predictiveinfo

Contents

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

Overview

predictiveinfo is a program within the sortseq_tools package which computes the mutual information between a linear energy matrix model and a data set. Models which are closer to reality will have a higher mutual information value.

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

Command-line usage

usage: sortseq predictiveinfo [-h] [-ds DATASET]
                              [-expt {None,sortseq,selex,dms,mpra}] [-s START]
                              [-e END] [-m M] [-o OUT]

Options:

-ds, --dataset	Undocumented
-expt, --exptype
	Undocumented Possible choices: None, sortseq, selex, dms, mpra
-s=0, --start=0
	Position to start your analyzed region
-e, --end	Position to end your analyzed region
-m, --m	Model file, otherwise input through the standard input.
-o, --out	Undocumented

Example Input and Output

The input table should be a sorted library data set (the model should be specified after the -m flag). You should use the –start and –end flags to specify the region in the data set that the model corresponds to.

Example Input Table:

seq    ct_0    ct_1  ...
AGTT   20      13
CCTA   35      40
...

Example Output Table:

info
.94

Example command to run the analysis:

sortseq predictive info -i my_dataset.txt -m my_linear_matrix_model.txt -s 5 -e 20