Package | Description |
---|---|
biolockj.exception |
This package contains
Exception subclasses specific to BioLockJ. |
biolockj.module | |
biolockj.module.assembly | |
biolockj.module.classifier |
This package contains Classifier specific
BioModule s that build bash scripts to generate
taxonomy reports from the sequences files. |
biolockj.module.classifier.r16s |
This package contains RDP and QIIME classifier modules that assign taxonomy to 16s sequences.
Output file formats are classifier specific so classifier requires a unique post-requisite ParserModule . |
biolockj.module.classifier.wgs |
This package contains Kraken, Kraken2, Humann2, MetaPhlAn classifier modules that assign taxonomy to WGS data.
As with all BioLockJ classifiers, these modules generate raw classifier output files from the sequence data. Include the corresponding ParserModule in the Config file to
generate standardized OTU abundance tables. |
biolockj.module.implicit.qiime |
This package contains
BioModule s that are implicitly added to QIIME pipeline as needed. |
biolockj.util |
Static utilities centralize and organize reusable core methods.
|
Modifier and Type | Class and Description |
---|---|
class |
ConfigConflictException |
class |
ConfigFormatException
ConfigFormatException is thrown if property is defined but the format is invalid.
|
class |
ConfigNotFoundException
ConfigNotFoundException is thrown if a required
Config property is undefined. |
class |
ConfigPathException
ConfigPathException is thrown if property is invalid file paths are encountered when processing the BioLockJ
configuration file.
|
class |
ConfigViolationException
ConfigViolationException is thrown at runtime due to application state violations caused by invalid module I/O
(sequences or metadata) as defined by
Config properties. |
class |
SpecialPropertiesException
This type of exception is thrown if an error occurs while processing a special type of property such as "exe."
properties or defaultProps.
|
Modifier and Type | Method and Description |
---|---|
protected String |
ScriptModuleImpl.getRuntimeParams(List<String> params,
String numThreadsParam)
Return all collectionProperty values separated by a space.
|
Modifier and Type | Method and Description |
---|---|
protected String |
GenomeAssembly.getCheckmParams()
Get standard Checkm runtime parameters.
|
protected String |
GenomeAssembly.getMetabatParams()
Get Metabat runtime parameters.
|
protected String |
GenomeAssembly.getMetaspadeParams()
Get Metaspade runtime parameters.
|
Modifier and Type | Method and Description |
---|---|
String |
ClassifierModule.getClassifierExe()
Get the executable required to classify your samples.
|
abstract String |
ClassifierModuleImpl.getClassifierExe() |
List<String> |
ClassifierModule.getClassifierParams()
Get optional list of parameters to append whenever the classifier executable is called.
|
abstract List<String> |
ClassifierModuleImpl.getClassifierParams() |
Modifier and Type | Method and Description |
---|---|
protected List<String> |
QiimeClosedRefClassifier.getBatch(List<String> lines,
int batchNum,
int index)
Method returns batch script lines for one batch.
|
String |
RdpClassifier.getClassifierExe()
RDP uses java to run a JAR file, so no special command is required
|
List<String> |
RdpClassifier.getClassifierParams()
Do not accept -t to define a database, since that instead requires the specific
property: "rdp.db"
If "rdp.hierCounts" is true, then skip any parameter for it here, it will added per file. |
Modifier and Type | Method and Description |
---|---|
String |
Metaphlan2Classifier.getClassifierExe()
Metaphlan runs python scripts, so no special command is required
|
String |
Humann2Classifier.getClassifierExe()
Get HumanN2 executable command: "exe.humann2"
|
String |
KrakenClassifier.getClassifierExe()
Get kraken executable command: "exe.kraken"
|
String |
Kraken2Classifier.getClassifierExe()
Get kraken executable command: "exe.kraken2"
|
List<String> |
Metaphlan2Classifier.getClassifierParams()
Obtain the metaphlan2 runtime params
|
List<String> |
Humann2Classifier.getClassifierParams()
Obtain the humann2 runtime params
|
List<String> |
KrakenClassifier.getClassifierParams()
Obtain the kraken runtime params
|
List<String> |
Kraken2Classifier.getClassifierParams()
Obtain the kraken2 runtime params
|
Modifier and Type | Method and Description |
---|---|
String |
QiimeClassifier.getClassifierExe()
QIIME calls python scripts, so no special command is required
|
List<String> |
QiimeClassifier.getClassifierParams()
Obtain the QIIME runtime params
|
protected String |
QiimeClassifier.getParams()
Subclasses call this method to check dependencies before picking OTUs to validate
Config ."qiime.params" |
protected List<String> |
QiimeClassifier.getPickOtuLines(String otuPickingScript,
File fastaDir,
String mapping,
File outputDir)
Subclasses call this method to add OTU picking lines by calling "add_qiime_labels.py" via OTU picking
script.
|
protected String |
QiimeClassifier.getVsearchParams()
Return runtime parameters for "qiime.vsearchParams"
|
Modifier and Type | Method and Description |
---|---|
protected static void |
BashScriptBuilder.buildMainScript(ScriptModule module)
Build the MIAN script.
|
static List<String> |
DockerUtil.buildSpawnDockerContainerFunction(BioModule module,
String startedFlag)
Build the "spawnDockerContainer" method, which takes container name, in/out port, and optionally script
path parameters.
|
protected static List<String> |
BashScriptBuilder.initMainScript(ScriptModule module)
Create the ScriptModule main script that calls all worker scripts.
|