simulate_evaluate

Contents

• simulate_evaluate
  • Overview
  • Command-line usage
  • Examples

Overview

simulate_evaluate is a program within the sortseq_tools package which uses an energy model to calculate the predicted energies of each sequence in a library. A simulated library must be evaluated before simulate_sort can be used.

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

Command-line usage

usage: sortseq simulate_evaluate [-h] [-m {RandomLinear,LinearEmat,Custom}]
                                 [-mp MODELPARAM] [-t {dna,rna,protein}]
                                 [-i I] [-o OUT]

Options:

-m, --modeltype
	Type of Model to use Possible choices: RandomLinear, LinearEmat, Custom
-mp, --modelparam
	Parameters should be entered as a list, with RandomLinear=[LengthofSeq],LinearEmat=[FileName]. If you are using a custom model enter a list of parameters with the first parameter being the python function name (for mymodel.py enter mymodel)
-t=dna, --type=dna
	Undocumented Possible choices: dna, rna, protein
-i=False, --i=False
	Read input from file instead of stdin
-o, --out	Undocumented

Examples

The input table to this function should be a library file. The model type needs to be specified using the -m flag. The file name of the model should be specified after the -mp flag.

Example Input Table:

seq    ct
ACTAG  10
AGGTA  5
...

Example Output Table:

seq    ct     val
ACTAG  10     -1.4
AGGTA  5      -.5
...