Package org.broadinstitute.hellbender.tools.spark.pathseq

Class PathSeqBuildReferenceTaxonomy

java.lang.Object

org.broadinstitute.hellbender.cmdline.CommandLineProgram

org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqBuildReferenceTaxonomy

All Implemented Interfaces:

org.broadinstitute.barclay.argparser.CommandLinePluginProvider

@DocumentedFeature
public class PathSeqBuildReferenceTaxonomy
extends CommandLineProgram

Build an annotated taxonomy datafile for a given microbe reference. The output file from this tool is required to run the PathSeq pipeline.

The tool reads the list of sequence accessions from the given reference. For each accession, it looks up the NCBI taxonomic ID of the corresponding organism and builds a taxonomic tree containing only organisms that are represented in the reference. The reference should only contain sequences from NCBI RefSeq and/or Genbank databases.

Input

• An indexed microbe reference in FASTA format (NCBI RefSeq/Genbank sequences)
• Downloaded NCBI RefSeq (and/or GenBank) catalog archive file(s)
• Downloaded NCBI taxonomy archive file

See argument documentation for information about where to download the archive files.

Output

• A binary file containing reference taxonomy information

Usage examples

 gatk PathSeqBuildReferenceTaxonomy \
   --reference microbe_reference.fasta \
   --output taxonomy.db \
   --refseq-catalog RefSeq-releaseXX.catalog.gz \
   --tax-dump taxdump.tar.gz \
   --min-non-virus-contig-length 2000
 

Notes

Often there are inconsistencies between the reference sequences, NCBI catalog, and taxonomy archive. To minimize this issue, ensure that the input files are retrieved on the same date.

Nested Class Summary

Nested classes/interfaces inherited from class org.broadinstitute.hellbender.cmdline.CommandLineProgram

CommandLineProgram.AutoCloseableNoCheckedExceptions

Field Summary

Fields

Modifier and Type	Field	Description
static final String	GENBANK_CATALOG_LONG_NAME
static final String	GENBANK_CATALOG_SHORT_NAME
String	genbankCatalogPath	This may be supplied alone or in addition to the RefSeq catalog in the case that sequences from GenBank are present in the reference.
static final String	MIN_NON_VIRUS_CONTIG_LENGTH_LONG_NAME
static final String	MIN_NON_VIRUS_CONTIG_LENGTH_SHORT_NAME
int	minNonVirusContigLength	Sequences from non-virus organisms less than this length will be filtered out such that any reads aligning to them will be ignored.
String	outputPath
protected final ReferenceInputArgumentCollection	referenceArguments
static final String	REFSEQ_CATALOG_LONG_NAME
static final String	REFSEQ_CATALOG_SHORT_NAME
String	refseqCatalogPath
static final String	TAX_DUMP_LONG_NAME
static final String	TAX_DUMP_SHORT_NAME
String	taxdumpPath

Fields inherited from class org.broadinstitute.hellbender.cmdline.CommandLineProgram

GATK_CONFIG_FILE, logger, NIO_MAX_REOPENS, NIO_PROJECT_FOR_REQUESTER_PAYS, QUIET, specialArgumentsCollection, tmpDir, useJdkDeflater, useJdkInflater, VERBOSITY

Constructor Summary

Constructors

Constructor	Description
PathSeqBuildReferenceTaxonomy()

Method Summary

Modifier and Type	Method	Description
Object	doWork()	Do the work after command line has been parsed.

Methods inherited from class org.broadinstitute.hellbender.cmdline.CommandLineProgram

customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getPluginDescriptors, getSupportInformation, getToolkitName, getToolkitShortName, getToolStatusWarning, getUsage, getVersion, instanceMain, instanceMainPostParseArgs, isBetaFeature, isExperimentalFeature, onShutdown, onStartup, parseArgs, printLibraryVersions, printSettings, printStartupMessage, runTool, setDefaultHeaders, warnOnToolStatus

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details

REFSEQ_CATALOG_LONG_NAME

public static final String REFSEQ_CATALOG_LONG_NAME

See Also:

• Constant Field Values

REFSEQ_CATALOG_SHORT_NAME

public static final String REFSEQ_CATALOG_SHORT_NAME

See Also:

• Constant Field Values

GENBANK_CATALOG_LONG_NAME

public static final String GENBANK_CATALOG_LONG_NAME

See Also:

• Constant Field Values

GENBANK_CATALOG_SHORT_NAME

public static final String GENBANK_CATALOG_SHORT_NAME

See Also:

• Constant Field Values

TAX_DUMP_LONG_NAME

public static final String TAX_DUMP_LONG_NAME

See Also:

• Constant Field Values

TAX_DUMP_SHORT_NAME

public static final String TAX_DUMP_SHORT_NAME

See Also:

• Constant Field Values

MIN_NON_VIRUS_CONTIG_LENGTH_LONG_NAME

public static final String MIN_NON_VIRUS_CONTIG_LENGTH_LONG_NAME

See Also:

• Constant Field Values

MIN_NON_VIRUS_CONTIG_LENGTH_SHORT_NAME

public static final String MIN_NON_VIRUS_CONTIG_LENGTH_SHORT_NAME

See Also:

• Constant Field Values

referenceArguments

@ArgumentCollection
protected final ReferenceInputArgumentCollection referenceArguments

outputPath

@Argument(doc="Local path for the output file. By convention, the extension should be \".db\"",
          shortName="O",
          fullName="output")
public String outputPath

refseqCatalogPath

@Argument(doc="Local path to catalog file (RefSeq-releaseXX.catalog.gz available at ftp://ftp.ncbi.nlm.nih.gov/refseq/release/release-catalog/)",
          fullName="refseq-catalog",
          shortName="RC",
          optional=true)
public String refseqCatalogPath

genbankCatalogPath

@Argument(doc="Local path to Genbank catalog file (gbXXX.catalog.XXX.txt.gz at ftp://ftp.ncbi.nlm.nih.gov/genbank/catalog/)",
          fullName="genbank-catalog",
          shortName="GC",
          optional=true)
public String genbankCatalogPath

This may be supplied alone or in addition to the RefSeq catalog in the case that sequences from GenBank are present in the reference.

taxdumpPath

@Argument(doc="Local path to taxonomy dump tarball (taxdump.tar.gz available at ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/)",
          fullName="tax-dump",
          shortName="TD")
public String taxdumpPath

minNonVirusContigLength

@Argument(doc="Minimum reference contig length for non-viruses",
          fullName="min-non-virus-contig-length",
          shortName="min-non-virus-contig-length",
          minValue=0.0,
          minRecommendedValue=500.0,
          maxRecommendedValue=10000.0)
public int minNonVirusContigLength

Sequences from non-virus organisms less than this length will be filtered out such that any reads aligning to them will be ignored. This is a quality control measure to remove shorter sequences from draft genomes that are likely to contain sequencing artifacts such as cross-species contamination or sequencing adapters. Note this may remove some bacteria plasmid sequences.

Constructor Details

PathSeqBuildReferenceTaxonomy

public PathSeqBuildReferenceTaxonomy()

Method Details

doWork

public Object doWork()

Description copied from class: CommandLineProgram

Do the work after command line has been parsed. RuntimeException may be thrown by this method, and are reported appropriately.

Specified by:

doWork in class CommandLineProgram

Returns:

the return value or null is there is none.