chameleontools 0.3.0

A Stealth-based pipeline that optimizes plasmids for bacterial transformations in non-model organisms.

Chameleon

UCSC TABI presents project Chameleon, a pipeline and software package that optimizes plasmids for bacterial transformation efficiency in non-model organisms.

Description

Chameleon is a software project written for UCSC TABI as a submission for the Best Software award for iGEM 2023. For more information on anything here, visit our team wiki

pstealth is a software pipeline included in Chameleon built around Stealth. Stealth is a bioinformatics tool written by our PI David L. Bernick here a UCSC. Stealth statistically finds and reports underrepresented kmer motifs within a genome. The original version of Stealth can be found here.

Chameleon is published as a python package to the Python Package Index (PyPI) under the package chameleontools. Find the PyPI page for the project here.

Installation

Installation steps are tailored to Mac/Unix-based operating systems. For instruction for Windows, skip to Windows OS

MacOS/Linux (Ubuntu 20.04)

Chameleon can be installed under the Python package chameleontools. Installation is made simple with the pip python package installer.

The pip installer should be automatically installed with most Python distributions. Check if you have properly installed python and pip installer, the output should look similar

usr:~$ python --version
Python 3.x.x
usr:~$ python -m pip --version
pip X.Y.Z from /<path>/<to>/<your>/pip (python 3.x.x)  

If your output looks similar, you can skip to Installing Chameleon.

Installing Python / pip

Follow this section if your output did not look the same as above.

If you do not have Python, get started by installing Python 3.10 or above from python.org, or through a distriubtion such as anaconda.

If you do not have a working pip installer, follow steps found here.

Validate you have a working Python / pip installer by running

usr:~$ python --version
Python 3.x.x
usr:~$ python -m pip --version
pip X.Y.Z from /<path>/<to>/<your>/pip (python 3.x.x)  

and making sure the output looks similar.

Installing Chameleon

Installing Chameleon is simple as running the command

usr:~$ pip install chameleontools
# OR
usr:~$ python -m pip install chameleontools

with a valid pip installer to install the chameleontools package from the Python Package Index (PyPI)

Windows Installation

Installation on Windows requires aPath environment variable be set for pstealth to be run as a CLI tool. Firstly, make sure Python 3.10+ is installed from python.org or other distribution.

Validate that Python and a valid pip installer are installed using the command in the command prompt or Windows powershell

C:\usr>python --version
Python 3.x.x
C:\usr>python -m pip --version 
pip X.Y.Z from C:\<path>\<to>\<your>\pip (python 3.x.x)

Install chameleontools with the command

C:\usr>python -m pip install chameleontools

If running pstealth gives an output that looks like the following

C:\usr>pstealth -h
'pstealth' is not recognized as an internal or external command,
operable program or batch file.
C:\usr>

continue to the following section. If pstealth runs normally (prints usage information), chameleontools is properly installed and you can ignore the following section.

Adding to Path

You must add the Python Scripts directory to your Path environment variables. This can be done by navigating to your Scripts directory where pstealth.exe is located. This is most likely under the path C:\Users\<USER>\AppData\Local\Programs\Python\Python3<x>\Scripts where <USER> is the local Windows user profile and Python3<x> represents the version of your Python installation (eg. Python312). Once naviagted to your Scripts directory, save the filepath.

In the Windows search (hitting the windows button), type and enter run and then enter sysdm.cpl into the dialog box that pops up. This opens up a new window titled System Properties. From there navigate to the Advance tab and select Environment Variables. From there, scroll until you see a Path variable, select, and click Edit. In the Edit Environment Variable window, select New and paste the filepath you saved into the new text box.

If you do not see a Path variable, simply select New in the Environment Variables window and create a new variable named Path with the value of your saved file path.

Once done, pstealth should be able to be used from the commandline as intended.

Usage

Plasmid-Stealth (pstealth) CLI tool

Once installed, the pipeline can be easily run with the command pstealth

# usage
pstealth --genome (-g) <genome infile> --plasmid (-p) <plasmid infile> --outfile -o [outfile | default: stdout] -[zPMmrs]
            Optional Args:
                --zScore (-z) -> [zscore cutoff value | default: -4]
                --pseudo (-P) [pseudo-count value | default: 0]
                --max (-M) [maximum motif size | default: 8]
                --min (-m) [minimum motif size | default: 1]
                --palindrome (-r) [Remove RC palindromes only | default: off]
                --silent (-s) [Hide report message | default: show]

The pstealth command takes two required arguments --plasmid (-p) and --genome (-g). --plasmid is the annotated plasmid which you wish to Stealth optimize in GenBank format (.gb/.gbk) --genome is the genomic sequence of the species you wish transform your plasmid into in GenBank or FastA format (.gb/.gbk || .fasta/.fa)

An example usage is as follows

usr:~$ pstealth -g M_aeruginosa.gb -p pSPDY.gb -o pSPDY_stealth.gb -r 
...
usr:~$ cat pSPDY_stealth.gb | head
LOCUS       pSPDY                   8825 bp    DNA     circular UNA 18-AUG-2023
DEFINITION  synthetic circular DNA.
ACCESSION
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct.
FEATURES             Location/Qualifiers
     misc_feature    1

The above example optimizes plasmid pSPDY.gb for transformation into species M_aeruginosa.gb, removing only reverse-complement palindrome motifs identified with StealthV0. The modifed plasmid is saved to a new file pSPDY_stealth.gb, keeping all the same annotations, only changing the plasmid sequence to remove underrepresented motifs in coding regions.

chameleontools Module

Development of chameleontools started when we wrote software to process the Stealth output of M.aeruginosa and realized we could write a pipeline to automate what was a manual and time consuming process. This software ultimately became what is now the StealthParser module.

We recognized the usefulness of having each submodule perform their own specific tasks and have written the chameleontools package in a way that reflects that ideal.

To import chameleontools as a Python module, simplly import it as follows

import chameleontools.<submodule>

The submodules supported for importing include

import chameleontools.ChromatoSeq # Motif removal from sequence
import chameleontools.CodonAnalyzer # Codon Analysis of CDS
import chameleontools.FastAreader 
import chameleontools.ORFfinder # Very basic ORF finder
import chameleontools.SeqParser # Plasmid and Genome input handling
import chameleontools.Stealth # Stealth analysis
import chameleontools.StealthParser # Stealth output parser

Visit each submodule's folder for detailed README documentation.

Contributing

Chameleon was created for the 2023 iGEM competition and will not be maintained on this repository after the conclusion of this year's iGEM cycle.

This software is published under the MIT license. Feel free to use any and all code provided by the project in any way and for any purpose.

Authors and acknowledgment

Stealth was written by our PI David L. Bernick at UC Santa Cruz who advised the development of the pstealth pipeline (contact: [e-mail])

Chameleon was written and contributed to by

• Tyler Gaw (contact: [e-mail])
• Allison Jaballas (contact: [e-mail])
• James Larbaleister (contact: [e-mail])

Special thanks to Reto Stamm (contact: [e-mail] | github) for guidance in developing and publishing a packge to the Python Package Index