kadhirvelm / dnacode

Code that allows users to manipulate DNA sequences in different ways

PySeqSimulator

Use '--calc fasta.fasta' to create a random sequence based on fasta.fasta Or Use '--load params' to create a random sequence based on the parameters in params Follow either command above with '--save file' to save the logistics data to file.

ReverseCompliment

Run it with a fasta file and it'll write the reverse compliment to the terminal.

InformationContent

Run it with a Stockholm formatted file as its input and it'll spit out the top ten lowest Shannon entropy columns, and the top fifty mutual information columns.

Pairwise Alignment:

Run it with a similarity matrix as the first argument and a sequence file as the second to get the first two sequences inside the sequence file aligned and printed to the terminal.

Crispi:

Run it with any fasta file and it'll create an output.txt with the best CRISPR/Cas9 NGG sites present in the file.'