java -cp .:jstacs-1.3.1.jar:lib/numericalMethods.jar:lib/bytecode.jar:lib/biojava-live.jar projects.dispom.Dispom home=path/to/data/directory/ fg=fgfile.txt bg=bgfile.txt init=best-random=100 p-val=1E-4
path/to/data/directory/fgfile.txt
but not in path/to/data/directory/bgfile.txt
, initialize Dispom with the best from 100 randomly drawn starting values, and search for motif occurrences with a p-value less than 1E-4
.
Under Windows, you must use ";" instead of ":" in the class path.
The arguments have the following meaningname | comment | type |
home | the path to the data directory, default = ./ | String |
ignore | the char that is used to mask comment lines in data files, e.g., '>' in a FASTA-file, default = > | Character |
fg | the file name of the foreground data file (the file containing sequences which are expected to contain binding sites of a common motif) | String |
bg | the file name of the background data file, OPTIONAL | String |
position | a switch whether to use uniform, skew-normal, or mixture position distribution, range={UNIFORM, SKEW_NORMAL, MIXTURE}, default = MIXTURE | String |
mean | the mean of the a priori TFBS distribution, default = 250.0 | Double |
sd | the sd of the a priori TFBS distribution, valid range = [1.0, Infinity], default = 150.0 | Double |
motifs | the number of motifs to be searched for, valid range = [1, 5], default = 1 | Integer |
length | the motif length that is used at the beginning, valid range = [1, 50], default = 15 | Integer |
flankOrder | The Markov order of the model for the flanking sequence and the background sequence, valid range = [0, 5], default = 0 | Integer |
motifOrder | The Markov order of the motif model, valid range = [0, 3], default = 0 | Integer |
bothStrands | a switch whether to use both strands or not, default = true | Boolean |
init | the method that is used for initialization, one of 'best-random= |
String=[Integer | String] |
adjust | a switch whether to adjust the motif length, i.e., either to shrink or expand, default = true | Boolean |
maxPos | a switch whether to use max. pos. in the heuristic or not, default = true | Boolean |
learning | a switch for the learning principle, range={ML, MAP, MCL, MSP}, default = MSP | String |
threads | the number of threads that are use to evaluate the objective function and its gradient, valid range = [1, 128], default = 4 | Integer |
starts | the number of independent starts of Dispom, valid range = [1, 100], default = 1 | Integer |
xml | the file name of the xml file the classifier is written to, default = ./classifier.xml | String |
p-val | a p-value for predicting binding sites, valid range = [0.0, 1.0], OPTIONAL | Double |