How To Install python3-pychopper on Ubuntu

Posted on April 1, 2023 (Last modified on May 20, 2023 )

3 minutes • 623 words

Introduction

In this tutorial we learn how to install python3-pychopper on Ubuntu.

What is `python3-pychopper`

python3-pychopper is:

Pychopper v2 is a Python module to identify, orient and trim full-length Nanopore cDNA reads. It is also able to rescue fused reads and provides the script ‘cdna_classifier.py’. The general approach of Pychopper v2 is the following:

Pychopper first identifies alignment hits of the primers across the length of the sequence. The default method for doing this is using nhmmscan with the pre-trained strand specific profile HMMs, included with the package. Alternatively, one can use the edlib backend, which uses a combination of global and local alignment to identify the primers within the read.
After identifying the primer hits by either of the backends, the reads are divided into segments defined by two consecutive primer hits. The score of a segment is its length if the configuration of the flanking primer hits is valid (such as SPP,-VNP for forward reads) or zero otherwise.
The segments are assigned to rescued reads using a dynamic programming algorithm maximizing the sum of used segment scores (hence the amount of rescued bases). A crucial observation about the algorithm is that if a segment is included as a rescued read, then the next segment must be excluded as one of the primer hits defining it was “used up” by the previous segment. This put constraints on the dynamic programming graph. The arrows in read define the optimal path for rescuing two fused reads with the a total score of l1 + l3.

A crucial parameter of Pychopper v2 is -q, which determines the stringency of primer alignment (E-value in the case of the pHMM backend). This can be explicitly specified by the user, however by default it is optimized on a random sample of input reads to produce the maximum number of classified reads.

There are three methods to install python3-pychopper on Ubuntu. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.

Install python3-pychopper Using apt-get

Update apt database with apt-get using the following command.

sudo apt-get update

After updating apt database, We can install python3-pychopper using apt-get by running the following command:

sudo apt-get -y install python3-pychopper

Install python3-pychopper Using apt

Update apt database with apt using the following command.

sudo apt update

After updating apt database, We can install python3-pychopper using apt by running the following command:

sudo apt -y install python3-pychopper

Install python3-pychopper Using aptitude

If you want to follow this method, you might need to install aptitude first since aptitude is usually not installed by default on Ubuntu. Update apt database with aptitude using the following command.

sudo aptitude update

After updating apt database, We can install python3-pychopper using aptitude by running the following command:

sudo aptitude -y install python3-pychopper

How To Uninstall python3-pychopper on Ubuntu

To uninstall only the python3-pychopper package we can use the following command:

sudo apt-get remove python3-pychopper

Uninstall python3-pychopper And Its Dependencies

To uninstall python3-pychopper and its dependencies that are no longer needed by Ubuntu, we can use the command below:

sudo apt-get -y autoremove python3-pychopper

Remove python3-pychopper Configurations and Data

To remove python3-pychopper configuration and data from Ubuntu we can use the following command:

sudo apt-get -y purge python3-pychopper

Remove python3-pychopper configuration, data, and all of its dependencies

We can use the following command to remove python3-pychopper configurations, data and all of its dependencies, we can use the following command:

sudo apt-get -y autoremove --purge python3-pychopper

Dependencies

python3-pychopper have the following dependencies:

References

python3-pychopper website

Summary

In this tutorial we learn how to install python3-pychopper package on Ubuntu using different package management tools: apt, apt-get and aptitude.