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License

All source code is available under an ISC license.

Copyright (c) 2011-2015, Nick Booher [email protected] and Erin Doyle [email protected].

Permission to use, copy, modify, and/or distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies.

THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.

Description

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:

  1. In talconfig.py, change the value of BASE_DIR to the full path of the parent folder of boglab_tools
  2. 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.

Usage

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'