OpenRDP
OpenRDP is an open-source re-implementation of the RDP recombination detection program.
RDP is a widely popular program for detecting recombination in genetic sequences - however, it has only been available as Windows binaries
(These binaries are not compatible with Windows 11).
The developers of RDP, specifically Darren Martin, kindly provided the source code for the most recent version (RDP5) and permission to modify and redistribute this code.
This program runs a suite of methods to detect recombination events by comparing a nucleotide sequence to other sequences in a multiple alignment.
We have re-implemented most of this code in the Python programming language, with the exception of some of the standalone third-party binaries (3Seq and GENECONV).
3Seq is released under the Creative Commons license (CC BY-NC-SA 4.0), which restricts commerical use.
Similarly, GENECONV is licensed for academic use and distribution, but commercial use is restricted.
For your convenience, we package these binaries along with their respective licenses.
Dependencies
- Python 3 (tested on version 3.8.10)
numpy version 1.17.4 or laterscipy version 1.5.0 or laterh5py version 3.8.0 or later
Installation
- Clone the OpenRDP repository:
git clone https://github.com/PoonLab/OpenRDP
If you do not have git installed, you can download a release.
- Switch into the package directory (
cd OpenRDP) and run the installation script using either:
sudo python3 setup.py install
if you have super-user privileges on the computer, or:
python3 setup.py install --user
to do a local (single user) install.
Usage
Command-line interface (CLI)
art@Wernstrom OpenRDP % openrdp -h
usage: openrdp [-h] [-o OUTFILE] [-c CFG] [-m [...]] [-q] infile
An open source implementation of RDP5.
positional arguments:
infile File containing sequence alignment (FASTA or CLUSTAL) format
options:
-h, --help show this help message and exit
-o OUTFILE, --outfile OUTFILE
Path to write CSV output
-c CFG, --cfg CFG Path to file that contains parameters. Defaults to
default.ini.
-m [ ...], --methods [ ...]
Space-delimited list of recombination methods to run.
Permitted values are: {geneconv bootscan maxchi siscan
chimaera threeseq rdp}. All methods are run if not specified.
-q, --quiet Hide progress messages
The simplest command will run all seven recombination detection methods under the default settings, and prints the results to the console:
You can specify a different configuration file using the -c flag. For example:
art@Wernstrom OpenRDP % openrdp -c tests/test_cfg.ini tests/test_neisseria.fasta
Loading configuration from openrdp/tests/test_cfg.ini
Starting 3Seq Analysis
Finished 3Seq Analysis
Starting GENECONV Analysis
Finished GENECONV Analysis
Setting up bootscan analysis...
Starting Scanning Phase of Bootscan/Recscan
Finished Scanning Phase of Bootscan/Recscan
Setting up maxchi analysis...
Setting up siscan analysis...
Setting up chimaera analysis...
Setting up rdp analysis...
Scanning triplet 1 / 4
Scanning triplet 0 / 4
Scanning triplet 2 / 4
Scanning triplet 3 / 4
Scanning triplet 1 / 4
Scanning triplet 2 / 4
Scanning triplet 3 / 4
Scanning triplet 4 / 4
Method Start End Recombinant Parent1 Parent2 Pvalue
------------------------------------------------------------------------
Geneconv 1 204 X64866 X64869 - 2.00E-05
Geneconv 151 195 X64860 X64869 - 2.10E-03
Geneconv 203 507 X64860 X64866 - 8.29E-03
Geneconv 539 759 X64860 X64866 - 1.54E-01
Geneconv 151 193 X64873 - - 2.20E-02
Geneconv 56 170 X64860 - - 2.73E-02
Bootscan 760 765 X64873 X64860 X64866 6.51E-02
MaxChi 439 482 X64860 X64866 X64869 4.04E-02
MaxChi 475 518 X64860 X64866 X64873 4.04E-02
MaxChi 475 518 X64860 X64869 X64873 4.04E-02
Siscan 2 45 X64860 X64866 X64869 7.64E-01
Siscan 2 45 X64860 X64866 X64873 7.49E-01
Siscan 2 45 X64860 X64869 X64873 7.64E-01
Siscan 2 45 X64866 X64869 X64873 7.65E-01
Chimaera 198 241 X64860 X64866 X64869 2.05E-02
Chimaera 179 265 X64866 X64869 X64873 4.70E-03
Chimaera 170 213 X64873 X64860 X64869 1.81E-03
3Seq 202 787 X64869 X64860 X64866 5.98E-10
3Seq 181 787 X64866 X64869 X64873 5.29E-06
RDP 6 504 X64860 X64866 X64869 6.87E-07
RDP 6 496 X64860 X64866 X64873 3.05E-02
RDP 6 479 X64860 X64869 X64873 3.40E-02
RDP 6 18 X64866 X64869 X64873 2.36E+01
You can also provide a parental reference sequence using the -r flag. For example:
(venv) sandeep@Jesry:~/OpenRDP$ openrdp -c tests/test_cfg.ini tests/short.fasta -r tests/short_ref.fasta
Loading configuration from tests/test_cfg.ini
Starting 3Seq Analysis
Finished 3Seq Analysis
Starting GENECONV Analysis
Finished GENECONV Analysis
Setting up bootscan analysis...
Starting Scanning Phase of Bootscan/Recscan
Finished Scanning Phase of Bootscan/Recscan
Setting up maxchi analysis...
Invalid option for 'win_size'.
Using default value (200) instead.
Setting up siscan analysis...
Invalid option for 'win_size'.
Using default value (200) instead.
Setting up chimaera analysis...
Invalid option for 'win_size'.
Using default value (200) instead.
Setting up rdp analysis...
Scanning triplet 1 / 15
Scanning triplet 3 / 15
Scanning triplet 2 / 15
Scanning triplet 4 / 15
Scanning triplet 5 / 15
Scanning triplet 7 / 15
Scanning triplet 6 / 15
Scanning triplet 8 / 15
Scanning triplet 9 / 15
Scanning triplet 10 / 15
Scanning triplet 11 / 15
Scanning triplet 13 / 15
Scanning triplet 12 / 15
Scanning triplet 14 / 15
Scanning triplet 15 / 15
Scanning triplet 1 / 15
Scanning triplet 2 / 15
Scanning triplet 3 / 15
Scanning triplet 4 / 15
Scanning triplet 5 / 15
Scanning triplet 6 / 15
Scanning triplet 7 / 15
Scanning triplet 8 / 15
Scanning triplet 9 / 15
Scanning triplet 10 / 15
Scanning triplet 11 / 15
Scanning triplet 12 / 15
Scanning triplet 13 / 15
Scanning triplet 14 / 15
Scanning triplet 15 / 15
Method Start End Recombinant Parent1 Parent2 Pvalue
------------------------------------------------------------------------
Siscan 2 205 A J R 7.84E-01
Siscan 2 205 A K R 7.56E-01
Siscan 2 205 A J K 7.77E-01
Siscan 2 205 B J R 7.77E-01
Siscan 3 205 B K R 7.34E-01
Siscan 2 205 B J K 7.57E-01
Siscan 2 205 C J R 7.77E-01
Siscan 2 205 C K R 7.08E-01
Siscan 2 205 C J K 7.62E-01
Siscan 2 205 D J R 7.84E-01
Siscan 2 205 D K R 7.58E-01
Siscan 3 205 D J K 7.57E-01
Siscan 2 205 E J R 7.67E-01
Siscan 2 205 E K R 7.08E-01
Siscan 2 205 E J K 7.60E-01
Using OpenRDP as a Python module
OpenRDP can be used as a Python module. In a typical workflow, we would start by creating an instance of the object class Scanner:
>>> from openrdp import Scanner
>>> scanner = Scanner(cfg="tests/test_cfg.ini")
Calling an instance of Scanner with no arguments, i.e., Scanner() loads the default package configuration file, default.ini.
We can also extract the configuration and modify specific settings:
>>> cfg = scanner.get_config()
>>> cfg
{'Geneconv': {'indels_as_polymorphisms': False, 'mismatch_penalty': 1, 'min_len': 1, 'min_poly': 2, 'min_score': 2, 'max_num': 1}, 'MaxChi': {'max_pvalue': '0.05', 'win_size': 40, 'strip_gaps': False, 'fixed_win_size': True, 'num_var_sites': 70, 'frac_var_sites': '0.1'}, 'Chimaera': {'max_pvalue': '0.05', 'win_size': 40, 'strip_gaps': False, 'fixed_win_size': True, 'num_var_sites': 70, 'frac_var_sites': '0.1'}, 'RDP': {'max_pvalue': '0.05', 'reference_sequence': 'None', 'window_size': 40, 'min_identity': 0, 'max_identity': 100}, 'Bootscan': {'max_pvalue': '0.1', 'win_size': 20, 'step_size': 5, 'num_replicates': 100, 'random_seed': 3, 'cutoff_percentage': '0.7', 'scan': 'distances', 'np': 2}, 'Siscan': {'max_pvalue': '0.8', 'win_size': 40, 'step_size': 5, 'strip_gaps': True, 'pvalue_perm_num': 1100, 'scan_perm_num': 100, 'random_seed': 3}}
>>> cfg["Siscan"]["win_size"] = 50
>>> scanner.set_config(cfg)
The Scanner object has a run_scans method that takes the input file path as its only argument:
>>> results = scanner.run_scans("tests/test_neisseria.fasta")
Scanner returns an instance of the object class ScanResults, which has a custom __str__ attribute:
>>> print(results)
Method Start End Recombinant Parent1 Parent2 Pvalue
------------------------------------------------------------------------
Geneconv 1 204 X64866 X64869 - 2.00E-05
Geneconv 151 195 X64860 X64869 - 2.10E-03
Geneconv 203 507 X64860 X64866 - 8.29E-03
Geneconv 539 759 X64860 X64866 - 1.54E-01
Geneconv 151 193 X64873 - - 2.20E-02
Geneconv 56 170 X64860 - - 2.73E-02
Bootscan 760 765 X64866 X64860 X64869 6.51E-02
MaxChi 475 518 X64860 X64866 X64869 4.04E-02
MaxChi 475 518 X64860 X64866 X64873 4.04E-02
MaxChi 439 482 X64860 X64869 X64873 4.04E-02
Siscan 2 55 X64860 X64866 X64869 7.52E-01
Siscan 2 55 X64860 X64866 X64873 7.67E-01
Siscan 2 55 X64860 X64869 X64873 7.65E-01
Siscan 2 55 X64866 X64869 X64873 7.65E-01
Chimaera 198 241 X64860 X64869 X64873 2.05E-02
Chimaera 170 213 X64866 X64860 X64873 1.81E-03
Chimaera 178 221 X64866 X64869 X64873 1.17E-02
3Seq 202 787 X64869 X64860 X64866 5.98E-10
3Seq 181 787 X64866 X64869 X64873 5.29E-06
RDP 6 15 X64860 X64866 X64869 3.11E+01
RDP 6 504 X64860 X64869 X64873 5.51E-07
RDP 36 481 X64866 X64869 X64873 1.89E-05
This object also has a method to write CSV-formatted results to a file:
>>> with open("results.csv", 'w') as outfile:
... results.write(outfile)
...
A ScanResults object also behaves like a dictionary for accessing specific results, which are stored as a list of dict objects for each detection method:
>>> list(results.keys())
['geneconv', 'bootscan', 'maxchi', 'siscan', 'chimaera', 'threeseq', 'rdp']
>>> results["geneconv"]
[{'start': 1, 'end': 204, 'recombinant': 'X64866', 'parent1': 'X64869', 'parent2': '-', 'pvalue': 2e-05}, {'start': 151, 'end': 195, 'recombinant': 'X64860', 'parent1': 'X64869', 'parent2': '-', 'pvalue': 0.0021}, {'start': 203, 'end': 507, 'recombinant': 'X64860', 'parent1': 'X64866', 'parent2': '-', 'pvalue': 0.00829}, {'start': 539, 'end': 759, 'recombinant': 'X64860', 'parent1': 'X64866', 'parent2': '-', 'pvalue': 0.15378}, {'start': 151, 'end': 193, 'recombinant': 'X64873', 'parent1': '-', 'parent2': '-', 'pvalue': 0.02202}, {'start': 56, 'end': 170, 'recombinant': 'X64860', 'parent1': '-', 'parent2': '-', 'pvalue': 0.02728}]
The actual dictionary can be accessed from ScanResults.dict.
Docker
If you prefer to use Docker to run OpenRDP, a Dockerfile has been included in this repository.
To build the Docker image, navigate to the location of the Dockerfile and run the following command:
docker build . -t openrdp
The following command can then be used to run all seven recombination detection methods under the default settings:
cat <input FASTA> | docker run -i --rm openrdp > <output CSV file>