org.broadinstitute.hellbender.tools.spark.pathseq

Class PSBuildReferenceTaxonomyUtils

java.lang.Object

org.broadinstitute.hellbender.tools.spark.pathseq.PSBuildReferenceTaxonomyUtils

public final class PSBuildReferenceTaxonomyUtils
extends java.lang.Object

Field Summary

Fields

Modifier and Type	Field and Description
protected static org.apache.logging.log4j.Logger	logger

Constructor Summary

Constructors

Constructor and Description
PSBuildReferenceTaxonomyUtils()

Method Summary

Modifier and Type	Method and Description
protected static java.util.Map<java.lang.String,java.lang.Integer>	buildAccessionToTaxIdMap(java.util.Map<java.lang.Integer,PSPathogenReferenceTaxonProperties> taxIdToProperties, PSTree tree, int minNonVirusContigLength) Create reference_name-to-taxid map (just an inversion on taxIdToProperties)
protected static PSTree	buildTaxonomicTree(java.util.Map<java.lang.Integer,PSPathogenReferenceTaxonProperties> taxIdToProperties) Returns a PSTree representing a reduced taxonomic tree containing only taxa present in the reference
static java.io.BufferedReader	getBufferedReaderGz(java.lang.String path) Gets a buffered reader for a gzipped file
static java.io.BufferedReader	getBufferedReaderTarGz(java.lang.String tarPath, java.lang.String fileName) Gets a Reader for a file in a gzipped tarball
protected static java.util.Set<java.lang.String>	parseCatalog(java.io.BufferedReader reader, java.util.Map<java.lang.String,scala.Tuple2<java.lang.String,java.lang.Long>> accessionToNameAndLength, java.util.Map<java.lang.Integer,PSPathogenReferenceTaxonProperties> taxIdToProperties, boolean bGenBank, java.util.Set<java.lang.String> accessionsNotFoundIn) Builds maps of reference contig accessions to their taxonomic ids and vice versa.
protected static void	parseNamesFile(java.io.BufferedReader reader, java.util.Map<java.lang.Integer,PSPathogenReferenceTaxonProperties> taxIdToProperties) Parses scientific name of each taxon and puts it in taxIdToProperties
protected static java.util.Collection<java.lang.Integer>	parseNodesFile(java.io.BufferedReader reader, java.util.Map<java.lang.Integer,PSPathogenReferenceTaxonProperties> taxIdToProperties) Gets the rank and parent of each taxon.
protected static java.util.Map<java.lang.String,scala.Tuple2<java.lang.String,java.lang.Long>>	parseReferenceRecords(java.util.List<htsjdk.samtools.SAMSequenceRecord> dictionaryList, java.util.Map<java.lang.Integer,PSPathogenReferenceTaxonProperties> taxIdToProperties) Build set of accessions contained in the reference.
static void	writeTaxonomyDatabase(java.lang.String filePath, PSTaxonomyDatabase taxonomyDatabase) Writes objects using Kryo to specified local file path.

Methods inherited from class java.lang.Object

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

Field Detail

logger

protected static final org.apache.logging.log4j.Logger logger

Constructor Detail

PSBuildReferenceTaxonomyUtils

public PSBuildReferenceTaxonomyUtils()

Method Detail

parseReferenceRecords

protected static java.util.Map<java.lang.String,scala.Tuple2<java.lang.String,java.lang.Long>> parseReferenceRecords(java.util.List<htsjdk.samtools.SAMSequenceRecord> dictionaryList,
                                                                                                                     java.util.Map<java.lang.Integer,PSPathogenReferenceTaxonProperties> taxIdToProperties)

Build set of accessions contained in the reference. Returns: a map from accession to the name and length of the record. If the sequence name contains the taxonomic ID, it instead gets added to taxIdToProperties. Later we merge both results into taxIdToProperties. Method: First, look for either "taxid||" or "ref||" in the sequence name. If neither of those are found, use the first word of the name as the accession.

parseCatalog

protected static java.util.Set<java.lang.String> parseCatalog(java.io.BufferedReader reader,
                                                              java.util.Map<java.lang.String,scala.Tuple2<java.lang.String,java.lang.Long>> accessionToNameAndLength,
                                                              java.util.Map<java.lang.Integer,PSPathogenReferenceTaxonProperties> taxIdToProperties,
                                                              boolean bGenBank,
                                                              java.util.Set<java.lang.String> accessionsNotFoundIn)

Builds maps of reference contig accessions to their taxonomic ids and vice versa. Input can be a RefSeq or Genbank catalog file. accNotFound is an initial list of accessions from the reference that have not been successfully looked up; if null, will be initialized to the accToRefInfo key set by default.

Returns a collection of reference accessions that could not be found, if any.

parseNamesFile

protected static void parseNamesFile(java.io.BufferedReader reader,
                                     java.util.Map<java.lang.Integer,PSPathogenReferenceTaxonProperties> taxIdToProperties)

Parses scientific name of each taxon and puts it in taxIdToProperties

parseNodesFile

protected static java.util.Collection<java.lang.Integer> parseNodesFile(java.io.BufferedReader reader,
                                                                        java.util.Map<java.lang.Integer,PSPathogenReferenceTaxonProperties> taxIdToProperties)

Gets the rank and parent of each taxon. Returns a Collection of tax ID's found in the nodes file that are not in taxIdToProperties (i.e. were not found in a reference sequence name using the taxid|\ tag or the catalog file).

buildAccessionToTaxIdMap

protected static java.util.Map<java.lang.String,java.lang.Integer> buildAccessionToTaxIdMap(java.util.Map<java.lang.Integer,PSPathogenReferenceTaxonProperties> taxIdToProperties,
                                                                                            PSTree tree,
                                                                                            int minNonVirusContigLength)

Create reference_name-to-taxid map (just an inversion on taxIdToProperties)

buildTaxonomicTree

protected static PSTree buildTaxonomicTree(java.util.Map<java.lang.Integer,PSPathogenReferenceTaxonProperties> taxIdToProperties)

Returns a PSTree representing a reduced taxonomic tree containing only taxa present in the reference

getBufferedReaderGz

public static java.io.BufferedReader getBufferedReaderGz(java.lang.String path)

Gets a buffered reader for a gzipped file

Parameters:

path - File path

Returns:

Reader for the file

getBufferedReaderTarGz

public static java.io.BufferedReader getBufferedReaderTarGz(java.lang.String tarPath,
                                                            java.lang.String fileName)

Gets a Reader for a file in a gzipped tarball

Parameters:

tarPath - Path to the tarball

fileName - File within the tarball

Returns:

The file's reader

writeTaxonomyDatabase

public static void writeTaxonomyDatabase(java.lang.String filePath,
                                         PSTaxonomyDatabase taxonomyDatabase)

Writes objects using Kryo to specified local file path. NOTE: using setReferences(false), which must also be set when reading the file. Does not work with nested objects that reference its parent.