How to Install and Uninstall python3-pychopper Package on Ubuntu 21.10 (Impish Indri)

Last updated: May 18,2024

1. Install "python3-pychopper" package

This is a short guide on how to install python3-pychopper on Ubuntu 21.10 (Impish Indri)


    
        
            $
        

        
            
                sudo apt update
            
                    
    
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            $
        

        
            
                sudo apt install
            
                        
                python3-pychopper
            
                    
    
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2. Uninstall "python3-pychopper" package

Please follow the instructions below to uninstall python3-pychopper on Ubuntu 21.10 (Impish Indri):


    
        
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                sudo apt remove
            
                        
                python3-pychopper
            
                    
    
    Copied


    
        
            $
        

        
            
                sudo apt autoclean && sudo apt autoremove
            
                    
    
    Copied

3. Information about the python3-pychopper package on Ubuntu 21.10 (Impish Indri)

Package: python3-pychopper
Architecture: all
Version: 2.5.0-1
Priority: optional
Section: universe/python
Source: pychopper
Origin: Ubuntu
Maintainer: Ubuntu Developers
Original-Maintainer: Debian Med Packaging Team
Bugs: https://bugs.launchpad.net/ubuntu/+filebug
Installed-Size: 345
Depends: python3-edlib, python3-matplotlib, python3-pandas, python3-parasail, python3-pytest, python3-seaborn, python3-six, python3-sphinx, python3-sphinx-rtd-theme, python3-tqdm, python3:any
Filename: pool/universe/p/pychopper/python3-pychopper_2.5.0-1_all.deb
Size: 120912
MD5sum: cda4cc502017d4eb771cb9480f98b759
SHA1: b5d98784fe636e580286c40ec1572ca9a187b883
SHA256: c49058f4de20b8f1a11d43ab0c9bd034b88ef4ab641cc577654a591437249479
SHA512: 8086d06d35a0b0e67945d70037d60c51ef8a5de4685417b2230d73a6e9cabfcf212608371ca6609c2b4fa28601720de254b08d9dbfa1c0b971009e6120cb869f
Homepage: https://github.com/nanoporetech/pychopper
Description-en: identify, orient and trim full-length Nanopore cDNA reads
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.
Description-md5: c82f4d6ea954d4a2adb49d0cbebcb404