Can I use the (protein disorder) predictor from the command line?
BioJava module biojava3-protein-disorder can be compiled into a single executable JAR file and run using
java -jar <jar_file_name>
command. The jar file can be downloaded from the BioJava repository biojava3-protein-disorder-3.0.2-SNAPSHOT.jar
Alternatively if you want to integrate the predictor into your code you can use API functions to perform the calculations.
Options supported by the command line executable
JRONN version 3.1b usage 1 August 2011: java -jar JRONN_JAR_NAME -i=inputfile <OPTIONS> 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 < n < (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.