gwaslab 3.4.37__py3-none-any.whl → 3.4.39__py3-none-any.whl

gwaslab/io_to_formats.py

@@ -1,6 +1,7 @@
 import pandas as pd
 import yaml
 import hashlib
+import copy
 from pysam import tabix_compress 
 from pysam import tabix_index
 from datetime import datetime
@@ -11,6 +12,8 @@ from gwaslab.g_Log import Log
 from gwaslab.bd_common_data import get_format_dict
 from gwaslab.bd_common_data import get_number_to_chr
 from gwaslab.g_version import gwaslab_info
+from gwaslab.bd_get_hapmap3 import gethapmap3
+
 # to vcf
 # to fmt
     ## vcf
@@ -19,7 +22,168 @@ from gwaslab.g_version import gwaslab_info
     ## annovar
     ## general : ldsc, plink, plink2, saige, regenie 
 ###################################################################################################################################################
+def _to_format(sumstats,
+              path="./sumstats",
+              fmt="gwaslab",   
+              extract=None,
+              exclude=None,
+              cols=None,
+              id_use="rsID",
+              hapmap3=False,
+              exclude_hla=False,
+              hla_range=(25,34),  
+              build=None, 
+              n=None,
+              no_status=False,
+              output_log=True,
+              to_csvargs=None,
+              float_formats=None,
+              xymt_number=False,
+              xymt=None,
+              chr_prefix="",
+              meta=None,
+              ssfmeta=False,
+              md5sum=False,
+              bgzip=False,
+              tabix=False,
+              tabix_indexargs={},
+              log=Log(),
+              verbose=True):
+    
+    if  to_csvargs is None:
+        to_csvargs = {}
+    if  float_formats is None:
+        float_formats={}
+    if cols is None:
+        cols=[]
+    if xymt is None:
+        xymt = ["X","Y","MT"]
+    onetime_log = copy.deepcopy(log)
+
+    #######################################################################################################
+    
+    formatlist= get_formats_list() + ["vep","bed","annovar","vcf"]
+    if fmt in formatlist:
+        onetime_log.write("Start to convert the output sumstats in: ",fmt, " format",verbose=verbose)
+    else:
+        raise ValueError("Please select a format to output")
+    suffix=fmt
+    
+    #######################################################################################################
+    # filter
+    output = sumstats.copy()
+    
+    if extract is not None:
+        onetime_log.write(" -Extracting {} variants from the main DataFrame...".format(len(extract)),verbose=verbose)
+        output = output.loc[output[id_use].isin(extract),:]
+        onetime_log.write(" -Extracted {} variants from the main DataFrame...".format(len(output)),verbose=verbose)
+    
+    if exclude is not None:
+        onetime_log.write(" -Excluding {} variants from the main DataFrame...".format(len(exclude)),verbose=verbose)
+        output = output.loc[~output[id_use].isin(exclude),:]
+        onetime_log.write(" -Excluded {} variants from the main DataFrame...".format(len(output)),verbose=verbose)
+    
+    #hla and hapmap3 #######################################################################################
+    
+    #exclude hla
+    if exclude_hla==True:
+        onetime_log.write(" -Excluding variants in MHC (HLA) region ...",verbose=verbose)
+        before = len(output)
+        is_hla = (output["CHR"].astype("string") == "6") & (output["POS"].astype("Int64") > hla_range[0]*1000000) & (output["POS"].astype("Int64") < hla_range[1]*1000000)
+        output = output.loc[~is_hla,:]
+        after = len(output)
+        onetime_log.write(" -Exclude "+ str(before - after) + " variants in MHC (HLA) region : {}Mb - {}Mb.".format(hla_range[0], hla_range[1]),verbose=verbose)
+        suffix = "noMHC."+suffix
+    
+    #extract hapmap3 SNPs
+    if hapmap3==True:
+        output = gethapmap3(output,build=build,verbose=verbose)
+        after = len(output)
+        onetime_log.write(" -Extract {} variants in Hapmap3 datasets for build {}.".format(after, build ),verbose=verbose)
+        suffix = "hapmap3."+suffix
+    
+    # add a n column
+    if n is not None:
+        output["N"] = n
+            
+    #######################################################################################################
+    #formatting float statistics
+    onetime_log.write(" -Formatting statistics ...",verbose=verbose)
+    
+    formats = {
+            'EAF': '{:.4g}', 
+            'MAF': '{:.4g}', 
+            'BETA': '{:.4f}', 
+            'SE': '{:.4f}',
+            'BETA_95U': '{:.4f}',
+            'BETA_95L': '{:.4f}',
+            'Z': '{:.4f}',
+            'CHISQ': '{:.4f}',
+            'F': '{:.4f}',
+            'OR': '{:.4f}',
+            'OR_95U': '{:.4f}',
+            'OR_95L': '{:.4f}',
+            'HR': '{:.4f}',
+            'HR_95U': '{:.4f}',
+            'HR_95L': '{:.4f}',
+            'INFO': '{:.4f}',
+            'P': '{:.4e}',
+            'MLOG10P': '{:.4f}',
+            'DAF': '{:.4f}'}
+    
+    for col, f in float_formats.items():
+        if col in output.columns: 
+            formats[col]=f
+    
+    for col, f in formats.items():
+        if col in output.columns: 
+            if str(output[col].dtype) in ["Float32","Float64","float64","float32","float16","float"]:
+                output[col] = output[col].map(f.format)
     
+    onetime_log.write(" -Float statistics formats:",verbose=verbose)  
+    keys=[]
+    values=[]
+    for key,value in formats.items():
+        if key in output.columns: 
+            keys.append(key)
+            values.append(value)
+    
+    onetime_log.write("  - Columns       :",keys,verbose=verbose) 
+    onetime_log.write("  - Output formats:",values,verbose=verbose) 
+        
+    ##########################################################################################################          
+    # output, mapping column names
+    
+    if fmt in get_formats_list() + ["vep","bed","annovar","vcf"]:
+        tofmt(output,
+              path=path,
+              fmt=fmt,
+              cols=cols,
+              suffix=suffix,
+              build=build,
+              verbose=verbose,
+                no_status=no_status,
+                log=onetime_log,
+                to_csvargs=to_csvargs,
+                chr_prefix=chr_prefix,
+                meta=meta,
+                ssfmeta=ssfmeta,
+                bgzip=bgzip,
+                tabix=tabix,
+                tabix_indexargs=tabix_indexargs,
+                md5sum=md5sum,
+                xymt_number=xymt_number,
+                xymt=xymt)
+    
+    if output_log is True:
+        log_path = path + "."+ suffix + ".log"
+        onetime_log.write(" -Saving log file to: {}".format(log_path),verbose=verbose)
+        onetime_log.write("Finished outputting successfully!",verbose=verbose)
+        try:
+            onetime_log.save(log_path, verbose=False)
+        except:
+            pass
+
 ###################################################################################################################################################
 def tofmt(sumstats,
           meta,
@@ -47,229 +211,74 @@ def tofmt(sumstats,
     if fmt in ["ssf"]: 
         xymt_number=True
         if "SNPID" in sumstats.columns:
-            if verbose: log.write(' - Replacing SNPID separator from ":" to "_"...')
+            log.write(' -Replacing SNPID separator from ":" to "_"...')
             sumstats["SNPID"] = sumstats["SNPID"].str.replace(":","_")
-    if verbose: log.write(" - Start outputting sumstats in "+fmt+" format...")
+    log.write(" -Start outputting sumstats in "+fmt+" format...")
     
     if "CHR" in sumstats.columns:
         if xymt_number is False and pd.api.types.is_integer_dtype(sumstats["CHR"]):
             sumstats["CHR"]= sumstats["CHR"].map(get_number_to_chr(xymt=xymt,prefix=chr_prefix))
         elif chr_prefix is not None:
             sumstats["CHR"]= chr_prefix + sumstats["CHR"].astype("string")
-    
-    ### calculate meta data
-    if "EAF" in sumstats.columns:
-        min_maf = sumstats["EAF"].min()
-    else:
-        min_maf = "Unknown"
-    
-    if "N" in sumstats.columns:
-        n_median =  sumstats["N"].median()
-        n_max = sumstats["N"].max()
-        n_min = sumstats["N"].min()
-    else:
-        n_median = "Unknown"
-        n_max = "Unknown"
-        n_min = "Unknown"
-
 
+    ####################################################################################################################
     if fmt=="bed":
         # bed-like format, 0-based, 
         # first 3 columns : chromosome, start, end
         # https://genome.ucsc.edu/FAQ/FAQformat.html#format1
-        is_snp = (sumstats["EA"].str.len() == sumstats["NEA"].str.len())
-        is_insert = (sumstats["EA"].str.len()>1) &(sumstats["NEA"].str.len()==1)
-        is_delete = (sumstats["EA"].str.len()==1) &(sumstats["NEA"].str.len()>1)
+        is_snp,is_insert,is_delete = _check_indel(sumstats,log,verbose)
+        log.write(" -formatting to 0-based bed-like file...")
+        log.write(" -format description: {}".format("https://genome.ucsc.edu/FAQ/FAQformat.html#format1"))
         
-        if verbose: log.write(" -Number of SNPs :",sum(is_snp))
-        if verbose: log.write(" -Number of Insertions :",sum(is_insert)) 
-        if verbose: log.write(" -Number of Deletions :",sum(is_delete)) 
-        
-        if verbose: log.write(" -formatting to 0-based bed-like file...")
-        # for snp  
-        # start = pos - 1 ; end = pos
-        # A/G
-        # AT/CG
-        sumstats.loc[is_snp,"START"]  = sumstats.loc[is_snp,"POS"]-1 
-        sumstats.loc[is_snp,"END"]    = sumstats.loc[is_snp,"POS"]-1 + sumstats.loc[is_snp,"NEA"].str.len()
-        sumstats.loc[is_snp,"NEA/EA"] = sumstats.loc[is_snp,"NEA"].astype("string")+"/"+sumstats.loc[is_snp,"EA"].astype("string")
-        
-        # for insertion
-        # start = pos : end = pos
-        # A/ATC -> -/TC
-        sumstats.loc[is_insert,"START"]  = sumstats.loc[is_insert,"POS"]
-        sumstats.loc[is_insert,"END"]    = sumstats.loc[is_insert,"POS"]
-        sumstats.loc[is_insert,"NEA/EA"] = "-/"+sumstats.loc[is_insert,"EA"].str.slice(start=1)
-        
-        # for deletion 
-        # start = pos - 1 +1; end = pos -1 +1+ len(Ref)
-        # ATC/A -> TC/-
-        sumstats.loc[is_delete,"START"]  = sumstats.loc[is_delete,"POS"]
-        sumstats.loc[is_delete,"END"]    = sumstats.loc[is_delete,"POS"] + sumstats.loc[is_delete,"NEA"].str.len() - 1
-        sumstats.loc[is_delete,"NEA/EA"] = sumstats.loc[is_delete,"NEA"].str.slice(start=1)+"/-"
-        
-        sumstats["STRAND"]="+"
+        sumstats = _adjust_position(sumstats, fmt, is_snp, is_insert, is_delete, log, verbose )
 
-        sumstats["START"] = sumstats["START"].astype("Int64")
-        sumstats["END"] = sumstats["END"].astype("Int64")
         ouput_cols=["CHR","START","END","NEA/EA","STRAND","SNPID"] + cols
 
-        sumstats = sumstats.loc[:,ouput_cols ]
-        path = path + "."+suffix
-        if verbose: log.write(" -Output columns:",sumstats.columns)
-        if verbose: log.write(" -Output path:",path) 
-        
-        sumstats.to_csv(path,sep="\t",index=None,header=None,**to_csvargs)
-        #tabix_compress
-        #tabix_index
-        if bgzip is True:
-            if verbose: log.write(" -bgzip compressing ...") 
-            tabix_compress(path, path+".gz",force=True)
-        if tabix is True:
-            if verbose: log.write(" -tabix indexing...")
-            if "preset" not in  tabix_indexargs:
-                tabix_indexargs["preset"] = "bed"
-            if "force" not in tabix_indexargs:
-                tabix_indexargs["force"] = True
-
-            tabix_index(path+".gz", **tabix_indexargs)
+        _output_bed_like(sumstats,  path, "bed", suffix, ouput_cols,to_csvargs,bgzip, tabix, tabix_indexargs, md5sum, log, verbose)
     ####################################################################################################################   
     elif fmt=="vep":
         # bed-like format, 1-based
         # first 6 columns : chromosome, start, end, allele, strand, identifier
         # https://asia.ensembl.org/info/docs/tools/vep/vep_formats.html
         
-        is_snp = (sumstats["EA"].str.len() == sumstats["NEA"].str.len())
-        is_insert = (sumstats["EA"].str.len()>1) &(sumstats["NEA"].str.len()==1)
-        is_delete = (sumstats["EA"].str.len()==1) &(sumstats["NEA"].str.len()>1)
-        
-        if verbose: log.write(" -Number of SNPs :",sum(is_snp)) 
-        if verbose: log.write(" -Number of Insertions :",sum(is_insert)) 
-        if verbose: log.write(" -Number of Deletions :",sum(is_delete)) 
+        is_snp,is_insert,is_delete = _check_indel(sumstats,log,verbose)
             
-        if verbose: log.write(" -formatting to 1-based bed-like file (for vep)...")
-        # for snp  
-        # start = pos ; end = pos
-        sumstats.loc[is_snp,"START"]  = sumstats.loc[is_snp,"POS"] + (sumstats.loc[is_snp,"NEA"].str.len() - 1 )
-        sumstats.loc[is_snp,"END"]    = sumstats.loc[is_snp,"POS"] + (sumstats.loc[is_snp,"NEA"].str.len() - 1 )
-        sumstats.loc[is_snp,"NEA/EA"] = sumstats.loc[is_snp,"NEA"].astype("string")+"/"+sumstats.loc[is_snp,"EA"].astype("string")
-        
-        # for insertion
-        # start = pos+1 ; end = pos
-        # A/ATC -> -/TC
-        sumstats.loc[is_insert,"START"]  = sumstats.loc[is_insert,"POS"] + 1
-        sumstats.loc[is_insert,"END"]    = sumstats.loc[is_insert,"POS"]
-        sumstats.loc[is_insert,"NEA/EA"] = "-/" + sumstats.loc[is_insert,"EA"].str.slice(start=1)
-        
-        # for deletion 
-        # start = pos ; end = pos + len(Ref) -1
-        # ATC/A -> TC/-
-        sumstats.loc[is_delete,"START"]  = sumstats.loc[is_delete,"POS"] + 1
-        sumstats.loc[is_delete,"END"]    = sumstats.loc[is_delete,"POS"] + (sumstats.loc[is_delete,"NEA"].str.len() -1)
-        sumstats.loc[is_delete,"NEA/EA"] = sumstats.loc[is_delete,"NEA"].str.slice(start=1)+"/-"
-           
-        sumstats["STRAND"]="+"
-        
-        sumstats["START"] = sumstats["START"].astype("Int64")
-        sumstats["END"] = sumstats["END"].astype("Int64")
+        log.write(" -formatting to 1-based bed-like file (for vep)...")
+        log.write(" -format description: {}".format("http://asia.ensembl.org/info/docs/tools/vep/vep_formats.html"))
+        sumstats = _adjust_position(sumstats, fmt, is_snp, is_insert, is_delete , log, verbose)
         
         ouput_cols=["CHR","START","END","NEA/EA","STRAND","SNPID"]+ cols
-        sumstats = sumstats.loc[:,ouput_cols]
-        path = path + "."+suffix+".gz"
-        if verbose: log.write(" -Output columns:",sumstats.columns)
-        if verbose: log.write(" -Output path:",path) 
 
-        sumstats.to_csv(path,sep="\t",index=None,header=None,**to_csvargs)
-        if md5sum is True: md5sum_file(path,log,verbose)
+        _output_bed_like(sumstats,  path,"vep", suffix, ouput_cols,to_csvargs,bgzip, tabix, tabix_indexargs, md5sum, log, verbose)
+
     ####################################################################################################################
     elif fmt=="annovar":
         # bed-like format, 1-based, 
         # first 3 columns : Chromosome ("chr" prefix is optional), Start, End, Reference Allelel, Alternative Allele
         # https://annovar.openbioinformatics.org/en/latest/user-guide/input/
-        is_snp = (sumstats["EA"].str.len() == sumstats["NEA"].str.len())
-        is_insert = (sumstats["EA"].str.len()>1) &(sumstats["NEA"].str.len()==1)
-        is_delete = (sumstats["EA"].str.len()==1) &(sumstats["NEA"].str.len()>1)
-        
-        if verbose: log.write(" -Number of SNPs :",sum(is_snp))
-        if verbose: log.write(" -Number of Insertions :",sum(is_insert)) 
-        if verbose: log.write(" -Number of Deletions :",sum(is_delete)) 
-        
-        if verbose: log.write(" -formatting to 1-based bed-like file...")
-        # for snp  
-        # start = pos ; end = pos
-        # A/G
-        # AT/CG
-        sumstats.loc[is_snp,"START"]  = sumstats.loc[is_snp,"POS"]
-        sumstats.loc[is_snp,"END"]    = sumstats.loc[is_snp,"POS"]-1 + sumstats.loc[is_snp,"NEA"].str.len()
-        sumstats.loc[is_snp,"NEA_out"] = sumstats.loc[is_snp,"NEA"].astype("string")
-        sumstats.loc[is_snp,"EA_out"] = sumstats.loc[is_snp,"EA"].astype("string")
-        
-        # for insertion
-        # start = pos : end = pos
-        # A/ATC -> -/TC
-        sumstats.loc[is_insert,"START"]  = sumstats.loc[is_insert,"POS"]+1
-        sumstats.loc[is_insert,"END"]   = sumstats.loc[is_insert,"POS"]+1
-        sumstats.loc[is_insert,"NEA_out"] = "-"
-        sumstats.loc[is_insert,"EA_out"] = sumstats.loc[is_insert,"EA"].str.slice(start=1)
-        
-        # for deletion 
-        # start = pos - 1 +1; end = pos -1 +1+ len(Ref)
-        # ATC/A -> TC/-
-        sumstats.loc[is_delete,"START"] = sumstats.loc[is_delete,"POS"]
-        sumstats.loc[is_delete,"END"]  = sumstats.loc[is_delete,"POS"]- 1 + sumstats.loc[is_delete,"NEA"].str.len() 
-        sumstats.loc[is_delete,"NEA_out"] = sumstats.loc[is_delete,"NEA"].str.slice(start=1)
-        sumstats.loc[is_delete,"EA_out"] = "-"
+        is_snp,is_insert,is_delete = _check_indel(sumstats,log,verbose)
+
+        log.write(" -formatting to 1-based bed-like file...")
+        log.write(" -format description: {}".format("https://annovar.openbioinformatics.org/en/latest/user-guide/input/"))
         
-        sumstats["START"] = sumstats["START"].astype("Int64")
-        sumstats["END"] = sumstats["END"].astype("Int64")
+        sumstats = _adjust_position(sumstats, fmt, is_snp, is_insert, is_delete, log, verbose )
 
         ouput_cols=["CHR","START","END","NEA_out","EA_out","SNPID"]+ cols
-        sumstats = sumstats.loc[:,ouput_cols]
-        path = path + "."+suffix
-        if verbose: log.write(" -Output columns:",sumstats.columns)
-        if verbose: log.write(" -Output path:",path) 
         
-        sumstats.to_csv(path,sep="\t",index=None,header=None,**to_csvargs)
-        #tabix_compress
-        #tabix_index
-        if bgzip is True:
-            if verbose: log.write(" -bgzip compressing ...") 
-            tabix_compress(path, path+".gz",force=True)
-            if md5sum is True: md5sum_file(path+".gz",log,verbose)
-        if tabix is True:
-            if verbose: log.write(" -tabix indexing...")
-            if "preset" not in tabix_indexargs:
-                tabix_indexargs["preset"] = "bed"
-            if "force" not in tabix_indexargs:
-                tabix_indexargs["force"] = True
-            tabix_index(path+".gz", **tabix_indexargs)
+        _output_bed_like(sumstats, path, fmt, suffix, ouput_cols,to_csvargs,bgzip, tabix, tabix_indexargs, md5sum, log, verbose)
+    
     ####################################################################################################################       
     elif fmt=="vcf":
-        if verbose: log.write(" -"+fmt+" format will be loaded...")
+        # GWAS-VCF
+        log.write(" -"+fmt+" format will be loaded...",verbose=verbose)
         meta_data,rename_dictionary = get_format_dict(fmt,inverse=True)
-        #loading format data
-        if verbose:             
-            log.write(" -"+fmt+" format meta info:")   
-            for key,value in meta_data.items():
-                if key not in ["format_fixed_header","format_contig_19","format_contig_38"]:
-                    log.write("  -",key," : ",value)
+        print_format_info(fmt=fmt, meta_data=meta_data,rename_dictionary=rename_dictionary,verbose=verbose, log=log, output=True, skip_meta_records=["format_fixed_header","format_contig_19","format_contig_38"])
         
         # determine which ID to use
         if "rsID" in sumstats.columns:
             rename_dictionary["rsID"]="ID"
         else:
             rename_dictionary["SNPID"]="ID" 
-
-        # logging
-        if verbose: 
-            log.write(" -gwaslab to "+fmt+" format dictionary:")  
-            keys=[]
-            values=[]
-            for key,value in rename_dictionary.items():
-                keys.append(key)
-                values.append(value)
-            log.write("  - gwaslab keys:",','.join(keys)) 
-            log.write("  - "+fmt+" values:",','.join(values)) 
         
         # get the columns to output
         ouput_cols=[]
@@ -277,12 +286,10 @@ def tofmt(sumstats,
             if i in rename_dictionary.keys():
                 ouput_cols.append(i)  
         ouput_cols = ouput_cols +["STATUS"]+ cols
-        sumstats = sumstats.loc[:,ouput_cols]
+        sumstats = sumstats[ouput_cols]
         sumstats = sumstats.rename(columns=rename_dictionary) 
         
-        # calculate meta data
-        harmonised = sum(sumstats["STATUS"].str.match( r"\w\w\w[0][0123][012][01234]", case=False, flags=0, na=False ) )
-        switchedalleles = sum(sumstats["STATUS"].str.match( r"\w\w\w[0][0123][12][24]", case=False, flags=0, na=False ) )
+        # replace : with _
         sumstats["ID"] = sumstats["ID"].str.replace(":","_")
         
         # process Allele frequency data
@@ -297,35 +304,21 @@ def tofmt(sumstats,
             if i in meta_data["format_format"]:
                 output_format.append(i)  
 
-        # Create vcf header
-        vcf_header= meta_data["format_fixed_header"] +"\n"+ meta_data["format_contig_"+str(build)]+"\n"
-        # Create sample header
-        vcf_header+="##SAMPLE=<ID={},TotalVariants={},VariantsNotRead=0,HarmonisedVariants={},VariantsNotHarmonised={},SwitchedAlleles={},StudyType={}>\n".format(meta["gwaslab"]["study_name"],len(sumstats),harmonised,len(sumstats)-harmonised,switchedalleles,meta["gwaslab"]["study_type"])
-        vcf_header+="##gwaslab_version="+gwaslab_info()["version"]+"\n"
-        
-        
-         #StudyID=meta["Name"]
-        #otalVariants = len(sumstats)
-        #HarmonisedVariants = 
-        #VariantsNotHarmonised = 
-        #StudyType=
-        ##SAMPLE=<ID=IEU-b-1,TotalVariants=9851866,VariantsNotRead=0,HarmonisedVariants=9851866,VariantsNotHarmonised=0,SwitchedAlleles=9851866,StudyType=Continuous>
-        
-        
         # determine path
         path = path + "."+suffix
-        if verbose: log.write(" -Output path:",path) 
-        if verbose: log.write(" -vcf header contig build:"+str(build)) 
         
+        
+        vcf_header =  _process_vcf_header(sumstats, meta, meta_data, build, log, verbose)
+
+        log.write(" -Writing sumstats to: {}...".format(path),verbose=verbose)
         # output header
         with open(path,"w") as file:
             file.write(vcf_header)
         
         with open(path,"a") as file:
-            if verbose: log.write(" -Output columns:"," ".join(meta_data["format_fixed"]+[meta["gwaslab"]["study_name"]]))
+            log.write(" -Output columns:"," ".join(meta_data["format_fixed"]+[meta["gwaslab"]["study_name"]]))
             file.write("\t".join(meta_data["format_fixed"]+[meta["gwaslab"]["study_name"]])+"\n")
-            if verbose: log.write(" -Outputing data...")
-            counter=0
+            log.write(" -Outputing data...")
             QUAL="."
             FILTER="PASS"
             for index,row in sumstats.iterrows():
@@ -337,112 +330,153 @@ def tofmt(sumstats,
                 INFO=str(row["INFO"])
                 FORMAT=":".join(output_format)
                 DATA=":".join(row[output_format].astype("string"))
-                file.write(CHROM+"\t"+POS+"\t"+ID+"\t"+REF+"\t"+ALT+"\t"+QUAL+"\t"+FILTER+"\t"+INFO+"\t"+FORMAT+"\t"+DATA+"\n")
-
-        if bgzip==True:
-            if verbose: log.write(" -bgzip compressing ...") 
-            tabix_compress(path, path+".gz",force=True)
-            if md5sum is True: md5sum_file(path+".gz",log,verbose)
-        if tabix==True:
-            if verbose: log.write(" -tabix indexing...")
-            if "preset" not in tabix_indexargs:
-                tabix_indexargs["preset"] = "vcf"
-            if "force" not in tabix_indexargs:
-                tabix_indexargs["force"] = True
-            tabix_index(path+".gz", **tabix_indexargs)
+                file.write("{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\n".format(CHROM, POS, ID, REF, ALT, QUAL, FILTER, INFO, FORMAT, DATA))
+        _bgzip_tabix_md5sum(path, fmt, bgzip, md5sum, tabix, tabix_indexargs, log, verbose)
+    
     ####################################################################################################################
-    elif fmt in get_formats_list():       
-        if verbose: log.write(" -"+fmt+" format will be loaded...")
+    elif fmt in get_formats_list():      
+        # tabular 
+        log.write(" -"+fmt+" format will be loaded...",verbose=verbose)
         meta_data,rename_dictionary = get_format_dict(fmt,inverse=True)
         print_format_info(fmt=fmt, meta_data=meta_data,rename_dictionary=rename_dictionary,verbose=verbose, log=log, output=True)
-        #if verbose:             
-        #    log.write(" -"+fmt+" format meta info:")   
-        #    for key,value in meta_data.items():
-        #        if type(value) is list:
-        #            log.write("  -",key," : ",','.join(value))
-        #        else:
-        #            log.write("  -",key," : ",value)
-        #if verbose: 
-        #    log.write(" -gwaslab to "+fmt+" format dictionary:",)  
-        #    keys=[]
-        #    values=[]
-        #    for key,value in rename_dictionary.items():
-        #        keys.append(key)
-        #        values.append(value)
-        #    log.write("  - gwaslab keys:",  ','.join(keys)) 
-        #    log.write("  - "+fmt+" values:"  , ','.join(values))
-        
-        # grab format cols that exist in sumstats
-        ouput_cols=[]
-        for i in sumstats.columns:
-            if i in rename_dictionary.keys():
-                ouput_cols.append(i)  
-        # + additional cols
-        ouput_cols = ouput_cols + cols
-        try:
-            if no_status == True:
-                ouput_cols.remove("STATUS")
-        except:
-            pass
-        sumstats = sumstats.loc[:,ouput_cols]
-        sumstats = sumstats.rename(columns=rename_dictionary) 
         
-
         ymal_path = path + "."+suffix+".tsv-meta.ymal"
         path = path + "."+suffix+".tsv.gz"
+        log.write(" -Output path:",path, verbose=verbose) 
         
-        if verbose: log.write(" -Output path:",path) 
+        sumstats,to_csvargs = _configure_output_cols_and_args(sumstats, rename_dictionary, cols, no_status, path, meta_data, to_csvargs, log, verbose)
         
-        if path is not None: 
-            if "format_separator" in meta_data.keys():
-                to_csvargs["sep"] = meta_data["format_separator"]
-            else:
-                to_csvargs["sep"]="\t"
-            if "format_na" in meta_data.keys():
-                to_csvargs["na_rep"] = meta_data["format_na"]
-            if "format_col_order" in meta_data.keys():
-                fixed_col =[]
-                other_col=[]
-                for i in meta_data["format_col_order"]:
-                    if i in sumstats.columns:
-                        fixed_col.append(i)
-                for i in sumstats.columns:
-                    if i not in meta_data["format_col_order"]:
-                        other_col.append(i)
-                
-                sumstats = sumstats.loc[:,fixed_col + other_col]
-                if verbose: log.write(" -Reordering columns...") 
-
-            if verbose: log.write(" -Output columns:",','.join(sumstats.columns))
-            sumstats.to_csv(path, index=None,**to_csvargs)
-
-        if md5sum is True: 
+        log.write(" -Writing sumstats to: {}...".format(path),verbose=verbose)
+        sumstats.to_csv(path, index=None,**to_csvargs)
+
+        if md5sum == True: 
             md5_value = md5sum_file(path,log,verbose)
         else:
             md5_value = calculate_md5sum_file(path)
         
         ## update ssf-style meta data and export to yaml file
-        if ssfmeta==True:
-            meta_copy = meta.copy()
-            if "format_cite_name" in meta_data.keys():
-                meta_copy["file_type"] = meta_data["format_cite_name"]
-            else:
-                meta_copy["file_type"] = fmt
-            meta_copy["minor_allele_freq_lower_limit"] = min_maf
-            meta_copy["data_file_name"] = path
-            meta_copy["data_file_md5sum"] = md5_value
-            meta_copy["date_last_modified"] = get_format_date_and_time()
-            meta_copy["samples"]["sample_size"] = n_max
-            meta_copy["gwaslab"]["samples"]["sample_size_min"] = n_min
-            meta_copy["gwaslab"]["samples"]["sample_size_median"] = n_median
-            meta_copy["gwaslab"]["variants"]["variant_number"] = len(sumstats)
-            if verbose: log.write(" -Exporting SSF-style meta data to {}".format(ymal_path)) 
-            with open(ymal_path, 'w') as outfile:
-                yaml.dump(meta_copy, outfile)
+        _configure_ssf_meta(sumstats, fmt, ssfmeta, meta, meta_data, path, md5_value, ymal_path, log, verbose)
+        
         return sumstats  
+####################################################################################################################
+def _configure_output_cols_and_args(sumstats, rename_dictionary, cols, no_status, path, meta_data, to_csvargs, log, verbose):
+    # grab format cols that exist in sumstats
+    ouput_cols=[]
+    for i in sumstats.columns:
+        if i in rename_dictionary.keys():
+            ouput_cols.append(i)  
+    
+    # + additional cols and remove duplicated
+    ouput_cols = list(set(ouput_cols + cols)) 
     
+    # remove STATUS
+    try:
+        if no_status == True:
+            ouput_cols.remove("STATUS")
+    except:
+        pass
+    
+    #filter and rename to target fromat headers
+    sumstats = sumstats[ouput_cols]
+    sumstats = sumstats.rename(columns=rename_dictionary) 
+
+    # configure target format args and reorder columns
+    if "format_separator" in meta_data.keys():
+        to_csvargs["sep"] = meta_data["format_separator"]
+    else:
+        to_csvargs["sep"]="\t"
+    if "format_na" in meta_data.keys():
+        to_csvargs["na_rep"] = meta_data["format_na"]
+    if "format_col_order" in meta_data.keys():
+        fixed_col =[]
+        other_col=[]
+        for i in meta_data["format_col_order"]:
+            if i in sumstats.columns:
+                fixed_col.append(i)
+        for i in sumstats.columns:
+            if i not in meta_data["format_col_order"]:
+                other_col.append(i)
+        sumstats = sumstats[fixed_col + other_col]
+    log.write(" -Output columns: {}".format(",".join(sumstats.columns)),verbose=verbose)
+    return sumstats, to_csvargs
+
+
+def _configure_ssf_meta(sumstats, fmt, ssfmeta, meta, meta_data, path, md5_value, ymal_path, log, verbose):
+    ### calculate meta data
+    if "EAF" in sumstats.columns:
+        min_maf = sumstats["EAF"].min()
+    else:
+        min_maf = "Unknown"
+    
+    if "N" in sumstats.columns:
+        n_median =  sumstats["N"].median()
+        n_max = sumstats["N"].max()
+        n_min = sumstats["N"].min()
+    else:
+        n_median = "Unknown"
+        n_max = "Unknown"
+        n_min = "Unknown"
+
+    if ssfmeta==True:
+        sumstats_meta_copy = meta.copy()
+        if "format_cite_name" in meta_data.keys():
+            sumstats_meta_copy["file_type"] = meta_data["format_cite_name"]
+        else:
+            sumstats_meta_copy["file_type"] = fmt
+        sumstats_meta_copy["minor_allele_freq_lower_limit"] = min_maf
+        sumstats_meta_copy["data_file_name"] = path
+        sumstats_meta_copy["data_file_md5sum"] = md5_value
+        sumstats_meta_copy["date_last_modified"] = get_format_date_and_time()
+        sumstats_meta_copy["samples"]["sample_size"] = n_max
+        sumstats_meta_copy["gwaslab"]["samples"]["sample_size_min"] = n_min
+        sumstats_meta_copy["gwaslab"]["samples"]["sample_size_median"] = n_median
+        sumstats_meta_copy["gwaslab"]["variants"]["variant_number"] = len(sumstats)
+        log.write(" -Exporting SSF-style meta data to {}".format(ymal_path),verbose=verbose) 
+        with open(ymal_path, 'w') as outfile:
+            yaml.dump(sumstats_meta_copy, outfile)
+
+
+
+def _output_bed_like(sumstats, path, fmt, suffix, ouput_cols,to_csvargs,bgzip, tabix, tabix_indexargs, md5sum, log, verbose):
+    sumstats = sumstats[ouput_cols]
+    path = path + "."+suffix
+    log.write(" -Output columns: {}".format(",".join(sumstats.columns)),verbose=verbose)
+    log.write(" -Writing sumstats to: {}...".format(path),verbose=verbose)
+    sumstats.to_csv(path,sep="\t",index=None,header=None,**to_csvargs)
+    _bgzip_tabix_md5sum(path, fmt, bgzip, md5sum, tabix, tabix_indexargs, log, verbose)
+
+
+def _bgzip_tabix_md5sum(path, fmt, bgzip, md5sum, tabix, tabix_indexargs, log, verbose):
+    if bgzip == True:
+        log.write(" -bgzip compressing : {}...".format(path+".gz"),verbose=verbose) 
+        tabix_compress(path, path+".gz",force=True)
+    if md5sum == True: 
+        if bgzip == True:
+            md5sum_file(path+".gz",log,verbose)
+        else:
+            md5sum_file(path,log,verbose)
+    if tabix == True and bgzip == True:
+        log.write(" -tabix indexing : : {}...".format(path+".gz.tbi"),verbose=verbose)
+        if "preset" not in  tabix_indexargs:
+            tabix_indexargs["preset"] = fmt
+        if "force" not in tabix_indexargs:
+            tabix_indexargs["force"] = True
+        tabix_index(path+".gz", **tabix_indexargs)    
+
+
+def _check_indel(sumstats,log,verbose):
+    is_snp = (sumstats["EA"].str.len() == sumstats["NEA"].str.len())
+    is_insert = (sumstats["EA"].str.len()>1) &(sumstats["NEA"].str.len()==1)
+    is_delete = (sumstats["EA"].str.len()==1) &(sumstats["NEA"].str.len()>1)
+    
+    log.write(" -Number of SNPs :",sum(is_snp))
+    log.write(" -Number of Insertions :",sum(is_insert)) 
+    log.write(" -Number of Deletions :",sum(is_delete)) 
+    return is_snp,is_insert,is_delete
+
+
 def md5sum_file(filename,log,verbose):
-    if verbose: log.write(" -md5sum hashing for the file:",filename) 
+    log.write(" -md5sum hashing for the file:",filename,verbose=verbose) 
     md5_hash = hashlib.md5()
     with open(filename,"rb") as f:
         # Read and update hash in chunks
@@ -451,7 +485,8 @@ def md5sum_file(filename,log,verbose):
     with open(filename+".md5sum","w") as f:
         out = str(md5_hash.hexdigest())
         f.write(out+"\n")
-        if verbose: log.write(" -md5sum path:",filename+".md5sum")    
+        log.write(" -md5sum path:",filename+".md5sum",verbose=verbose)    
+        log.write(" -md5sum: {}".format(out),verbose=verbose) 
         return out
 
 def calculate_md5sum_file(filename):
@@ -466,4 +501,102 @@ def calculate_md5sum_file(filename):
 def get_format_date_and_time():
     now = datetime.now()
     dt_string = now.strftime("%Y-%m-%d-%H:%M:%S")
-    return dt_string
+    return dt_string
+
+
+def _adjust_position(sumstats, fmt,is_snp, is_insert, is_delete, log, verbose):
+    log.write(" -Adjusting positions in format-specific manner..",verbose=verbose) 
+    if fmt=="bed":
+        sumstats.loc[is_snp,"START"]  = sumstats.loc[is_snp,"POS"]-1 
+        sumstats.loc[is_snp,"END"]    = sumstats.loc[is_snp,"POS"]-1 + sumstats.loc[is_snp,"NEA"].str.len()
+        sumstats.loc[is_snp,"NEA/EA"] = sumstats.loc[is_snp,"NEA"].astype("string")+"/"+sumstats.loc[is_snp,"EA"].astype("string")
+        
+        # for insertion
+        # start = pos : end = pos
+        # A/ATC -> -/TC
+        sumstats.loc[is_insert,"START"]  = sumstats.loc[is_insert,"POS"]
+        sumstats.loc[is_insert,"END"]    = sumstats.loc[is_insert,"POS"]
+        sumstats.loc[is_insert,"NEA/EA"] = "-/"+sumstats.loc[is_insert,"EA"].str.slice(start=1)
+        
+        # for deletion 
+        # start = pos - 1 +1; end = pos -1 +1+ len(Ref)
+        # ATC/A -> TC/-
+        sumstats.loc[is_delete,"START"]  = sumstats.loc[is_delete,"POS"]
+        sumstats.loc[is_delete,"END"]    = sumstats.loc[is_delete,"POS"] + sumstats.loc[is_delete,"NEA"].str.len() - 1
+        sumstats.loc[is_delete,"NEA/EA"] = sumstats.loc[is_delete,"NEA"].str.slice(start=1)+"/-"
+        sumstats["STRAND"]="+"
+    elif fmt=="vep":
+        sumstats.loc[is_snp,"START"]  = sumstats.loc[is_snp,"POS"] + (sumstats.loc[is_snp,"NEA"].str.len() - 1 )
+        sumstats.loc[is_snp,"END"]    = sumstats.loc[is_snp,"POS"] + (sumstats.loc[is_snp,"NEA"].str.len() - 1 )
+        sumstats.loc[is_snp,"NEA/EA"] = sumstats.loc[is_snp,"NEA"].astype("string")+"/"+sumstats.loc[is_snp,"EA"].astype("string")
+        
+        # for insertion
+        # start = pos+1 ; end = pos
+        # A/ATC -> -/TC
+        sumstats.loc[is_insert,"START"]  = sumstats.loc[is_insert,"POS"] + 1
+        sumstats.loc[is_insert,"END"]    = sumstats.loc[is_insert,"POS"]
+        sumstats.loc[is_insert,"NEA/EA"] = "-/" + sumstats.loc[is_insert,"EA"].str.slice(start=1)
+        
+        # for deletion 
+        # start = pos ; end = pos + len(Ref) -1
+        # ATC/A -> TC/-
+        sumstats.loc[is_delete,"START"]  = sumstats.loc[is_delete,"POS"] + 1
+        sumstats.loc[is_delete,"END"]    = sumstats.loc[is_delete,"POS"] + (sumstats.loc[is_delete,"NEA"].str.len() -1)
+        sumstats.loc[is_delete,"NEA/EA"] = sumstats.loc[is_delete,"NEA"].str.slice(start=1)+"/-"
+        sumstats["STRAND"]="+"
+    elif fmt=="annovar":
+        # for snp  
+        # start = pos ; end = pos
+        # A/G
+        # AT/CG
+        sumstats.loc[is_snp,"START"]  = sumstats.loc[is_snp,"POS"]
+        sumstats.loc[is_snp,"END"]    = sumstats.loc[is_snp,"POS"]-1 + sumstats.loc[is_snp,"NEA"].str.len()
+        sumstats.loc[is_snp,"NEA_out"] = sumstats.loc[is_snp,"NEA"].astype("string")
+        sumstats.loc[is_snp,"EA_out"] = sumstats.loc[is_snp,"EA"].astype("string")
+        # for insertion
+        # start = pos : end = pos
+        # A/ATC -> -/TC
+        sumstats.loc[is_insert,"START"]  = sumstats.loc[is_insert,"POS"]+1
+        sumstats.loc[is_insert,"END"]   = sumstats.loc[is_insert,"POS"]+1
+        sumstats.loc[is_insert,"NEA_out"] = "-"
+        sumstats.loc[is_insert,"EA_out"] = sumstats.loc[is_insert,"EA"].str.slice(start=1)
+        
+        # for deletion 
+        # start = pos - 1 +1; end = pos -1 +1+ len(Ref)
+        # ATC/A -> TC/-
+        sumstats.loc[is_delete,"START"] = sumstats.loc[is_delete,"POS"]
+        sumstats.loc[is_delete,"END"]  = sumstats.loc[is_delete,"POS"]- 1 + sumstats.loc[is_delete,"NEA"].str.len() 
+        sumstats.loc[is_delete,"NEA_out"] = sumstats.loc[is_delete,"NEA"].str.slice(start=1)
+        sumstats.loc[is_delete,"EA_out"] = "-"
+
+    
+    sumstats["START"] = sumstats["START"].astype("Int64")
+    sumstats["END"] = sumstats["END"].astype("Int64")
+    return sumstats
+
+def _process_vcf_header(sumstats, meta, meta_data, build, log, verbose):
+    
+    log.write(" -Creating VCF file header...",verbose=verbose)
+    log.write("  -VCF header contig build:"+str(build),verbose=verbose) 
+    
+    # calculate meta data
+    harmonised = sum(sumstats["STATUS"].str.match( r"\w\w\w[0][0123][012][01234]", case=False, flags=0, na=False ) )
+    switchedalleles = sum(sumstats["STATUS"].str.match( r"\w\w\w[0][0123][12][24]", case=False, flags=0, na=False ) )
+
+    # Create vcf header
+    vcf_header = meta_data["format_fixed_header"] +"\n"+ meta_data["format_contig_"+str(build)]+"\n"
+
+    # Create sample header
+    vcf_header+="##SAMPLE=<ID={},TotalVariants={},VariantsNotRead=0,HarmonisedVariants={},VariantsNotHarmonised={},SwitchedAlleles={},StudyType={}>\n".format(
+                    meta["gwaslab"]["study_name"], len(sumstats), harmonised, len(sumstats)-harmonised, switchedalleles, meta["gwaslab"]["study_type"])
+    vcf_header+="##gwaslab_version="+gwaslab_info()["version"]+"\n"
+
+    log.write("  -ID:{}".format( meta["gwaslab"]["study_name"]),verbose=verbose) 
+    log.write("  -StudyType:{}".format(meta["gwaslab"]["study_type"]),verbose=verbose) 
+    log.write("  -TotalVariants:{}".format(len(sumstats)),verbose=verbose) 
+    log.write("  -HarmonisedVariants:{}".format(harmonised),verbose=verbose) 
+    log.write("  -VariantsNotHarmonised:{}".format(len(sumstats)-harmonised),verbose=verbose) 
+    log.write("  -SwitchedAlleles:{}".format(switchedalleles),verbose=verbose) 
+
+    return vcf_header
+