AncestryDNA
===========



AncestryDNA to PED-MAP
------------------------


.. code-block:: console

   #1. Convert AncestryDNA files to 23andme --> AncestryDNAto23andme()
   #2. Convert 23andme files to BED-BIM-FAM --> 23andmetoBED-BIM-FAM()
   #That function will generates three files 23andmetoBED.bed, 23andmetoBED.bim, and 23andmetoBED.fam
   # Step 3 
   ./plink --bfile 23andmetoBED --recode vcf --out output_file
    

   
   

AncestryDNA to RAW
------------------------

.. code-block:: console

   #1. Convert AncestryDNA files to 23andme --> AncestryDNAto23andme()
   #2. Convert 23andme files to BED-BIM-FAM --> 23andmetoBED-BIM-FAM()
   #That function will generates three files 23andmetoBED.bed, 23andmetoBED.bim, and 23andmetoBED.fam
   # Step 3 
   ./plink --bfile 23andmetoBED --recodeA --out output_file



AncestryDNA to BED-BIM-FAM
------------------------------


.. code-block:: console

   #1. Convert AncestryDNA files to 23andme --> AncestryDNAto23andme()
   #2. Convert 23andme files to BED-BIM-FAM --> 23andmetoBED-BIM-FAM()
   #That function will generates three files 23andmetoBED.bed, 23andmetoBED.bim, and 23andmetoBED.fam
 



AncestryDNA to GEN-SAMPLE
------------------------------


.. code-block:: console

   #1. Convert AncestryDNA files to 23andme --> AncestryDNAto23andme()
   #2. Convert 23andme files to BED-BIM-FAM --> 23andmetoBED-BIM-FAM()
   #That function will generates three files 23andmetoBED.bed, 23andmetoBED.bim, and 23andmetoBED.fam
   # Step 3 
   ./plink --bfile 23andmetoBED  --export oxford --out output_file
 



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


.. code-block:: console

   #Make a directory in which 23andme files will be saved.
   if not os.path.isdir("23andme"):
      os.mkdir("23andme")
  
   #Read AncestryDNA files from the directory
   _ancestry  = os.listdir('./AncestryDNA')
   for files in _ancestry:
      
      if ".txt" in files and "temp" not in files:
         if os.stat("./AncestryDNA"+os.sep+files).st_size == 0:
         continue
      else:
         data = pd.read_csv("./AncestryDNA"+os.sep+files,sep="\t",skiprows=18)
        
         new = pd.DataFrame()
         new['Rsid'] = data['rsid'].values
         new['Chromosome'] = data['chromosome'].values
         new['position'] = data['position'].values
         
         #Merge genotype data
         new['genotype'] = data['allele2']+ data['allele1']
         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')
         
         files = files.replace("ancestry","23andme")
        
         #Save each file in "23andme" directory
         new.to_csv("./23andme"+os.sep+files, sep="\t",index=False,header=False) 



AncestryDNA to VCF
------------------------


.. code-block:: console

   #1. Convert AncestryDNA files to 23andme --> AncestryDNAto23andme()
   #2. Convert 23andme files to BED-BIM-FAM --> 23andmetoBED-BIM-FAM()
   #That function will generates three files 23andmetoBED.bed, 23andmetoBED.bim, and 23andmetoBED.fam
   # Step 3 
   ./plink --bfile 23andmetoBED --recode vcf --out output_file



AncestryDNA to HAPS-LEGEND-SAMPLE
--------------------------------------


.. code-block:: console

   #1. Convert AncestryDNA files to 23andme --> AncestryDNAto23andme()
   #2. Convert 23andme files to BED-BIM-FAM --> 23andmetoBED-BIM-FAM()
   #That function will generates three files 23andmetoBED.bed, 23andmetoBED.bim, and 23andmetoBED.fam
   # Step 3 
   ./plink --bfile 23andmetoBED --recode vcf --out output_file
    
   # Step 4
   bcftools convert output_file.vcf  -h  output_file2