The following functions read the contents of 23andMe genotypes

In [1]: 
def GetAlleles(filename):
    """ Read the alleles in filename """ 
    allele = dict()
    with open(filename, 'rb') as tsvfile:
        for row in tsvfile:
            line = row[:row.find('#')].strip(' \r\n')   # strip comments and line endings
            if (len(line) == 0):                        # skip empty lines
                continue
            field = line.split('\t')
            if (len(field) != 4):                       # print error for lines missing fields
                print "ERROR: %s" % str(field)
                continue
            allele[field[0]] = field[3]
    return allele

def GetCoordinates(filename):
    """ Read the chromosome and positions of alleles in filename """ 
    chrPos = dict()
    with open(filename, 'rb') as tsvfile:
        for row in tsvfile:
            line = row[:row.find('#')].strip(' \r\n')   # strip comments and line endings
            if (len(line) == 0):                        # skip empty lines
                continue
            field = line.split('\t')
            if (len(field) != 4):                       # print error for lines missing fields
                print "ERROR: %s" % str(field)
                continue
            chrPos[field[0]] = (field[1], int(field[2]))
    return chrPos

Now let's test it on an example by printing 20 random alleles

In [20]: 
genomePosition = GetCoordinates("genomeA.txt")
allelesA = GetAlleles("genomeA.txt")

N = 0
for gId, gType in allelesA.iteritems():
    chromo, pos = genomePosition[gId]
    print "%15s, %2s, %10d, %2s" % (gId, chromo, pos, gType)
    N += 1
    if (N == 20):
        break
print "alleles = ", len(allelesA)

      rs7299872, 12,   55233823, AG
     rs11866519, 16,   87500210, AG
      rs1898321,  9,   86682315, TT
      rs7060463,  X,   68757767,  T
      rs6035331, 20,    1994112, CT
       rs572753,  2,   45072029, GT
      rs2176056,  2,  147722211, AG
      rs2176051, 18,   27039561, TT
     rs17597441, 19,   32605173, GG
     rs16913433, 11,   24891999, AA
     rs16913434,  9,  111448624, TT
      rs6873488,  5,  153597371, GG
       rs386161,  5,   57916579, GG
     rs10737544,  1,  168891735, AG
      rs7789112,  7,   78125648, GG
     rs12795043, 11,  125970673, GG
     rs12795042, 11,  133658168, CC
      rs1544914,  2,   49654260, TT
     rs11637530, 15,   61366854, CT
     rs17069507,  3,   63924956, AA
alleles =  960613

Next well add functions to get simple allele stats.

In [7]: 
def CountGenotypes(genotypeDict):
    """ Counts the distinct genotypes in filename """ 
    typecount = dict()
    for gId, gType in genotypeDict.iteritems():
        typecount[gType] = typecount.get(gType, 0) + 1 
    return typecount

def ClassifyTypes(typeCountDict):
    """ Combine genotype counts into classes """
    sHom, sHet, sHem = 0, 0, 0
    iHom, iHet, iHem = 0, 0, 0
    nCnt = 0
    for gtype, count in typeCountDict.iteritems():
        if (len(gtype) == 1):
            if (gtype in "ACGT"):
                sHem += count
            elif (gtype in "ID"):
                iHem += count
            else:
                nCnt += count
        else:
            if (gtype[0] == gtype[1]):
                if (gtype[0] in "ACGT"):
                    sHom += count
                elif (gtype[0] in "ID"):
                    iHom += count
                else:
                    nCnt += count
            else:
                if ((gtype[0] in "ACGT") and (gtype[1] in "ACGT")):
                    sHet += count
                elif ((gtype[0] in "ID") and (gtype[1] in "ID")):
                    iHet += count
                else:
                    nCnt += count
    return (sHom, sHet, sHem, iHom, iHet, iHem, nCnt)

Let's test them too.

In [10]: 
aTypes = CountGenotypes(allelesA)
print "Allele types =", aTypes

aClass = ClassifyTypes(aTypes)
print
print "Homozygous SNP: %d" % aClass[0]
print "Heterozygous SNP: %d" % aClass[1]
print "Hemizygous SNP: %d" % aClass[2]
print "Homozygous indel: %d" % aClass[3]
print "Heterozygous indel: %d" % aClass[4]
print "Hemizygous indel: %d" % aClass[5]
print "No-calls: %d" % aClass[6]

Allele types = {'AA': 146024, 'A': 6582, 'AC': 25290, 'GT': 25300, 'I': 113, 'G': 7147, 'AG': 109096, 'DI': 28, 'CC': 173040, 'TT': 146257, 'CG': 1001, 'C': 7199, 'D': 34, 'GG': 172136, '--': 24139, 'II': 666, 'T': 6500, 'AT': 593, 'DD': 148, 'CT': 109320}

Homozygous SNP: 637457
Heterozygous SNP: 270600
Hemizygous SNP: 27428
Homozygous indel: 814
Heterozygous indel: 28
Hemizygous indel: 147
No-calls: 24139

Consider the following pedigree given in class: A pedigree of genotypes

In [29]: 
allelesD = GetAlleles("genomeD.txt")
allelesE = GetAlleles("genomeE.txt")
allelesG = GetAlleles("genomeG.txt")

FixTotal, FixError = 0, 0
HetTotal, HetError = 0, 0
for gId in allelesG.iterkeys():
    momsAllele = allelesD[gId]
    popsAllele = allelesE[gId]
    kidsAllele = allelesG[gId]
    if (momsAllele == '--') or (popsAllele == '--') or (kidsAllele == '--'):
        continue
    if (len(kidsAllele) == 2):
        if ((momsAllele[0] == momsAllele[-1]) and (popsAllele[0] == popsAllele[-1])):
            if (momsAllele[0] == popsAllele[0]):
                FixTotal += 1
                if (kidsAllele[0] != kidsAllele[-1]):
                    FixError += 1
                elif (kidsAllele[0] != momsAllele[0]):
                    print momsAllele, popsAllele, kidsAllele
                    FixError += 1
            else:
                HetTotal += 1
                if (kidsAllele[0] == kidsAllele[-1]):
                    HetError += 1
                elif ((kidsAllele[0] not in momsAllele+popsAllele) or (kidsAllele[-1] not in momsAllele+popsAllele)):
                    print momsAllele, popsAllele, kidsAllele
                    HetError += 1
print "Fixed Alleles = %d, Trio Errors = %d, Error %% = %2.4f" % (FixTotal, FixError, (100.0*FixError)/FixTotal)
print "Opposite Alleles = %d, Trio Errors = %d, Error %% = %2.4f" % (HetTotal, HetError, (100.0*HetError)/HetTotal)

AA AA GG
TT TT AA
TT TT CC
GG GG AA
Fixed Alleles = 429611, Trio Errors = 45, Error % = 0.0105
Opposite Alleles = 53828, Trio Errors = 141, Error % = 0.2619
In [22]: 
HetHetHetCount = 0
for gId in allelesG.iterkeys():
    momsAllele = allelesD[gId]
    if (momsAllele[0] == momsAllele[-1]):
        continue
    popsAllele = allelesE[gId]
    if (popsAllele[0] == popsAllele[-1]):
        continue
    kidsAllele = allelesG[gId]
    if (kidsAllele[0] != kidsAllele[-1]):
        HetHetHetCount += 1
print HetHetHetCount, (100.0*HetHetHetCount)/len(allelesG)

52507 5.46637585954
In []: