Basic Usage - drivenbyentropy/aptasuite GitHub Wiki
To open the GUI, either double-click on the executable jar file called aptasuite-x.y.z.jar or call the jar file from command line without parameters (x.y.z corresponds to the version you downloaded):
$ java -jar aptasuite-x.y.z.jar
Then, follow the instructions on the screen to get started.
AptaSUITE consists of a series of methods which can either be called individually or chained together to create data workflows.
The basic call of AptaSUITE complies with the following pattern:
java -jar /path/to/aptasuite.jar -option1 [-option2] ... [-optionN] -config path/to/configuration/fileCurrently, the following options are available:
usage: AptaSUITE [-cluster] -config <path> [-export
<pool,cycles,clusters,structure>] [-help] [-net] [-parse |
-simulate] [-predict <structure,bppm>] [-trace]
-cluster Applies AptaCLUSTER to the
dataset using the parameters
as specified in the
configuration file
-config <path> Path to the configuration file
for APTASuite
-export <pool,cycles,clusters,structure> Writes the specified <data> to
file. Multiple arguments must
be comma-separated with not
spaces in between. Arguments:
pool: every unique aptamer of
the selection together with
the counts of all selection
cycles
cycles: the aptamers sequences
as present in the specified
selection cycles. Each aptamer
will be written to file as
many times as its cardinality
in the pool.
clusters: Exports the clusters
for the specified cycles
sorted by cluster size
structures: writes the
structural data for the
aptamer pool to file.
-help print this message
-net Experimental branch: AptaNET
-parse Runs AptaPLEX and creates a
new aptamer pool and
associated selection cycles
according to the configuration
file. Note, this option is
mutually exclusive with
-simulate.
-predict <structure,bppm> Performs several structural
predictions of all aptamers in
the pool and stores them on
disk.
Arguments:
structure: Predicts the
context probabilities for each
nuceotide position of every
species in the pool
bppm: Predicts the base pair
probabilities for each
possible pair of nucleodites
in every species.
-simulate Creates a new aptamer pool
using AptaSIM according to the
configuration file. Note, this
option is mutually exclusive
with -parse
-trace Applies AptaTRACE to the
dataset using the parameters
as specified in the
configuration file
For example, in order to import a SELEX experiment (using AptaPLEX) into AptaSUITE and export all unique species along with their corresponding counts in each selection cycle, AptaSUITE can be called as follows:
java -jar aptasuite.jar -parse -export pool -config path/to/configuration/file
Note that with the default configuration, importing data (-parse), predicting secondary structure information (-structures), as well as clustering data (-cluster) only need to be performed once as the results are stored on disk and retrieved on subsequent calls to AptaSUITE. For instance, in order to run AptaTRACE on the same data imported before, the following call suffices:
java -jar aptasuite.jar -structures -trace -config path/to/configuration/file
If instead
java -jar aptasuite.jar -parse -structures -trace -config path/to/configuration/file
is called, any previous data for this experiment will be deleted from disk and imported again. Similarly, after predicting all secondary structures (-structures), AptaTRACE can be called with different parameters by modifying the configuration file and issuing the following command:
java -jar aptasuite.jar -trace -config path/to/configuration/file