fromto_mutrate

Contents

• fromto_mutrate
  • Overview
  • Command-line usage
  • Example Input and Output

Overview

fromto_mutrate is a program which characterizes the biases in mutations within your library. Specifically, given a wild type sequence. It calculates the probability of occurance of all bases.

After you install `sortseq_tools`_, this program will be available to run at the command line.

Command-line usage

usage: sortseq fromto_mutrate [-h] [-t {dna,rna,protein}] [-o OUT]

Options:

-t=dna, --type=dna
	Undocumented Possible choices: dna, rna, protein
-o, --out	Undocumented

Example Input and Output

An unsorted library (or a sorted library with an unsorted counts bin ‘’ct’‘) must be used as input.

Example Input Table:

seq    ct
ACA    9
GGG    7
...

Example Output Table:

wt   obs   mut
A    A     .97
A    C     .01
A    G     .01
...

The final column ‘’mut’’ gives the probability that we will see the base in the column ‘’obs’’ given the wt base is what is shown in the column ‘’wt’‘.

The analysis could be performed using the example command:

sortseq fromto_mutrate -i unsorted_lib.txt -o my_mutrates.txt