public class RdpParser extends ParserModuleImpl implements ApiModule
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 |
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RdpParser() |
Modifier and Type | Method and Description |
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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 boolean |
isValid(OtuNode node)
|
void |
parseSamples()
Parse all
RdpClassifier reports in the input directory.Build an RdpNode for each line.If isValid(OtuNode) ,Create ParsedSample for the OtuNodeImpl.getSampleId() if not yet
created. |
String |
version()
Changes to a module class should be accompanied by a increment in version.
|
addOtuNode, addParsedSample, buildOtuCountFiles, checkDependencies, getDepricatedOtuCountFields, getHitsPerSample, getOtuCountField, getParsedSample, getParsedSamples, getSampleIds, getSummary, getUniqueOtus, 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
moduleComplete, moduleFailed
buildScript, buildScriptForPairedReads, getJobParams, getMainScript, getScriptDir, getScriptErrors, getTimeout, getWorkerScriptFunctions
public void parseSamples() throws Exception
RdpClassifier
reports in the input directory.RdpNode
for each line.isValid(OtuNode)
,ParsedSample
for the OtuNodeImpl.getSampleId()
if not yet
created.
OtuNodeImpl.getCount()
(1) to ParsedSample
OTU count.
Sample QIIME report line (head 7A_reported.tsv):
FCABK7W:1:2105:21787:12788#/1 Root rootrank 1.0 Bacteria domain 1.0 Firmicutes phylum 1.0 Clostridia class 1.0
Clostridiales order 1.0 Ruminococcaceae family 1.0 Faecalibacterium genus 1.0
parseSamples
in interface ParserModule
parseSamples
in class ParserModuleImpl
Exception
- if error occurs while parsing classifier reportsprotected boolean isValid(OtuNode node)
isValid
in class ParserModuleImpl
node
- OtuNode build from 1 line of a ClassifierModule
output fileOtuNode
is validpublic String getDescription()
ApiModule
getDetails
.getDescription
in interface ApiModule
public String getCitationString()
ApiModule
getCitationString
in interface ApiModule