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This directory contains the source code for the TALEN Targeter, Old TALEN Targeter, and TAL Effector Targeter tools from the TALE-NT website.
Dependencies and Set Up
boglab_tools requires Python 2.6+ and biopython.
By default the tools expect to be located at /opt/boglab/talent. Changing this requires editing 2 files:
- In talconfig.py, change the value of BASE_DIR to the full path of the parent folder of boglab_tools
- In findTAL.py find the line that says 'with open(BASE_DIR + "/talent/re_dict_dump", "rb") as re_dict_file:' and change 'talent' to 'boglab_tools'
Note that off-target counting with findTAL.py won't work unless tfcount is installed, and findRvdTAL.py and findPairedRvdTALs.py won't work unless you install the C libraries and cython wrappers from talesf and talesf/paired.
Here's a mapping between the the tools on the site and the scripts in boglab_tools:
- TALEN Targeter - findTAL.py
- TALEN Targeter (old version with design guidelines) - findTAL_old.py
- TAL Effector Targeter - findSingleTALsite.py
- Target Finder - findRvdTAL.py
- Paired Target Finder - findPairedRvdTALs.py
You can run any of the scripts by doing:
python findTAL.py OPTIONS
You can find out what options exist for any of them by doing:
python findTAL.py --help
The command for running findTAL.py with the default parameters from the site is:
python findTAL.py --filter '0' --gspec --min '15' --max '30' --arraymin '15' --arraymax '20' --fasta 'filemx4P32.fasta' --outpath 'fileOgILYO.txt' --logpath '79637.log'
- --min and --max are the minimum and maximum spacer length
- --arraymin and --arraymax are the minimum and maximum RVD sequence length
- --fasta is the path to the file containing your input sequences in FASTA format
- --gspec tells the script to use NH instead of NN for G
- --outpath is where you want the output file to go
- --logpath is the path to write the process log to; if you leave this out it will print this to stdout on your terminal
To search for off-target sites in a custom genome, run findTAL.py as above, but add the options '--offtargets --offtargets-fasta PATH_TO_CUSTOM_GENOME'