public class Kraken2Parser extends KrakenParser
NUM_OTUS
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 |
---|
Kraken2Parser() |
Modifier and Type | Method and Description |
---|---|
protected void |
parseSample(File file)
Construct a new KrakenNode
|
void |
parseSamples()
Parse all
Kraken2Classifier reports in the input directory.Cache the leaf counts Build an Kraken2Node for each line.If ParserModuleImpl.isValid(OtuNode) ,Create ParsedSample for the OtuNodeImpl.getSampleId() if not
yet created. |
addOtuNode, getCitationString, getDescription
addParsedSample, buildOtuCountFiles, checkDependencies, getDepricatedOtuCountFields, getHitsPerSample, getOtuCountField, getParsedSample, getParsedSamples, getSampleIds, getSummary, getUniqueOtus, isValid, runModule, setNumHitsFieldName, validateModuleOrder
buildScript, executeTask, getDockerImageName, getDockerImageOwner, getDockerImageTag, getWorkerScriptFunctions, isValidInputModule, 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, getInputFiles, getLogDir, getMenuPlacement, getMetadata, getModuleDir, getOutputDir, getPostRequisiteModules, getPreRequisiteModules, getPropDefault, getPropDescMap, getPropType, getPropTypeMap, getResourceDir, getTempDir, getTitle, hashCode, init, listProps, setAlias, toString
clone, finalize, getClass, notify, notifyAll, wait, wait, wait
getDescription, getDetails, getMenuPlacement, getPropType, getTitle, isValidProp, listProps
checkDependencies, cleanUp, executeTask, getAlias, getDockerImageName, getDockerImageOwner, getDockerImageTag, getID, getInputFiles, getLogDir, getMetadata, getModuleDir, getOutputDir, getPostRequisiteModules, getPreRequisiteModules, getPropDefault, getResourceDir, getSummary, getTempDir, init, isValidInputModule, setAlias, version
moduleComplete, moduleFailed
buildScript, buildScriptForPairedReads, getJobParams, getMainScript, getScriptDir, getScriptErrors, getTimeout, getWorkerScriptFunctions
protected void parseSample(File file) throws Exception
KrakenParser
parseSample
in class KrakenParser
file
- KrakenClassifier output fileException
- if any errors occurpublic void parseSamples() throws Exception
Kraken2Classifier
reports in the input directory.Kraken2Node
for each line.ParserModuleImpl.isValid(OtuNode)
,ParsedSample
for the OtuNodeImpl.getSampleId()
if not
yet created.
OtuNodeImpl.getCount()
(1) to ParsedSample
OTU count.
Sample Kraken report line (head 7A_reported.tsv) :
FCC6MMAACXX:8:1101:1968:2100#GTATTCTC/1
d__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_vulgatus
parseSamples
in interface ParserModule
parseSamples
in class KrakenParser
Exception
- if error occurs while parsing classifier reports