public class KrakenParser extends ParserModuleImpl implements ApiModule
NUM_OTUSBLJ_OPTIONSGZIP_EXT, LOG_EXT, PDF_EXT, RETURN, SH_EXT, TAB_DELIM, TSV_EXT, TXT_EXTLOG_DIR, MAIN_SCRIPT_PREFIX, NO_VERSION, OUTPUT_DIR, RES_DIR, TEMP_DIR| Constructor and Description |
|---|
KrakenParser() |
| Modifier and Type | Method and Description |
|---|---|
void |
addOtuNode(OtuNode node)
Each sample with taxonomic assignments from a
ClassifierModule is parsed by
ParserModule.parseSamples() to produce a ParsedSample. |
String |
getCitationString()
At a minimum, this should return the name and/or url for the wrapped tool.
|
String |
getDescription()
Briefly describe what this module does.
|
protected void |
parseSample(File file)
Construct a new KrakenNode
|
void |
parseSamples()
Parse all
KrakenClassifier reports in the input directory.Cache the leaf counts Build an KrakenNode for each line.If ParserModuleImpl.isValid(OtuNode),Create ParsedSample for the OtuNodeImpl.getSampleId() if not
yet created. |
addParsedSample, buildOtuCountFiles, checkDependencies, getDepricatedOtuCountFields, getHitsPerSample, getOtuCountField, getParsedSample, getParsedSamples, getSampleIds, getSummary, getUniqueOtus, isValid, runModule, setNumHitsFieldName, validateModuleOrderbuildScript, executeTask, getDockerImageName, getDockerImageOwner, getDockerImageTag, getWorkerScriptFunctions, isValidInputModule, markStatus, moduleComplete, moduleFailed, runBioLockJ_CMDbuildScriptForPairedReads, getJobParams, getMainScript, getRuntimeParams, getScriptDir, getScriptErrors, getTimeout, hasScripts, isValidPropaddGeneralProperty, 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, toStringclone, finalize, getClass, notify, notifyAll, wait, wait, waitgetDescription, getDetails, getMenuPlacement, getPropType, getTitle, isValidProp, listPropscheckDependencies, cleanUp, executeTask, getAlias, getDockerImageName, getDockerImageOwner, getDockerImageTag, getID, getInputFiles, getLogDir, getMetadata, getModuleDir, getOutputDir, getPostRequisiteModules, getPreRequisiteModules, getPropDefault, getResourceDir, getSummary, getTempDir, init, isValidInputModule, setAlias, versionmoduleComplete, moduleFailedbuildScript, buildScriptForPairedReads, getJobParams, getMainScript, getScriptDir, getScriptErrors, getTimeout, getWorkerScriptFunctionspublic void addOtuNode(OtuNode node) throws Exception
ParserModuleClassifierModule is parsed by
ParserModule.parseSamples() to produce a ParsedSample. As each file is processed, this method
is called to add the OtuNode to the ParsedSample with the same sample
ID (if valid).addOtuNode in interface ParserModuleaddOtuNode in class ParserModuleImplnode - OtuNodeException - if unable to add the OTU nodepublic void parseSamples()
throws Exception
KrakenClassifier reports in the input directory.KrakenNode 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 ParserModuleparseSamples in class ParserModuleImplException - if error occurs while parsing classifier reportsprotected void parseSample(File file) throws Exception
file - KrakenClassifier output fileException - if any errors occurpublic String getDescription()
ApiModulegetDetails.getDescription in interface ApiModulepublic String getCitationString()
ApiModulegetCitationString in interface ApiModule