#crt-mod

Project to modify the CRISPR Recognition Tool and related wrapper in order to make the results more usable in more contexts.

Added features, thus far:

• Output FASTA files
• Run in multiple threads (can run MUCH faster than other versions)
• Simplified distribution - a working crt.jar file is included.

##Child of CRT Wrapper This is a command-line utility that goes a farther in terms of usability and performance than the original CRT wrapper project.

CRT is a command-line utility that wraps the 'CRISPR Recognition Tool' published by Bland et al. (BMC Bioinformatics 2007, 8(1):209) and available at http://www.room220.com/crt/

While the original CRT tool only accepts as input a FASTA-formatted sequence with only one sequence in it (typically a whole genome), the CRT wrapper accepts multi-sequence files in various formats (see here for a complete list).

Version

The current version is 2.0rev1. This is dependent on THIS project, not any predecessor.

##Installation

To install the CRT wrapper you must go through the following steps:

• Ensure a Python interpreter (ver 2.6 or 2.7; 3.0+ are not supported) is installed in your system. Get it here.
• Ensure the Biopython library is installed.
• Go to http://github.com/caseyh/crt-mod/zipball/master. A file named caseyh-crt-mod-xxxx.zip will download.
• Unzip this file.
• Ensure the file crt-mod/crt-mod.py is in your PATH, either by moving it to a directory already in your PATH or by adding this directory to the PATH. Alternatively you can add it as an alias.
• crt-mod should now be accessible from the command line; you can test it by typing crt-mod --version

##Usage A list of options can be obtained by using the --help or -h option. A description of the meaning of the CRT options --min-nr, --min-rl, etc. can be found at the CRT website.

##Example Example of use:

crt-mod -i my_sequences.fasta fasta -o annotated_CRISPRs.txt

or to output fasta files:

crt-mod -i my_sequences.fasta fasta -o CRISPRS.fasta -f

or to set the number of running threads:

crt-mod -i my_sequences.fasta fasta -o annotated_CRISPRs.txt -a 4

Dev Folder

This contains things that were used or modified in development. For example, dev/cli/src includes the modified java source code necessary for this project. The dev directory also contains various jars that were compiled to work in different java environments as a number of errors were encountered.