pro.parseq.GenomeExplorer

Class Explorer

java.lang.Object

pro.parseq.GenomeExplorer.Explorer

public class Explorer
extends Object

Reference genome sequences explorer class It wraps samtools functionality to provide it over your references References should be located in separate folders inside the "parent" references folder Each reference's folder should include 3 files: - reference fasta file - reference index file - reference dictionary file

Author:

Alexander Afanasyev aafanasyev@parseq.pro

Constructor Summary

Constructors

Constructor and Description
Explorer(String referencesFolderPath) Instantiates Explorer class Finds all references inside the "parent" folder specified

Method Summary

Modifier and Type	Method and Description
long	getContigLength(String reference, String contig) Get reference's contig length
List<String>	getReferenceContigsList(String reference) Get contigs list for reference specified
Set<String>	getReferenceGenomesList() Get available references
String	getReferenceSequence(String reference, String contig, long start, long stop, ReferenceSequenceCase sequenceCase) Get reference genome sequence for parameters specified
List<htsjdk.samtools.SAMSequenceRecord>	getReferenceSequencesList(String reference) Get references sequences for reference specified
boolean	hasContig(String reference, String contig) Returns true if reference's contig list contains contig of specified name
boolean	hasReference(String reference) Returns true if references dictionary contains mapping for specified reference name

Methods inherited from class java.lang.Object

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

Constructor Detail

Explorer

public Explorer(String referencesFolderPath)
         throws IllegalReferencesFolderPathException

Instantiates Explorer class Finds all references inside the "parent" folder specified

Parameters:

referencesFolderPath - "Parent" folder to search references in

Throws:

IllegalReferencesFolderPathException - If specified "parent" folder is not a directory

Method Detail

getReferenceGenomesList

public Set<String> getReferenceGenomesList()

Get available references

Returns:

Set of available references inside referencesFolder

hasReference

public boolean hasReference(String reference)

Returns true if references dictionary contains mapping for specified reference name

Parameters:

reference - Reference name to look for

Returns:

Whether reference is in the references dictionary

hasContig

public boolean hasContig(String reference,
                         String contig)
                  throws NoSuchReferenceException

Returns true if reference's contig list contains contig of specified name

Parameters:

reference - Reference name to look in

contig - Contig name to look for

Returns:

Whether contig is in the reference's contigs list

Throws:

NoSuchReferenceException - If there is no such reference name in the references dictionary

getContigLength

public long getContigLength(String reference,
                            String contig)
                     throws NoSuchReferenceException,
                            ContigNotFoundException

Get reference's contig length

Parameters:

reference - Reference genome name

contig - Contig id

Returns:

Reference's contig length

Throws:

NoSuchReferenceException - If there is no such reference name in the references dictionary

ContigNotFoundException - If there is no reference's contig of name specified

getReferenceSequencesList

public List<htsjdk.samtools.SAMSequenceRecord> getReferenceSequencesList(String reference)

Get references sequences for reference specified

Parameters:

reference - To get sequences of

Returns:

Sequences list, or null if no such reference

getReferenceContigsList

public List<String> getReferenceContigsList(String reference)

Get contigs list for reference specified

Parameters:

reference - To get contigs of

Returns:

Contigs list, or null if no such reference

getReferenceSequence

public String getReferenceSequence(String reference,
                                   String contig,
                                   long start,
                                   long stop,
                                   ReferenceSequenceCase sequenceCase)

Get reference genome sequence for parameters specified

Parameters:

reference - To get sequence of

contig - To get sequence of

start - To get sequence from (1-based inclusive)

stop - To get sequence to (1-based inclusive)

sequenceCase - Preferred sequence case

Returns:

Reference genome sequence bases for parameters specified, of null if no such reference