edmundkorley / text2dna Goto Github PK

We need to further encode the binary representations of ASCII values into the four bases of DNA. We can do this with either of the following methods:

1. Parse two bits of the binary string into A, T, C, or G assigning each of the four permutations of 0 and 1 to A, T, C, or G (e.g. 00=>A, 01=>T, 10=>C, 11=>G)
2. Change our code that takes decimal ASCII values from returning a binary string to returning a base-4 string, and assign each of 0, 1, 2, and 3 to A, T, C, and G (e.g. 0=>A, 1=>T, 2=>C, 3=>G)

We need to further encode the base-4 representations of ASCII values into the four bases of DNA.

Algorithm

1. Assign each of 0, 1, 2, and 3 to A, T, C, and G (e.g. 0=>A, 1=>T, 2=>C, 3=>G)
2. Take an array of strings "**input" where each index points to a string containing a base-4 representation of some ASCII value
3. Create an array of strings "**transformed" that points in each place to a string of A's,T's,C's, and G's representing the base-4 number that lives at the same index in "**input"
4. Return "**transformed"

• Transform command line arguments (treat as strings for now) from char * to int * of corresponding integer ASCII values.
• Transform further to char * array of binary equivalent of ASCII values.
• [TENTATIVE] Merge char * array of binary numbers into single char *. This depends on how the delimiting of characters work in the memories algorithm.
• Read further about how delimiting of characters work in memories algorithm.

The goal would be do the encoding very efficiently in C/C++, given we know the range of ASCII values and can use low-level memory-efficient data structures, then expose functionality as a module in Node/Python.

Since we have an encoder, having a decoder will be useful for testing. We can start it within this project, but it probably makes sense to move this to a separate repo later on.