23andme
=======

23andme to PED-MAP
------------------------


.. code-block:: console

   #1. Convert 23andme to BED-BIM-FAM --> 23andmetoBED-BIM-FAM()
   #That function will generates three files 23andmetoBED.bed, 23andmetoBED.bim, and 23andmetoBED.fam
   # Step 2 
   ./plink --bfile 23andmetoBED --recode --out output_file
   

23andme to RAW
------------------------

.. code-block:: console

   #1. Convert 23andme to BED-BIM-FAM --> 23andmetoBED-BIM-FAM()
   #That function will generates three files 23andmetoBED.bed, 23andmetoBED.bim, and 23andmetoBED.fam
   # Step 2 
   ./plink --bfile 23andmetoBED --recodeA --out output_file



23andme to BED-BIM-FAM
------------------------


.. code-block:: console


   # Place 23andme files in a new directory. 
   # input_file is actually input directory.
    
   if not os.path.isdir(input_file):
      print("Directory "+input_file+" does not exists...! Kindly place 23andme files in that directory.")
      exit(0)
   files = []
   allfiles = os.listdir("./"+input_file+"/")
   personname = [] 
   sexinfo = "0"
   for loop in allfiles:
      if ".23andme" in loop:
      
         data = loop.split(".")[0].split("_")
         personname.append(data[0])
         print(data)
         if data[5] =="XX":
            sexinfo = "2"
         elif data[5] =="XY":
            sexinfo = "1"
         else:
            sexinfo = "0" 
         #os.rename("tutorialsdir","tutorialsdirectory")
         os.system("./plink --23file ./"+input_file+os.sep+loop+" --snps-only --make-bed  --out ./"+input_file+os.sep+data[0])
         if os.path.exists("./"+input_file+os.sep+data[0]+".fam"):
            data2 = pd.read_csv("./"+input_file+os.sep+data[0]+".fam",header=None, sep="\s+")
            data2[0] = data[0]
            data2[1] = data[0]
            data2[4] = sexinfo    
            data2.to_csv("./"+input_file+os.sep+data[0]+".fam",sep="\t",header=False,index=False)
   allfiles =  os.listdir("./"+input_file+"/")
   count=0
   files=[]
   for loop in allfiles:
      if ".txt" in loop and ".bed" not in loop and ".fam" not in loop and ".bim" not in loop:
         print(loop)
         x = loop.split("_")[0]
         x = x + ".fam"
         me = os.path.exists("./"+input_file+os.sep+x)
         if me==True:
            x = x.split(".")[0]
            x = "./"+input_file+os.sep+x +".bed " + "./"+input_file+os.sep+x + ".bim " +  "./"+input_file+os.sep+x + ".fam"	
            files.append(x)
         else:
            count=count+1
         print(count," People removed due to missing fam file")
   with open("./"+input_file+os.sep+"All.txt", "w") as filehandle:
      for listitem in files:
        filehandle.write('%s\n' % listitem)
    
   os.system("./plink --merge-list ./"+input_file+os.sep+"/All.txt --make-bed --out 23andmetoBED")
    
   if os.path.exists("23andmetoBED.bed"):
      exit(0)
   else:
      allfiles =  os.listdir("./"+input_file+"/")
      count=0
      for loop in allfiles:
         if ".bed" in loop:
            x = loop
            x = x.split(".")[0]
    
            command = "./plink --bfile ./"+input_file+os.sep+x+" --exclude 23andmetoBED-merge.missnp --make-bed --out ./"+input_file+os.sep + x
            os.system(command)
      allfiles =  os.listdir("./"+input_file+"/")
      files=[]
      
      for loop in allfiles:
         if ".txt" in loop and ".bed" not in loop and ".fam" not in loop and ".bim" not in loop:
            print(loop)
            x = loop.split("_")[0]
            x = x + ".fam"
            me = os.path.exists("./"+input_file+os.sep+x)
            if me==True:
               x = x.split(".")[0]
               x = "./"+input_file+os.sep+x +".bed " + "./"+input_file+os.sep+x + ".bim " +  "./"+input_file+os.sep+x + ".fam"	
               files.append(x)
            else:
               count=count+1
            print(count," People removed due to missing fam file")
      with open("./"+input_file+os.sep+"All.txt", "w") as filehandle:
        for listitem in files:
            filehandle.write('%s\n' % listitem)      
      os.system("./plink --merge-list ./"+input_file+os.sep+"/All.txt --make-bed --out 23andmetoBED") 



23andme to GEN-SAMPLE
------------------------


.. code-block:: console

   #1. Convert 23andme to BED-BIM-FAM --> 23andmetoBED-BIM-FAM()
   #That function will generates three files 23andmetoBED.bed, 23andmetoBED.bim, and 23andmetoBED.fam
   # Step 2 
   ./plink --bfile 23andmetoBED  --export oxford --out output_file
 



23andme to VCF
------------------------

.. code-block:: console

   #1. Convert 23andme to BED-BIM-FAM --> 23andmetoBED-BIM-FAM()
   #That function will generates three files 23andmetoBED.bed, 23andmetoBED.bim, and 23andmetoBED.fam
   # Step 2 
   ./plink --bfile 23andmetoBED --recode vcf --out output_file



23andme to AncestryDNA
------------------------


.. code-block:: console


  
   # Make a directory in which AncestryDNA files will be saved.
   if not os.path.isdir("AncestryDNA"):
      os.mkdir("AncestryDNA")
   _23andmefiles  = os.listdir("./"+input_file)


   #Read files one-by-one
   for files in _23andmefiles:
      # 23andme files are in .txt file format
      if "23andme.txt" in files and "temp" not in files:

         #Check size
         if os.stat("./"+input_file+os.sep+files).st_size == 0:
            continue
         else:
            print(files)
            data = pd.read_csv("./"+input_file+os.sep+files,sep="\t", comment='#',header=None,low_memory=False)
            new = pd.DataFrame()
            new['Rsid'] = data[0].values
            new['Chromosome'] = data[1].values
            new['position'] = data[2].values


            #Split genotype into allele1 and allele2
            new['allele1'] = data[3].str[0]
            new['allele2'] =data[3].str[1]

            #Change chromosome numbers
            new['Chromosome'] = new['Chromosome'].replace(23, 'X')
            new['Chromosome'] = new['Chromosome'].replace(24, 'Y')
            new['Chromosome'] = new['Chromosome'].replace(25, 'XY')
            new['Chromosome'] = new['Chromosome'].replace(26, 'MT')


            #Rename file name
            files = files.replace("23andme","ancestry")
            new.to_csv("./AncestryDNA"+os.sep+files, sep="\t",index=False)



23andme to HAPS-LEGEND-SAMPLE
--------------------------------


.. code-block:: console

   #1. Convert 23andme to BED-BIM-FAM --> 23andmetoBED-BIM-FAM()
   #That function will generates three files 23andmetoBED.bed, 23andmetoBED.bim, and 23andmetoBED.fam
   # Step 2 
   ./plink --bfile 23andmetoBED --recode vcf --out output_file
    
   # Step 3
   bcftools convert output_file.vcf  -h  output_file2