3. Recipe 3: Play with kDataFrame¶

3.1. Description¶

In Recipe 1 we saved a kDataFrame to the disk with the file name kf1.mqf

Create kDataFrame with kmerSize = 21
Insert some random kmers with random counts
Query by each kmer and check the count
Insert a pre-exist kmer and check it’s count

3.2. Implementation¶

3.2.1. Importing¶

[1]:

import kProcessor as kp

3.2.2. Kmers List¶

[2]:

kmers = ["CTGACTACTCAGAGCTAGCCT", "CGTAACCTATGCTAGCTAGAT"]

3.2.3. Instantiate an object from the class kDataFrameMQF¶

[3]:

kf = kp.kDataFrameMQF(21) # Empty kDataFrame

3.2.4. Print the size of the kDataFrame¶

[4]:

print(f"kf size: {kf.size()}")

kf size: 0

3.3. Insert the first kmer and set count to 1 & the second kmer with count 10¶

[5]:

print("Inserting 2 kmers")
kf.insert(kmers[0], 1)
kf.insert(kmers[1], 10)

Inserting 2 kmers

[5]:

True

3.3.1. Print the size of the kDataFrame & counts of kmer1 and kmer2¶

[6]:

print("kf size: %d" % kf.size())

# Print the first kmer count
print("Kmer1 Count: %d" % kf.count(kmers[0]))
print("Kmer2 Count: %d" % kf.count(kmers[1]))

kf size: 2
Kmer1 Count: 1
Kmer2 Count: 10

3.3.2. Insert a duplicate kmer without count¶

[7]:

print("[*] Inserting kmer 1 again")
kf.insert(kmers[0])

[*] Inserting kmer 1 again

[7]:

True

3.3.3. Print the first kmer count again¶

[8]:

print("Kmer1 Count: %d" % kf.count(kmers[0]))

Kmer1 Count: 2

3.3.4. Erase kmer1 from the kDataFrame¶

[9]:

print("[*] Erasing kmer1")
kf.erase(kmers[0])

[*] Erasing kmer1

[9]:

True

3.3.5. Print the first kmer count again and the kDataframe Size¶

[10]:

print("Kmer1 Count: %d" % kf.count(kmers[0]))
print("kf size: %d" % kf.size())

Kmer1 Count: 0
kf size: 1

3.4. Complete Script¶

import kProcessor as kp

kmers = ["CTGACTACTCAGAGCTAGCCT", "CGTAACCTATGCTAGCTAGAT"]
kf = kp.kDataFrameMQF(21) # Empty kDataFrame
print(f"kf size: {kf.size()}")

print("Inserting 2 kmers")
kf.insert(kmers[0], 1)
kf.insert(kmers[1], 10)

print("kf size: %d" % kf.size())

# Print the first kmer count
print("Kmer1 Count: %d" % kf.count(kmers[0]))
print("Kmer2 Count: %d" % kf.count(kmers[1]))

print("[*] Inserting kmer 1 again")
kf.insert(kmers[0])

print("Kmer1 Count: %d" % kf.count(kmers[0]))


print("[*] Erasing kmer1")
kf.erase(kmers[0])

print("Kmer1 Count: %d" % kf.count(kmers[0]))
print("kf size: %d" % kf.size())

print("Kmer1 Count: %d" % kf.count(kmers[0]))
print("kf size: %d" % kf.size())