Given a string $$s$$, its $$k$$-mer composition¹ composition($$k$$, $$s$$) is the collection of all $$k$$-mer substrings of $$s$$ (including repeated $$k$$-mers). For example,

>>> composition(3, 'TATGGGGTGC')
['ATG', 'GGG', 'GGG', 'GGT', 'GTG', 'TAT', 'TGC', 'TGG']

Note that we have listed $$k$$-mers in lexicographic order² (i.e., how they would appear in a dictionary) rather than in the order of their appearance in TATGGGGTGC. We have done this because the correct ordering of the reads is unknown when they are generated.

Assignment

Write a function composition that takes three arguments: i) an integer $$k \in \mathbb{N_0}$$, ii) the location of a FASTA file containing a DNA string $$s$$ and iii) another file location. The function must generate the $$k$$-mer composition of strings $$s$$, and write the lexicographically ordered $$k$$-mers in FASTA format to the file whose location is passed as the third argument.

Example

In the following interactive session, we assume the FASTA files data01.fna³ and output01.fna⁴ to be located in the current directory.

>>> composition(5, 'data01.fna', 'output01.fna')
>>> print(open('output01.fna').read().rstrip())
>seq01
AATCC
>seq02
ATCCA
>seq03
CAATC
>seq04
CCAAC
>seq05
TCCAA