public class Scope
extends java.lang.Object
UberProperties
. This sets the baseline so that all properties used in the course of any of the SCOPE modules are initialized to valid variables that
represent the default settings of that algorithm. These values can then be modified either by loading in a new parameter file using the
-pf
flag or by specifying specific parameter values using the flag for that value. Each flag has a direct mapping to a
parameter in the default properties file. Calling SCOPE with the -h flag will cause parsing to stop immediately and the flag-properties
mappings to be displayed to stdout.
When the flags and param files are parsed, they are parsed from left to right, with flags that are further right taking precendence over flags that are further left.
-did BeamDriverClassName -- driver.id
: specifies the name (id) of the driver that will be used. Must be a (perhaps
subclass of) BeamDriver.-scorer ScorerClassName -- scorer.id
: specifies the type of scorer that will be run.-sgs 'key'|'keyFile'|'groupFile' -- seq.group.source
: specifies where the group of genes will be coming from.
groupFile
indicates that all the genes are read out of a group file. key
specifies that all the genes match a
given key--most likely a regulon. keyFile
specifies that multiple groups will be read, each specified by a key in the
keyFile. Each group will get it's own BeamDriver. The filename that corresponds to the key
, keyFile
or
groupFile
is specified by the seq.group.id
property.-sgi filename|keyName -- seq.group.id
: Specifies the file name of the keyFile
or groupFile
or
specifies the key
.-root directory -- out.root
: Specifies the root where output files will be placed.-drb 'true'|'false' -- driver.run.beam
: Toggles BEAM on and off-drbp 'true'|'false' -- driver.run.bipartites
: Toggles SPACER on and off-amb -- 'LO'|'GR'|'LOGR'|'none' -- ambiguizer.method
: Specifies which version of PRISM will be run on the output of
BEAM.-sgmm filename -- seq.group.motif.master
: Specifies the name of the file where the known motif definitions can be found.
This may be changed to move between consensus definitions and motif list definitions.-f
flag. When running multiple drivers, if one encounters an error or exception, all others will
stop. This flag overrides that and allows the other drivers to keep executing. This only works in single threaded mode.
There are many more flags. They can be most easily understood by using the -h flag to get the flag-parameter pairings and then looking at the default parameter file for descriptions of what each parameter is used for and what the default value is.
One important note is that when keyFile is used for seq.group.source, a seperate driver is created for each regulon. This has some major implications (obviously) on the way in which BeamDrivers are written.
-artificial
flag, which takes as an optional parameter
an id to identify a specific test run. When this flag is used, the genome, group, knownMotif list, and various root directories are all
changed. The roots have their own absolute paths, since each artificial test run generates it's own genome and we don't want these to be
ported or to clutter up the main directory. The genome (seq.id
), group (seq.group.source
and
seq.group.id
, and know motifs (seq.motifs.known.id
) are all set to correspond to the id given by the
-id
flag. For example the call
beam+ -id BP_0 -artificial
Will set all these parameters to point to an artificial test set that was generated with an id of BP_0.
Artificial test set generation was never ported over to the current version of SCOPE. Therefore, test sets must be generated in the old version and moved over to the new version. See Creating artificial test sets for more information.
BeamDriver
,
Scorer
Modifier and Type | Field and Description |
---|---|
private static UberProperties |
clHash |
(package private) static org.apache.log4j.Logger |
logger |
Constructor and Description |
---|
Scope() |
Modifier and Type | Method and Description |
---|---|
private static void |
driverError(java.lang.Throwable t,
boolean force) |
static BeamDriver[] |
getDrivers(UberProperties properties)
Creates the appropriate sets of driver(s) as defined by the properties.
|
static void |
main(java.lang.String[] args) |
static UberProperties |
parseCommands(java.lang.String[] args)
Parses command line flags and sets properties accordingly.
|
private static void |
printHelp() |
private static UberProperties clHash
static org.apache.log4j.Logger logger
private static void driverError(java.lang.Throwable t, boolean force)
public static BeamDriver[] getDrivers(UberProperties properties) throws java.lang.Exception
java.lang.Exception
public static void main(java.lang.String[] args)
public static UberProperties parseCommands(java.lang.String[] args)
private static void printHelp()