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
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)
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
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.