mpa.ProfileMut

Overview

It is often useful to compute the mutation rate within a set of sequences, e.g., in order to validate the composition of a library. This can be accomplished using the profile mut class as follows:

Usage

>>> import mpathic as mpa
>>> mpa.ProfileMut(dataset_df = valid_dataset)

Example Input:

ct                     seq

259  TAATGTGAGTTAGCTCACTCAT
41  TAAAGTGAGTTAGCTCACTCAT
36  TAATGTGAGTAAGCTCACTCAT
35  TAGTGTGAGTTAGCTCACTCAT
34  TAATGTTAGTTAGCTCACTCAT
34  TTATGTGAGTTAGCTCACTCAT
...

Example Output:

    pos wt      mut

0     0  T  0.23819
1     1  A  0.24141
2     2  A  0.24118
3     3  T  0.24016
4     4  G  0.24093
5     5  T  0.24001
...

Class Details

class profile_mut.ProfileMut(**kwargs)

Parameters:

dataset_df: (pandas dataframe)

Input data frame containing a valid dataset.

bin: (int)

A bin number specifying which counts to use

start: (int)

An integer specifying the sequence start position

end: (int)

An integer specifying the sequence end position

err: (boolean)

If true, include error estimates in computed mutual information

Returns:

mut_df: (pandas data frame)

A pandas dataframe containing results.