pyTanFinder is a python tool to search tandem repeats in genomic or long-read data by running, parsing and processing TandemRepeatFinder (Benson, 1999) output.
The pyTanFinder paper has been published. Please cite:
Kirov, I., Gilyok, M., Knyazev, A., & Fesenko, I. (2018). Pilot satellitome analysis of the model plant, Physcomitrella patens, revealed a transcribed and high-copy IGS related tandem repeat. Comparative Cytogenetics, 12(4), 493.
The program was developed in frame of the RNF grant (№17-14-01189). Our website: Plantprotlab.com
pyTanFinder is user friendly command line tool to run TRF software and parse the results followed by clustering of similar tandem repeats. The output of this program is a fasta file of all tandem repeats and table containing unique TR sequences with the estimated abundancy in genome. In addition, pyTanFinder also genearates html report containing the histograms of distribution of TR monomer size and number of connections of each monomer into individual cluster.
Download pyTanFinder from Github repository and proceed with installation instruction
pyTanFinder requires:
- TRF executable file (Can be donwload here).
For linux system it has to be made executable before run (e.g. run command
chmod +x trf409.linux64)
wget 'http://tandem.bu.edu/trf/downloads/trf409.linux64'
chmod +x trf409.linux64- blastn and makeblastdb programs. The paths to these programs can be set via
-bpand-mpflags, respectively - python v3.6
python packages to be installed: biopython, networkx
(run command:
pip install matplotlib biopython networkx) - for Ubuntu tkinter is required (run command
sudo apt-get install python3-tk)
usage: pyTanFinder.py fasta [-h] [-minM MINMONLENGTH] [-maxM MAXMONLENGTH] [-minMN MINMONNUM] [-minA MINABUNDANCY] [-px PREFIX] [--no_blast] [--no_html] [--no_runTRF] [-tp TRF_PATH] [-bp BLAST_PATH] [-mp MAKE_BLAST]
positional arguments:
fasta - fasta file where tandem repeats will be found
optional arguments:
-h, --help show this help message and exit
-minM - minimum length for tandem repeat
-maxM - maximum length for tandem repeat
-minMN - minimum number of repetitions
-minA - minimum abundancy of a repeat in genome, bp
-px - prefix that will be used for file and sequence names
--no_blast - do not run blast (useful when it already was run before)
--no_html - do not make html report
--no_runTRF - do not run TRF (useful when it already was run before)
-tp - path to TRF executable
-bp - path to blastn executable
-mp - path to makeblastdb executable
- now Docker container for pyTanFinder is available ( Linux only! ). Thus itis much easy to run it now without installation of any dependencies!
- To run pyTanFinder via Docker:
- Install Docker
- Obtain copy of pyTanFinder image
docker pull ilyakirov/pytanfinder2 - Go to the directory with your fasta file
- Command to run docker
docker run --name ptf1 -v $("pwd"):/data ilyakirov/pytanfinder2 /data/<YOUR SEQUENCE FILE>
- Some explantaions (for example your fasta file name is sequence.fasta ):
docker run --name ptf1 -v $("pwd"):/data ilyakirov/pytanfinder2 /data/sequence.fasta - This command will mount your current repository (
$("pwd")) to the Docker container folder /data . - When you run container it will now see your files in the current folder but the path to the files will be /data/ e.g. /data/sequence.fasta in the example above.
- If you need to add some pyTanFinder arguments (e.g. prefix 'lu') you should add them in the following way (actually it is a normal way:))
docker run --name ptf1 -v $("pwd"):/data ilyakirov/pytanfinder2 -px lu /data/sequence.fasta - After this step the pyTanFinder will start to work. BUT! in the end you will NOT see any output files because they are insight of the container. So, you need to copy them to your folder on the computer. It can be the following command (coping in the current directory):
docker cp ptf1:/src/app/pyTanFinder/out_pyTanFinder .
- After this step the results (out_pyTanFinder folder) will appear in the current folder.
Ilya Kirov
This project is licensed under the MIT License