public class AwkFastaConverter extends SeqModuleImpl implements ApiModule
Modifier and Type | Field and Description |
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protected static String |
FUNCTION_CONVERT_454
Name of the bash function used to conver 454 format to BioLockJ friendly Illumina format:
"convert454"
|
protected static String |
FUNCTION_CONVERT_TO_FASTA
Name of the bash function that converts the file format to Fasta: "convertToFastA"
|
protected static String |
FUNCTION_GUNZIP
Name of the bash function used to decompress gzipped files: "decompressGzip"
|
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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AwkFastaConverter() |
Modifier and Type | Method and Description |
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List<List<String>> |
buildScript(List<File> files)
Return an inner list of lines to execute for each sample.
|
void |
cleanUp()
|
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.
|
String |
getDetails()
A extension of
getDescription . |
String |
getDockerImageName()
Get the docker image to use for this module.
|
String |
getDockerImageOwner()
Get the name of the docker hub user that owns the image to use for this module.
|
String |
getDockerImageTag()
Get the version / tag to use for the docker image.
|
List<File> |
getSeqFiles(Collection<File> files)
Return only sequence files for sample IDs found in the metadata file.
If Config ."metadata.required" = "Y", an
error is thrown to list the files that cannot be matched to a metadata row. |
List<String> |
getWorkerScriptFunctions()
This method generates the required bash functions used by the module scripts.
|
protected static String |
unzip(File file,
String targetPath)
Build script line to decompress gzipped sequence file.
|
getInputFiles, getSummary, isValidInputModule
buildScriptForPairedReads, checkDependencies, executeTask, getJobParams, getMainScript, getRuntimeParams, getScriptDir, getScriptErrors, getTimeout, hasScripts, isValidProp
addGeneralProperty, addGeneralProperty, addGeneralProperty, addNewProperty, addNewProperty, cacheInputFiles, compareTo, equals, findModuleInputFiles, getAlias, getDescription, getFileCache, getID, 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, getMenuPlacement, getPropType, getTitle, isValidProp, listProps
checkDependencies, executeTask, getAlias, getID, getInputFiles, getLogDir, getMetadata, getModuleDir, getOutputDir, getPostRequisiteModules, getPreRequisiteModules, getPropDefault, getResourceDir, getSummary, getTempDir, init, isValidInputModule, setAlias, version
buildScriptForPairedReads, getJobParams, getMainScript, getScriptDir, getScriptErrors, getTimeout
protected static final String FUNCTION_CONVERT_454
protected static final String FUNCTION_CONVERT_TO_FASTA
protected static final String FUNCTION_GUNZIP
public List<List<String>> buildScript(List<File> files) throws Exception
ScriptModuleImpl
buildScript
in interface ScriptModule
buildScript
in class ScriptModuleImpl
files
- Files in the input directory that contain only forward readsException
- if unable to generate script linespublic void cleanUp() throws Exception
Config
."internal.seqType" = "fasta"Config
."internal.seqHeaderChar" =
SeqUtil.FASTA_HEADER_DEFAULT_DELIM
cleanUp
in interface BioModule
cleanUp
in class BioModuleImpl
Exception
- if errors occurpublic List<File> getSeqFiles(Collection<File> files) throws SequnceFormatException
SeqModule
Config
."metadata.required" = "Y", an
error is thrown to list the files that cannot be matched to a metadata row.getSeqFiles
in interface SeqModule
getSeqFiles
in class SeqModuleImpl
files
- Module input filesSequnceFormatException
- If Config
."metadata.required" =
"Y" but sequence files found that do not have a corresponding record in the metadata
file or if invalid metadata prevents parsing SEQ files.public List<String> getWorkerScriptFunctions() throws Exception
getWorkerScriptFunctions
in interface ScriptModule
getWorkerScriptFunctions
in class ScriptModuleImpl
Exception
- if errors occurprotected static String unzip(File file, String targetPath)
file
- Gzipped filetargetPath
- Output file namepublic String getDockerImageOwner()
BioModule
getDockerImageOwner
in interface BioModule
getDockerImageOwner
in class BioModuleImpl
public String getDockerImageName()
BioModule
getDockerImageName
in interface BioModule
public String getDockerImageTag()
BioModule
getDockerImageTag
in interface BioModule
getDockerImageTag
in class BioModuleImpl
public String getDescription()
ApiModule
getDetails
.getDescription
in interface ApiModule
public String getDetails()
ApiModule
getDescription
. Beyond the brief description, give details such as
the interaction between properties.getDetails
in interface ApiModule
getDetails
in class BioModuleImpl
public String getCitationString()
ApiModule
getCitationString
in interface ApiModule