lead] = 1
 
     ####################################################################################################    
     final_shape_col = "SHAPE"

gwaslab/viz_plot_stackedregional.py

@@ -57,7 +57,9 @@ def plot_stacked_mqq(objects,
                         fig_args=None,
                         region_hspace=0.05,
                         subplot_height=4,
+                        region_lead_grids = None,
                         region_lead_grid_line=None,
+                        region_ld_legends = None,
                         fontsize=9,
                         font_family="Arial",
                         build="99", 
@@ -85,6 +87,8 @@ def plot_stacked_mqq(objects,
         region_chromatin_height = len(region_chromatin_files) * region_chromatin_height
     if region_chromatin_labels is None:
         region_chromatin_labels = []
+    if region_ld_legends is None:
+        region_ld_legends = [0]
     if title_args is None:
         title_args = {"family":"Arial"}
     else:
@@ -125,7 +129,9 @@ def plot_stacked_mqq(objects,
                                           'width_ratios':[mqqratio,1]},
                                           **fig_args)
         plt.subplots_adjust(hspace=region_hspace)
-
+    
+    if region_lead_grids is None:
+        region_lead_grids = [i for i in range(len(axes))]
     ##########################################################################################################################################
     mqq_args_for_each_plot = _sort_args(mqq_args, n_plot)
     ##########################################################################################################################################
@@ -149,6 +155,10 @@ def plot_stacked_mqq(objects,
             figax = (fig,axes[index],axes[-1])
         elif mode=="mqq":
             figax = (fig,axes[index,0],axes[index,1])
+        if index in region_ld_legends:
+            region_ld_legend = True
+        else:
+            region_ld_legend = False
         #################################################################
         if index==0:
             # plot last m and gene track 
@@ -164,6 +174,7 @@ def plot_stacked_mqq(objects,
                             fontsize=fontsize,
                             font_family=font_family,
                             region_lead_grid=False,
+                            region_ld_legend=region_ld_legend,
                             gtf_path="default",
                             rr_ylabel=False,
                             figax=figax,
@@ -192,7 +203,7 @@ def plot_stacked_mqq(objects,
                             font_family=font_family,
                             mode=mode,
                             rr_ylabel=False,
-                            region_ld_legend=False,
+                            region_ld_legend=region_ld_legend,
                             gtf_path=None,
                             figax=figax,
                             _get_region_lead=True,
@@ -257,7 +268,7 @@ def plot_stacked_mqq(objects,
     
     ##########################################################################################################################################
     # draw the line for lead variants
-    _draw_grid_line_for_lead_variants(mode, lead_variants_is,lead_variants_is_color, n_plot, axes, region_lead_grid_line,region_chromatin_files)
+    _draw_grid_line_for_lead_variants(mode, lead_variants_is,lead_variants_is_color, n_plot, axes, region_lead_grid_line,region_chromatin_files,region_lead_grids)
     
     ##########################################################################################################################################  
     _drop_old_y_labels(axes, n_plot)
@@ -275,21 +286,24 @@ def _drop_old_y_labels(axes, n_plot):
     for index in range(n_plot):
         axes[index].set_ylabel("")
 
-def _draw_grid_line_for_lead_variants(mode, lead_variants_is,lead_variants_is_color, n_plot, axes, region_lead_grid_line,region_chromatin_files):
+def _draw_grid_line_for_lead_variants(mode, lead_variants_is,lead_variants_is_color, n_plot, axes, region_lead_grid_line,region_chromatin_files,region_lead_grids):
     if len(region_chromatin_files)>0:
         n_plot_and_track = n_plot+2
     else:
         n_plot_and_track = n_plot+1
+    
+    plotted=[None]
     if mode=="r":
         for index, sig_is in lead_variants_is.items():
-            for j, sig_i in enumerate(sig_is):
-                try:
-                    region_lead_grid_line["color"]=lead_variants_is_color[index][j]
-                except:
-                    pass
-                if sig_i is not None:
-                    for each_axis_index in range(n_plot_and_track):    
-                        axes[each_axis_index].axvline(x=sig_i, zorder=2,**region_lead_grid_line)
+            if index in region_lead_grids:
+                for j, sig_i in enumerate(sig_is):
+                    try:
+                        region_lead_grid_line["color"] = lead_variants_is_color[index][j]
+                    except:
+                        pass
+                    if sig_i not in plotted:
+                        for each_axis_index in range(n_plot_and_track):  
+                            axes[each_axis_index].axvline(x=sig_i, zorder=2,**region_lead_grid_line)
 
 def _add_new_y_label(mode, fig, gene_track_height,n_plot,subplot_height ,fontsize,font_family):
     gene_track_height_ratio = gene_track_height/(gene_track_height + n_plot*subplot_height)

{gwaslab-3.4.47.dist-info → gwaslab-3.4.48.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: gwaslab
-Version: 3.4.47
+Version: 3.4.48
 Summary: A collection of handy tools for GWAS SumStats
 Author-email: Yunye <yunye@gwaslab.com>
 Project-URL: Homepage, https://cloufield.github.io/gwaslab/
@@ -12,19 +12,19 @@ Requires-Python: <3.11,>=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE
 License-File: LICENSE_before_v3.4.39
-Requires-Dist: pandas !=1.5,>=1.3
-Requires-Dist: numpy <2,>=1.21.2
-Requires-Dist: matplotlib !=3.7.2,<3.9,>=3.5
-Requires-Dist: seaborn >=0.12
-Requires-Dist: scipy >=1.12
-Requires-Dist: pySAM ==0.22.1
-Requires-Dist: Biopython >=1.79
-Requires-Dist: adjustText <=0.8,>=0.7.3
-Requires-Dist: liftover >=1.1.13
-Requires-Dist: scikit-allel >=1.3.5
-Requires-Dist: pyensembl ==2.2.3
-Requires-Dist: gtfparse ==1.3.0
-Requires-Dist: h5py >=3.10.0
+Requires-Dist: pandas!=1.5,>=1.3
+Requires-Dist: numpy<2,>=1.21.2
+Requires-Dist: matplotlib!=3.7.2,<3.9,>=3.5
+Requires-Dist: seaborn>=0.12
+Requires-Dist: scipy>=1.12
+Requires-Dist: pySAM==0.22.1
+Requires-Dist: Biopython>=1.79
+Requires-Dist: adjustText<=0.8,>=0.7.3
+Requires-Dist: liftover>=1.1.13
+Requires-Dist: scikit-allel>=1.3.5
+Requires-Dist: pyensembl==2.2.3
+Requires-Dist: gtfparse==1.3.0
+Requires-Dist: h5py>=3.10.0
 
 # GWASLab
 
@@ -51,7 +51,7 @@ Warning: Known issues of GWASLab are summarized in [https://cloufield.github.io/
 ### install via pip
 
 ```
-pip install gwaslab==3.4.45
+pip install gwaslab==3.4.46
 ```
 
 ```python

{gwaslab-3.4.47.dist-info → gwaslab-3.4.48.dist-info}/RECORD

@@ -6,18 +6,18 @@ gwaslab/bd_get_hapmap3.py,sha256=asNjQYeGfQi8u3jnfenRvDdKMs5ptql5wpcUzqMlwUI,393
 gwaslab/cache_manager.py,sha256=HOTnSkCOyGEPLRl90WT8D_6pAdI8d8AzenMIDGuCeWc,28113
 gwaslab/g_Log.py,sha256=C3Zv-_6c3C9ms8bgQ-ytplz22sjk7euqXYkWr9zNeAs,1573
 gwaslab/g_Phenotypes.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-gwaslab/g_Sumstats.py,sha256=TUcFQFyODS_-FYMdXDvrBijG4Qtfi1igIWM-eEgb0nc,35352
+gwaslab/g_Sumstats.py,sha256=U5la-fJCSTN8FNxXjcULcPH8MV9D6YgMaVFNesMTa_o,35854
 gwaslab/g_SumstatsPair.py,sha256=20snPb4SlI6ftMGVjgxAuyxsxYRQF-GzzlBSnoB-3Lo,8851
 gwaslab/g_SumstatsT.py,sha256=u_DighLMnMxwTLnqm-B58pA0G6WXRj6pudPyKMVKjSU,2133
 gwaslab/g_Sumstats_summary.py,sha256=FECvvFXJVKaCX5dggBvvk9YvJ6AbdbcLfjltysX7wEE,6380
 gwaslab/g_meta.py,sha256=htWlgURWclm9R6UqFcX1a93WN27xny7lGUeyJZOtszQ,2583
 gwaslab/g_vchange_status.py,sha256=jLoVzMJFhB5k_cJKzHuBNc2HZGBWydAunCNa0n_d54g,1923
-gwaslab/g_version.py,sha256=_mujOAftzn4ic9p92turA93xxg-RqxoWIqVfJLiNaSg,1886
+gwaslab/g_version.py,sha256=kB6LiBYcRZElabjDUUEBhF5c5SVUq8vHO0pctDfBqkw,1886
 gwaslab/hm_casting.py,sha256=FqP4EQl83Q2OKLw004OgLIvUH795TVCGwziLk5jsHqY,11368
 gwaslab/hm_harmonize_sumstats.py,sha256=1hjUdle2DSKHGBp2BktfFqf-QHU_q2xWl_mPhiYc_ZA,78616
 gwaslab/hm_rsid_to_chrpos.py,sha256=ODWREO0jPN0RAfNzL5fRzSRANfhiksOvUVPuEsFZQqA,6552
 gwaslab/io_preformat_input.py,sha256=AZ43WGqVTzbo3XtClWhjRjsj6pBR9stw6JBL_TZ461U,20673
-gwaslab/io_read_ldsc.py,sha256=8S9n4imgl4d0WPms_GYld-6uUM5z7iWGiCA-M814kzY,12123
+gwaslab/io_read_ldsc.py,sha256=wsYXpH50IchBKd2dhYloSqc4YgnDkiwMsAweaCoN5Eo,12471
 gwaslab/io_read_tabular.py,sha256=EG-C6KhCutt4J4LlOMgXnqzJvU-EZXzVhMvaDFnHrMM,2380
 gwaslab/io_to_formats.py,sha256=m57dGoqmHzAE1E27j9YxYKVCA12_lKd1qCnZtp0WZLw,29401
 gwaslab/io_to_pickle.py,sha256=HhePU0VcaGni0HTNU0BqoRaOnrr0NOxotgY6ISdx3Ck,1833
@@ -28,18 +28,19 @@ gwaslab/ldsc_parse.py,sha256=MBnfgcWlV4oHp9MoDRh1mpilaHhAR15Af77hMFn4-5k,10564
 gwaslab/ldsc_regressions.py,sha256=yzbGjgNV7u-SWXNPsh9S8y9mK97Bim_Nmad9G9V18ZU,30078
 gwaslab/ldsc_sumstats.py,sha256=O0olsDxKlh1MJ1gAuEN1t40rxhajOEwOQ20ak7xoDrI,26245
 gwaslab/qc_check_datatype.py,sha256=kW68uk4dTLOU2b1dHoVat6n0loundDysAjIqxsXW28Q,3379
-gwaslab/qc_fix_sumstats.py,sha256=-DQz5dPW6YXXVP-LV2Txa4lJrpZHhqAoKNny6IYAW18,93100
+gwaslab/qc_fix_sumstats.py,sha256=aTX5jf7MVpp6XTiP-rbEyaLAQFsn1gyH9vEH4SLH-GY,93199
 gwaslab/run_script.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+gwaslab/util_abf_finemapping.py,sha256=LRcopjtkT-iXtKPAJIzR4qjPdhD7nrS_BGit4EW89FM,3054
 gwaslab/util_ex_calculate_ldmatrix.py,sha256=Z_spxbq6SHDS0v84I59YTTF40iyLQIOZbt0dmEcNJjw,15417
 gwaslab/util_ex_calculate_prs.py,sha256=9uJ588Sdj4V0vw3OZ9NeLECwOvW67f0IdLandVPS5RY,9442
 gwaslab/util_ex_gwascatalog.py,sha256=--Gde9HrsikfYTeFqSaYz0gUODr9wmv_gV6GZGNlElg,7688
 gwaslab/util_ex_ldproxyfinder.py,sha256=wWNW9wITWozj23gT41LR00WxU-rrHpGKbxs2H_3jEyM,9431
-gwaslab/util_ex_ldsc.py,sha256=a-OwyWmDcyinTPRfCNSeNYm6beVsydFeYmRAXAPcRnI,18350
+gwaslab/util_ex_ldsc.py,sha256=dd3QUNX7eOJY_z4mkKIE9Ey_SQGE4ox0efhq28ah_LE,18592
 gwaslab/util_ex_plink_filter.py,sha256=pK1Yxtv9-J4rMOdVAG7VU9PktvI6-y4FxBiVEH0QuRs,1673
 gwaslab/util_ex_process_h5.py,sha256=ynFvo3zxgvOxWYL565v2IQf8P6iEuq7UlKQ_ULxrd6Y,2831
 gwaslab/util_ex_process_ref.py,sha256=GQ0ZEWLxGpHLdBs3tqnAqKn3Pqx1A1YvNbYrBLBvXeg,17126
 gwaslab/util_ex_run_2samplemr.py,sha256=5c0DGF694T9j0Y58L2I7pr1_Z1hfpaatIgix7P5oPA8,9127
-gwaslab/util_ex_run_clumping.py,sha256=Y8KeUKuSpGc1a8iI_VKUgVQpAVBd7O9F11p85jY4oW4,7868
+gwaslab/util_ex_run_clumping.py,sha256=bs9CJENMhwVXolCNygaYtso5ikPrdPMiV13tGA0ttxg,7915
 gwaslab/util_ex_run_coloc.py,sha256=u57h8wPbTCOf6aY5u5DpzK1gv7inuDT8a15UGo-1ras,6288
 gwaslab/util_ex_run_susie.py,sha256=TXqiwBVq1io7XSlLF2_gNsYgxDLiKNnYE9pIjRWJ1Hc,5315
 gwaslab/util_in_calculate_gc.py,sha256=MWOXVzJv7SZx4i2_ncRiqsiEOADc7EfghaUzgGy4jaE,2219
@@ -52,22 +53,22 @@ gwaslab/util_in_get_density.py,sha256=kpKXH69acMkeYVG5vs-VbJC3COhmuLBfYco-wuOxgj
 gwaslab/util_in_get_sig.py,sha256=9kq1GXacknO2YnVmsTli1GlPA728ASweTZ3UKm3Wszo,38783
 gwaslab/util_in_meta.py,sha256=5K9lIZcIgUy0AERqHy1GvMN2X6dp45JUUgopuDLgt4o,11284
 gwaslab/util_in_snphwe.py,sha256=-KpIDx6vn_nah6H55IkV2OyjXQVXV13XyBL069WE1wM,1751
-gwaslab/viz_aux_annotate_plot.py,sha256=R-1GT89E4NEBAMNTYzNawdi9rjQV5LCnODgnYOOKsys,32184
+gwaslab/viz_aux_annotate_plot.py,sha256=UTOx-OpFsM_UVphBHxqQZwCFI8bjwwB6CMsgFbAfheQ,32215
 gwaslab/viz_aux_chromatin.py,sha256=7cGmej5EkKO7fxR1b5w8r1oRRl9ofVzFRG52SCYWtz0,4109
-gwaslab/viz_aux_quickfix.py,sha256=Z6ZNEAUFuWVDTzH-qGreNGxPxJLCmqhXtBrvDOgo4g8,18308
+gwaslab/viz_aux_quickfix.py,sha256=5XM-J9D2yp5FVbK6YQKEhSCqAYBLNWSQms9WjpXxVn8,18313
 gwaslab/viz_aux_reposition_text.py,sha256=iRIP-Rkltlei068HekJcVubiqPrunBqvAoSQ1eHk04M,4304
 gwaslab/viz_aux_save_figure.py,sha256=nL-aoE8Kg06h7FgleGRBIZjhI-6w5gpn3E1HWMwBig8,2664
 gwaslab/viz_plot_compare_af.py,sha256=qtXW45-Sq_ugK8ZfqBYMpmf58SKi3lB3YyHnzn_akcE,5344
-gwaslab/viz_plot_compare_effect.py,sha256=iA74jMzh-G65U6BeXyQro08tPlJWpNyvtrjFsYHLvFM,49505
+gwaslab/viz_plot_compare_effect.py,sha256=lV-4KSQatTSsYqzEGGTkBu17I2VlVyVh1uJr-kCq630,49585
 gwaslab/viz_plot_forestplot.py,sha256=xgOnefh737CgdQxu5naVyRNBX1NQXPFKzf51fbh6afs,6771
 gwaslab/viz_plot_miamiplot.py,sha256=rCFEp7VNuVqeBBG3WRkmFAtFklbF79BvIQQYiSY70VY,31238
-gwaslab/viz_plot_miamiplot2.py,sha256=SWv82D8UBbREKsk8EoKth-2w68l6FbXyVLsb_E1hh8o,15882
-gwaslab/viz_plot_mqqplot.py,sha256=udOTBKSX239KLFNauhHGDJHp0Viu18NkGwFn5GtAHuM,63297
+gwaslab/viz_plot_miamiplot2.py,sha256=Jg5j9qsr8gGydU8AOKU8xRZTNH_3QM8Nxv61Vh12aG0,15732
+gwaslab/viz_plot_mqqplot.py,sha256=q_c_ZDRdirEcdHHnb030h7dTUWAFy9OVuzwbdCzZ3gU,64580
 gwaslab/viz_plot_qqplot.py,sha256=psQgVpP29686CEZkzQz0iRbApzqy7aE3GGiBcazVvNw,7247
-gwaslab/viz_plot_regional2.py,sha256=6Dfbq5vFm5B63nLUpaTrlq96x4CruIgJu0TXXq3a_Ck,34546
+gwaslab/viz_plot_regional2.py,sha256=tBoGox-4ngL5o_twdIjk_VW6Iam3JDyrPKuttm6_4Sg,36862
 gwaslab/viz_plot_regionalplot.py,sha256=8u-5-yfy-UaXhaxVVz3Y5k2kBAoqzczUw1hyyD450iI,37983
 gwaslab/viz_plot_rg_heatmap.py,sha256=PidUsgOiEVt6MfBPCF3_yDhOEytZ-I1q-ZD6_0pFrV4,13713
-gwaslab/viz_plot_stackedregional.py,sha256=HISwtPDV84mT3PS41e2sXq77GPBujgSKVX1mQ4bEeKs,15820
+gwaslab/viz_plot_stackedregional.py,sha256=AoGMer73P3y-21A2qityrDX-_sIJFRgKzkm8i9zVxKA,16420
 gwaslab/viz_plot_trumpetplot.py,sha256=ZHdc6WcVx0-oKoj88yglRkmB4bS9pOiEMcuwKW35Yvo,42672
 gwaslab/data/formatbook.json,sha256=N2nJs80HH98Rsu9FxaSvIQO9J5yIV97WEtAKjRqYwiY,38207
 gwaslab/data/reference.json,sha256=k8AvvgDsuLxzv-NCJHWvTUZ5q_DLAFxs1Th3jtL313k,11441
@@ -77,9 +78,9 @@ gwaslab/data/hapmap3_SNPs/hapmap3_db150_hg19.snplist.gz,sha256=qD9RsC5S2h6l-OdpW
 gwaslab/data/hapmap3_SNPs/hapmap3_db151_hg38.snplist.gz,sha256=Y8ZT2FIAhbhlgCJdE9qQVAiwnV_fcsPt72usBa7RSBM,10225828
 gwaslab/data/high_ld/high_ld_hla_hg19.bed.gz,sha256=R7IkssKu0L4WwkU9SrS84xCMdrkkKL0gnTNO_OKbG0Y,219
 gwaslab/data/high_ld/high_ld_hla_hg38.bed.gz,sha256=76CIU0pibDJ72Y6UY-TbIKE9gEPwTELAaIbCXyjm80Q,470
-gwaslab-3.4.47.dist-info/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
-gwaslab-3.4.47.dist-info/LICENSE_before_v3.4.39,sha256=GhLOU_1UDEKeOacYhsRN_m9u-eIuVTazSndZPeNcTZA,1066
-gwaslab-3.4.47.dist-info/METADATA,sha256=G_RLrYWZe0z6Wbvyl_g7rXnJKoZ6HFKUHM66ogtfyug,7765
-gwaslab-3.4.47.dist-info/WHEEL,sha256=y4mX-SOX4fYIkonsAGA5N0Oy-8_gI4FXw5HNI1xqvWg,91
-gwaslab-3.4.47.dist-info/top_level.txt,sha256=PyY6hWtrALpv2MAN3kjkIAzJNmmBTH5a2risz9KwH08,8
-gwaslab-3.4.47.dist-info/RECORD,,
+gwaslab-3.4.48.dist-info/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
+gwaslab-3.4.48.dist-info/LICENSE_before_v3.4.39,sha256=GhLOU_1UDEKeOacYhsRN_m9u-eIuVTazSndZPeNcTZA,1066
+gwaslab-3.4.48.dist-info/METADATA,sha256=4Cqofc_AlsSBNtwKwiLBFiDtQsh8UUvWiM_XhBYksxw,7752
+gwaslab-3.4.48.dist-info/WHEEL,sha256=Mdi9PDNwEZptOjTlUcAth7XJDFtKrHYaQMPulZeBCiQ,91
+gwaslab-3.4.48.dist-info/top_level.txt,sha256=PyY6hWtrALpv2MAN3kjkIAzJNmmBTH5a2risz9KwH08,8
+gwaslab-3.4.48.dist-info/RECORD,,

{gwaslab-3.4.47.dist-info → gwaslab-3.4.48.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (70.2.0)
+Generator: setuptools (73.0.1)
 Root-Is-Purelib: true
 Tag: py3-none-any