BioJava:CookBook3:ProteinDisorderCLI.html

<h2 id="can-i-use-the-protein-disorder-predictor-from-the-command-line">Can I use the (protein disorder) predictor from the command line?</h2>

<p>BioJava module <em>biojava3-protein-disorder</em> can be compiled into a single
executable JAR file and run using <java> java -jar <jar_file_name>
&lt;/java&gt; command. The jar file can be downloaded from the BioJava
repository
[biojava3-protein-disorder-3.0.2-SNAPSHOT.jar](http://www.biojava.org/download/maven/org/biojava/biojava3-protein-disorder/)</jar_file_name></java></p>

<p>Alternatively if you want to integrate the predictor into your code you
can use <a href="BioJava:CookBook3:ProteinDisorder" title="wikilink"> API functions</a>
to perform the calculations.</p>

<h2 id="options-supported-by-the-command-line-executable">Options supported by the command line executable</h2>

<div class="highlighter-rouge"><pre class="highlight"><code>JRONN version 3.1b usage 1 August 2011:
java -jar JRONN_JAR_NAME -i=inputfile &lt;OPTIONS&gt;

Where -i=input file 
    Input file can contain one or more FASTA formatted sequences.

All OPTIONS are optional

Supported OPTIONS are: 
    -o=output file
    -d=disorder value
    -f=V or H 
    -s=statistics file
    -n=number of threads to use

OPTION DETAILED DESCRIPTION:
    -o full path to the output file, if not specified 
    standard out is used

    -d the value of disorder, defaults to 0.5

    -f output format, V for vertical, where the letters 
    of the sequence and corresponding disorder values are 
    output in two column layout. H for horizontal, where the
    disorder values are provided under the letters of the 
    sequence. Letters and values separated by tabulation in
    this case. Defaults to V.

    -s the file name to write execution statistics to.

    -n the number of threads to use. Defaults to the number of 
    cores available on the computer. n=1 mean sequential 
    processing. Valid values are 1 &lt; n &lt; (2 x num_of_cores)
    Default value will give the best performance.
    
EXAMPLES: 

    Predict disorder values for sequences from input file /home/input.fasta
    output the results to the standard out. Use default disorder value
    and utilise all cpus available on the computer.

    java -jar JRONN.JAR -i=/home/input.fasta
    
    Predict disorder values for sequences from input file /home/input.fasta
    output the results in horizontal layout to the /home/jronn.out, collect 
    execution statistics to /home/jronn.stat.txt file and limit the number 
    of threads to two. 
    
    java -jar JRONN.JAR -i=/home/input.fasta -o=/home/jronn.out -d=0.6 -n=2 -f=H
     
    The arguments can be provided in any order.
</code></pre>
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