Command Line Interface (CLI)

To execute CRT from the command line:  java -cp CRT1.2-CLI.jar crt [options] inputFile [outputFile]
    java -cp CRT1.2-CLI.jar -- executes a java program called crt, which is the main class defined in the file CRT1.2-CLI.jar;  -cp (class path)
    [options] -- optional; specifies input for the crt program; if no options are given, default values are used; see options below
    inputFile -- required; must be a file in FASTA format
    outputFile -- optional; file to which results are to be written;  if no file is given, results will be written a file named "a.out"

For example
    java -cp CRT1.2-CLI.jar crt ecoli.fna
    java -cp CRT1.2-CLI.jar crt ecoli.fna ecoli.out
    java -cp CRT1.2-CLI.jar crt -minNR 3 -minRL 21 ecoli.fna

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OPTIONS

        -minNR        minimum number of repeats a CRISPR must contain; default 3
        -minRL        minimum length of a CRISPR's repeated region;  default 19
        -maxRL        maximum length of a CRISPR's repeated region;  default 38
        -minSL        minimum length of a CRISPR's non-repeated region (or spacer region);  default 19
        -maxSL        maximum length of a CRISPR's non-repeated region (or spacer region);  default 48
        -screen        print results to the screen, instead of a file; default 0; (range: 0-1)
        -searchWL    length of search window used to discover CRISPRs; (range: 6-9)

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Simplier Execution of CRT using aliases

If operating within a Unix environment, execution of CRT can be made simplier using aliases.  Aliases allow the shortening of long commands.  In this case, we can substitute "java -cp CRT1.2-CLI.jar crt" with "crt".  To do this, type the command listed below at the prompt.

Bash shell syntax
    alias crt="java -cp CRT1.2-CLI.jar crt"
      
C shell (csh) or tcsh shell syntax
    alias crt "java -cp CRT1.2-CLI.jar crt"

This allows the program to be executed as follows.
    crt ecoli.fna
    crt ecoli.fna ecoli.out
    crt -minNR 3 -minRL 21 ecoli.fna

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To make an alias permanent, place it in your shell's corresponding .rc file. For csh this is .cshrc and for bash, this is .bashrc.  (You may have to type 'source .bashrc' or restart the shell before the change takes effect.)  Click here for more details.

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