4. Recipe 4: Itaration on kDataFrame kmers

4.1. Description

1. Create kDataFrame with kmerSize = 21
2. Insert some random kmers with random counts
3. Iterate over kDataFrames kmers and print Kmer and Count
4. Save the result in dictionary

4.2. Implementation

4.2.1. Importing

import kProcessor as kp
import random

4.2.2. Create kmers list with 4 kmers

kmers = ["ATCATACTGATCGATCGATGC", "CGTAACCTATGCTAGCTAGAT", "CTGACTACTCAGAGCTAGCCT","CAATCGCTGATACGATACGTA"]

4.2.3. Create an empty kDataFrame

kf2 = kp.kDataFrameMQF(21)

4.2.4. Insert all kmers using a for loop

for kmer in kmers:
    random_count = random.randint(1,100) # generate random count between 1 and 100
    print("Inserting kmer: %s with count %d" % (kmer, random_count))
    kf2.insert(kmer, random_count)

Inserting kmer: ATCATACTGATCGATCGATGC with count 99
Inserting kmer: CGTAACCTATGCTAGCTAGAT with count 22
Inserting kmer: CTGACTACTCAGAGCTAGCCT with count 35
Inserting kmer: CAATCGCTGATACGATACGTA with count 82

4.2.5. Iterate over all kmers and print their count and save them in a dictionary

# Create empty dictionary
kf2_data = {}

# create iterator with the first position in the kDataFrame
it = kf2.begin()

while(it != kf2.end()):

    # Get the kmer string
    kmer = it.getKmer()

    # Get the kmer count
    count = it.getCount()

    # Print the data
    print("retrieved kmer: %s with count: %d" % (kmer, count))

    # Save data in a dictionary
    kf2_data[kmer] = count

    it.next() # Extremely Important!

retrieved kmer: AGGCTAGCTCTGAGTAGTCAG with count: 35
retrieved kmer: ATCTAGCTAGCATAGGTTACG with count: 22
retrieved kmer: ATCATACTGATCGATCGATGC with count: 99
retrieved kmer: CAATCGCTGATACGATACGTA with count: 82

4.2.6. Dump the dictionary data to a file

with open("kf2_data.tsv", 'w') as kf2:
    kf2.write("kmer\tcount\n")
    for kmer,count in kf2_data.items():
        kf2.write("%s\t%d\n" % (kmer, count))

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4.3. Complete Script

import kProcessor as kp
import random

kmers = ["ATCATACTGATCGATCGATGC", "CGTAACCTATGCTAGCTAGAT", "CTGACTACTCAGAGCTAGCCT","CAATCGCTGATACGATACGTA"]

kf2 = kp.kDataFrameMQF(21)

for kmer in kmers:
    random_count = random.randint(1,100) # generate random count between 1 and 100
    print("Inserting kmer: %s with count %d" % (kmer, random_count))
    kf2.insert(kmer, random_count)

# Create empty dictionary
kf2_data = {}

# create iterator with the first position in the kDataFrame
it = kf2.begin()

while(it != kf2.end()):

    # Get the kmer string
    kmer = it.getKmer()

    # Get the kmer count
    count = it.getCount()

    # Print the data
    print("retrieved kmer: %s with count: %d" % (kmer, count))

    # Save data in a dictionary
    kf2_data[kmer] = count

    it.next() # Extremely Important!


with open("kf2_data.tsv", 'w') as kf2:
    kf2.write("kmer\tcount\n")
    for kmer,count in kf2_data.items():
        kf2.write("%s\t%d\n" % (kmer, count))

4.4. Output CSV

%%bash
cat kf2_data.tsv

kmer    count
AGGCTAGCTCTGAGTAGTCAG   35
ATCTAGCTAGCATAGGTTACG   22
ATCATACTGATCGATCGATGC   99
CAATCGCTGATACGATACGTA   82