simulate_library

Contents

• simulate_library
  • Overview
  • Command-line usage
  • Examples Inputs and outputs

Overview

simulate_library is a program within the sortseq_tools package which creates a library of random mutants from an initial wildtype sequence and mutation rate.

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

Command-line usage

usage: sortseq simulate_library [-h] [-w WTSEQ] [-m MUTRATE] [-n NUMSEQS]
                                [-bp BASEPROB] [-t {dna,rna,protein}] [-o OUT]

Options:

-w, --wtseq	Wild Type Sequence
-m=0.09, --mutrate=0.09
	Mutation Rate, given fractionally. For example enter .1, not 10 percent
-n=100000, --numseqs=100000
	Number of Sequences
-bp, --baseprob
	If you would like to use custom base probabilities, this is the filename of a probability array.
-t=dna, --type=dna
	Undocumented Possible choices: dna, rna, protein
-o, --out	Undocumented

Examples Inputs and outputs

To generate a library of mutated sequences you could use the command:

sortseq simulate_library -w ACAGGGTTAC -n 50000 -m .2

This will output a simulated library of the form:

seq           ct
ACAGGGTTAC    100
ACGGGGTTAC    50
...