public class RemoveScarcePathwayCounts extends Humann2CountModule
BLJ_OPTIONS
GZIP_EXT, LOG_EXT, PDF_EXT, RETURN, SH_EXT, TAB_DELIM, TSV_EXT, TXT_EXT
LOG_DIR, MAIN_SCRIPT_PREFIX, NO_VERSION, OUTPUT_DIR, RES_DIR, TEMP_DIR
Constructor and Description |
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RemoveScarcePathwayCounts() |
Modifier and Type | Method and Description |
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void |
checkDependencies()
Validate module dependencies:
Require
Config . exists
Require Config . is positive integer
Require Config . is positive integer
Verify Config . is positive integer if set
Start the AWS DB sync to S3 if a novel DB has been configure and
"aws.copyDbToS3" is enabled
|
String |
getSummary()
Produce summary message with min, max, mean, and median number of pathways.
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protected void |
logScarceData(TreeMap<String,TreeSet<String>> map,
File file)
Save a list of low count pathways or samples to the module temp directory.
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protected TreeMap<String,TreeSet<String>> |
removeScarcePathwayCounts(File file,
Set<String> scarcePathways)
Remove Pathway Counts below the
Config ."report.minCount" |
void |
runModule()
This method executes the modules primary Java routine.
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getInputFiles, getPreRequisiteModules, isHumann2CountModule, isValidInputModule
buildScript, executeTask, getDockerImageName, getDockerImageOwner, getDockerImageTag, getWorkerScriptFunctions, markStatus, moduleComplete, moduleFailed, runBioLockJ_CMD
buildScriptForPairedReads, getJobParams, getMainScript, getRuntimeParams, getScriptDir, getScriptErrors, getTimeout, hasScripts, isValidProp
addGeneralProperty, addGeneralProperty, addGeneralProperty, addNewProperty, addNewProperty, cacheInputFiles, cleanUp, compareTo, equals, findModuleInputFiles, getAlias, getDescription, getDetails, getFileCache, getID, getLogDir, getMenuPlacement, getMetadata, getModuleDir, getOutputDir, getPostRequisiteModules, getPropDefault, getPropDescMap, getPropType, getPropTypeMap, getResourceDir, getTempDir, getTitle, hashCode, init, listProps, setAlias, toString
clone, finalize, getClass, notify, notifyAll, wait, wait, wait
buildScriptForPairedReads, getJobParams, getMainScript, getScriptDir, getScriptErrors, getTimeout
cleanUp, getAlias, getID, getLogDir, getMetadata, getModuleDir, getOutputDir, getPostRequisiteModules, getPropDefault, getResourceDir, getTempDir, init, setAlias, version
public void checkDependencies() throws Exception
ScriptModuleImpl
Config
. exists
Config
. is positive integer
Config
. is positive integer
Config
. is positive integer if set
checkDependencies
in interface BioModule
checkDependencies
in class Humann2CountModule
Exception
- thrown if missing or invalid dependencies are foundpublic String getSummary() throws Exception
getSummary
in interface BioModule
getSummary
in class ScriptModuleImpl
Exception
- if any error occurspublic void runModule() throws Exception
JavaModule
runModule
in interface JavaModule
runModule
in class JavaModuleImpl
Exception
- thrown if any runtime error occursprotected void logScarceData(TreeMap<String,TreeSet<String>> map, File file) throws Exception
map
- TreeMap(sampleId, TreeSet(data)) of Pathways found in too few samples or pathwaysfile
- Output fileException
- if errors occurprotected TreeMap<String,TreeSet<String>> removeScarcePathwayCounts(File file, Set<String> scarcePathways) throws Exception
Config
."report.minCount"file
- input filescarcePathways
- Set of pathway names to be eliminatedException
- if errors occur