TASSELpy.net.maizegenetics.dna.snp package¶

Subpackages¶

Submodules¶

TASSELpy.net.maizegenetics.dna.snp.CoreGenotypeTable module¶

class TASSELpy.net.maizegenetics.dna.snp.CoreGenotypeTable.CoreGenotypeTable(*args, **kwargs)[source]¶

Bases: TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable

Methods

`alleleDefinitions`(*args)	For the first signature: Returns allele values as strings for all sites.
`allelePresenceForAllSites`(*args)	Returns sequence of true/false values indicating whether taxon at each site matches a specific allele (based on frequency).
`allelePresenceForAllTaxa`(*args)	Returns sequence of true/false values indicating whether site at
`allelePresenceForSitesBlock`(*args)	Returns sequence of true/false values indicating whether taxon at site
`alleles`(*args)	Returns all alleles at given site in order of frequency.
`allelesBySortType`(*args)	Returns all alleles at given site in order defined by scope
`allelesSortedByFrequency`(*args)	Return sorted list of alleles from highest frequency to lowest at given site in genotype table.
`bitStorage`(*args)	Returns BitStorage for this Genotype
`castTo`(pyType)	Casts this object to another java/python type
`chromosomalPosition`(*args)	Returns the physical position at given site
`chromosome`(*args)	Returns Chromosome for given site or with matching name
`chromosomeName`(*args)	Return chromosome name for given site
`chromosomeSiteCount`(*args)	Return number of sites for given chromosome
`chromosomes`(*args)	Return all chromosomes
`chromosomesOffsets`(*args)	Returns starting site for each chromosome
`clone`(*args)	Creates and returns a copy of this object
`compositeAlignments`(*args)	Returns individual genotype tables within this genotype table
`depth`(*args)	Returns allele depth object (null if not present)
`depthForAlleles`(*args)	Returns depth count for each diploid allele at the given taxon and site
`diploidAsString`(*args)	Returns String representation of diploid allele value at site.
`equals`(*args)	Indicates whether some other object is “equal to” this one
`firstLastSiteOfChromosome`(*args)	Get the first (inclusive) and last (exclusive) site of the specified
`genoCounts`(*args)	Returns counts of all diploid combinations from highest frequency to lowest for whole genotype table.
`genomeVersion`(*args)	Gets the Genome Assembly
`genosSortedByFrequency`(*args)	Returns sorted list of diploid values from highest frequency to lowest at given site in genotype table.
`genotype`(*args)	Returns diploid value (genotype) for a given taxon and site
`genotypeAllSites`(*args)	Returns sequence of diploid allele values for all taxa for given site.
`genotypeAllTaxa`(*args)	Returns sequence of diploid allele values for all taxa for given site.
`genotypeArray`(*args)	Returns diploid values for given taxon and site.
`genotypeAsString`(*args)	Returns string representation of diploid values returned by genotype() for given taxon and site.
`genotypeAsStringArray`(*args)	Returns string representation of diploid values returned by genotypeArray() for given taxon and site.
`genotypeAsStringRange`(*args)	Returns string representation of diploid alleles for given taxon in specified range (end site excluded).
`genotypeAsStringRow`(*args)	Returns string representation of diploid alleles for given taxon for all sites.
`genotypeMatrix`(*args)	Returns the immutable genotype matrix.
`genotypeRange`(*args)	Returns sequence of diploid allele values for given taxon in specified range (end site excluded).
`getArray`(size)	Gets an empty wrapped java array that can accept the type of the wrapped
`getClass`(*args)	Returns the runtime class of this Object.
`getDblArray`(rows[, cols])	Gets an empty wrapped java array that can accept the type of other wrapped java arrays: i.e.
`haplotypeAllelePresenceForAllSites`(*args)	Returns sequence of true/false values indicating whether taxon at each
`haplotypeAllelePresenceForAllTaxa`(*args)	Returns a sequence of true/false values indicating whether site at each taxon for given parent matches a specific allele (based on frequency).
`haplotypeAllelePresenceForSitesBlock`(*args)	Returns sequence of true/false values indicating whether taxon at sites (in given blocks, 64 sites per block including start block but excluding end block) for given parent matches a specific allele (based on frequency).
`hasAlleleProbabilities`(*args)	Returns true if this genotype table has allele probabilities
`hasDepth`(*args)	Returns true if this genotype table has sequencing depth
`hasReference`(*args)	Returns whether this genotype table has defined reference sequence.
`hashCode`(*args)	Returns a hash code vlaue for the object
`heterozygousCount`(*args)	Returns number of heterozygous taxa at given site
`heterozygousCountForTaxon`(*args)	Returns number of heterozygous sites at given taxon
`indelSize`(*args)	Returns size of indel at given site.
`isAllPolymorphic`(*args)	Returns whether all sites are polymorphic
`isHeterozygous`(*args)	Returns whether allele values at given taxon and site are heterozygous.
`isIndel`(*args)	Returns whether given site is an indel
`isPhased`(*args)	Returns whether this genotype table is phased
`isPolymorphic`(*args)	Returns whether given site is polymorphic
`isPositiveStrand`(*args)	Returns whether is positive strand at given site
`majorAllele`(*args)	Returns most common allele at given site.
`majorAlleleAsString`(*args)	Returns most common allele at given site.
`majorAlleleCount`(*args)	Returns the major allele count for given site
`majorAlleleFrequency`(*args)	Returns frequency for major allele at given site.
`majorMinorCounts`(*args)	Returns counts of all major/minor allele combinations from highest frequency to lowest for whole genotype table.
`maxNumAlleles`(*args)	Returns max number of alleles defined for any given site
`minorAllele`(*args)	Returns most common minor allele at given site.
`minorAlleleAsString`(*args)	Returns most common minor allele at given site.
`minorAlleleCount`(*args)	Returns the minor allele count for given site
`minorAlleleFrequency`(*args)	Returns frequency for most common minor allele at given site.
`minorAlleles`(*args)	Returns all minor alleles at given site.
`numChromosomes`(*args)	Return number of chromosomes
`numberOfSites`(*args)	Returns total number of sites of this genotype table
`numberOfTaxa`(*args)	Returns the number of taxa
`physicalPositions`(*args)	Returns all physical positions
`positions`(*args)	Return the position list for the gneotype table
`referenceAllele`(*args)	Returns reference diploid allele values at given site.
`referenceAlleleForAllSites`(*args)	Returns reference sequence of diploid allele values.
`referenceAlleles`(*args)	Returns reference sequence of diploid allele values for given taxon in specified range (end site not included).
`retainsRareAlleles`(*args)	Returns true if this genotype table retains rare alleles.
`siteName`(*args)	Get SNP ID for specified site
`siteOfPhysicalPosition`(*args)	Returns sites of given physical position/SNP ID in chromosome.
`siteScore`(*args)	Returns the site score of the given taxon and site
`siteScores`(*args)	Returns the site scores
`taxa`(*args)	Return taxa list of this genotype table
`taxaName`(*args)	Returns taxa name at given index
`toString`(*args)	Returns a string representation of the object
`totalGametesNonMissingForSite`(*args)	Returns total number of non-missing allele values for given site.
`totalGametesNonMissingForTaxon`(*args)	Returns total number of non-missing allele values for given taxon.
`totalNonMissingForSite`(*args)	Returns total number of non-missing taxa for given site.
`totalNonMissingForTaxon`(*args)	Returns total number of non-missing sites for given taxon.
`wrap_existing_array`(arr_instance)	Wraps a java array of this class’s type

__init__(*args, **kwargs)[source]¶

Instantiates a CoreGenotypeTable

Signature:	CoreGenotypeTable (GenotypeCallTable genotype, PositionList positionList, TaxaList taxaList, SiteScore siteScore, AlleleDepth alleleDepth)
Signature:	CoreGenotypeTable (GenotypeCallTable genotype, PositionList positionList, TaxaList taxaList)

TASSELpy.net.maizegenetics.dna.snp.FilterGenotypeTable module¶

class TASSELpy.net.maizegenetics.dna.snp.FilterGenotypeTable.FilterGenotypeTable(*args, **kwargs)[source]¶

Bases: TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable

Methods

alleleDefinitions(*args) For the first signature: Returns allele values as strings for all sites.

allelePresenceForAllSites(*args) Returns sequence of true/false values indicating whether taxon at each site matches a specific allele (based on frequency).

allelePresenceForAllTaxa(*args) Returns sequence of true/false values indicating whether site at

allelePresenceForSitesBlock(*args) Returns sequence of true/false values indicating whether taxon at site

alleles(*args) Returns all alleles at given site in order of frequency.

allelesBySortType(*args) Returns all alleles at given site in order defined by scope

allelesSortedByFrequency(*args) Return sorted list of alleles from highest frequency to lowest at given site in genotype table.

bitStorage(*args) Returns BitStorage for this Genotype

castTo(pyType) Casts this object to another java/python type

chromosomalPosition(*args) Returns the physical position at given site

chromosome(*args) Returns Chromosome for given site or with matching name

chromosomeName(*args) Return chromosome name for given site

chromosomeSiteCount(*args) Return number of sites for given chromosome

chromosomes(*args) Return all chromosomes

chromosomesOffsets(*args) Returns starting site for each chromosome

clone(*args) Creates and returns a copy of this object

compositeAlignments(*args) Returns individual genotype tables within this genotype table

depth(*args) Returns allele depth object (null if not present)

depthForAlleles(*args) Returns depth count for each diploid allele at the given taxon and site

diploidAsString(*args) Returns String representation of diploid allele value at site.

equals(*args) Indicates whether some other object is “equal to” this one

firstLastSiteOfChromosome(*args) Get the first (inclusive) and last (exclusive) site of the specified

functionalFilters(genoTable[, sitesFilter, ...])

genoCounts(*args) Returns counts of all diploid combinations from highest frequency to lowest for whole genotype table.

genomeVersion(*args) Gets the Genome Assembly

genosSortedByFrequency(*args) Returns sorted list of diploid values from highest frequency to lowest at given site in genotype table.

genotype(*args) Returns diploid value (genotype) for a given taxon and site

genotypeAllSites(*args) Returns sequence of diploid allele values for all taxa for given site.

genotypeAllTaxa(*args) Returns sequence of diploid allele values for all taxa for given site.

genotypeArray(*args) Returns diploid values for given taxon and site.

genotypeAsString(*args) Returns string representation of diploid values returned by genotype() for given taxon and site.

genotypeAsStringArray(*args) Returns string representation of diploid values returned by genotypeArray() for given taxon and site.

genotypeAsStringRange(*args) Returns string representation of diploid alleles for given taxon in specified range (end site excluded).

genotypeAsStringRow(*args) Returns string representation of diploid alleles for given taxon for all sites.

genotypeMatrix(*args) Returns the immutable genotype matrix.

genotypeRange(*args) Returns sequence of diploid allele values for given taxon in specified range (end site excluded).

getArray(size) Gets an empty wrapped java array that can accept the type of the wrapped

getBaseAlignment(*args)

signature:	getBaseAlignment ()

getBaseSitesShown(*args) Returns sites from original alignment that are viewable (not filtered) by

getClass(*args) Returns the runtime class of this Object.

getDblArray(rows[, cols]) Gets an empty wrapped java array that can accept the type of other wrapped java arrays: i.e.

getInstance(*args) This returns FilterGenotypeTable with only specified subTaxaList.

getInstanceRemoveIDs(*args) Removes specific IDs

getInstanceRemoveSiteNames(*args) Removes specific named sites

haplotypeAllelePresenceForAllSites(*args) Returns sequence of true/false values indicating whether taxon at each

haplotypeAllelePresenceForAllTaxa(*args) Returns a sequence of true/false values indicating whether site at each taxon for given parent matches a specific allele (based on frequency).

haplotypeAllelePresenceForSitesBlock(*args) Returns sequence of true/false values indicating whether taxon at sites (in given blocks, 64 sites per block including start block but excluding end block) for given parent matches a specific allele (based on frequency).

hasAlleleProbabilities(*args) Returns true if this genotype table has allele probabilities

hasDepth(*args) Returns true if this genotype table has sequencing depth

hasReference(*args) Returns whether this genotype table has defined reference sequence.

hashCode(*args) Returns a hash code vlaue for the object

heterozygousCount(*args) Returns number of heterozygous taxa at given site

heterozygousCountForTaxon(*args) Returns number of heterozygous sites at given taxon

indelSize(*args) Returns size of indel at given site.

isAllPolymorphic(*args) Returns whether all sites are polymorphic

isHeterozygous(*args) Returns whether allele values at given taxon and site are heterozygous.

isIndel(*args) Returns whether given site is an indel

isPhased(*args) Returns whether this genotype table is phased

isPolymorphic(*args) Returns whether given site is polymorphic

isPositiveStrand(*args) Returns whether is positive strand at given site

isSiteFilter(*args)

signature:	isSiteFilter ()

isSiteFilterByRange(*args)

signature:	isSiteFilterByRange ()

isTaxaFilter(*args)

signature:	isTaxaFilter ()

majorAllele(*args) Returns most common allele at given site.

majorAlleleAsString(*args) Returns most common allele at given site.

majorAlleleCount(*args) Returns the major allele count for given site

majorAlleleFrequency(*args) Returns frequency for major allele at given site.

majorMinorCounts(*args) Returns counts of all major/minor allele combinations from highest frequency to lowest for whole genotype table.

maxNumAlleles(*args) Returns max number of alleles defined for any given site

minorAllele(*args) Returns most common minor allele at given site.

minorAlleleAsString(*args) Returns most common minor allele at given site.

minorAlleleCount(*args) Returns the minor allele count for given site

minorAlleleFrequency(*args) Returns frequency for most common minor allele at given site.

minorAlleles(*args) Returns all minor alleles at given site.

numChromosomes(*args) Return number of chromosomes

numberOfSites(*args) Returns total number of sites of this genotype table

numberOfTaxa(*args) Returns the number of taxa

physicalPositions(*args) Returns all physical positions

positions(*args) Return the position list for the gneotype table

referenceAllele(*args) Returns reference diploid allele values at given site.

referenceAlleleForAllSites(*args) Returns reference sequence of diploid allele values.

referenceAlleles(*args) Returns reference sequence of diploid allele values for given taxon in specified range (end site not included).

retainsRareAlleles(*args) Returns true if this genotype table retains rare alleles.

reverseTranslateSite(*args) Returns site of this FilterGenotypeTable based on given site from

siteName(*args) Get SNP ID for specified site

siteOfPhysicalPosition(*args) Returns sites of given physical position/SNP ID in chromosome.

siteScore(*args) Returns the site score of the given taxon and site

siteScores(*args) Returns the site scores

taxa(*args) Return taxa list of this genotype table

taxaName(*args) Returns taxa name at given index

toString(*args) Returns a string representation of the object

totalGametesNonMissingForSite(*args) Returns total number of non-missing allele values for given site.

totalGametesNonMissingForTaxon(*args) Returns total number of non-missing allele values for given taxon.

totalNonMissingForSite(*args) Returns total number of non-missing taxa for given site.

totalNonMissingForTaxon(*args) Returns total number of non-missing sites for given taxon.

translateSite(*args)

signature:	translateSite (int site)

translateTaxon(*args)

signature:	translateTaxon (int taxon)

wrap_existing_array(arr_instance) Wraps a java array of this class’s type

__init__(*args, **kwargs)[source]¶

static functionalFilters(genoTable, sitesFilter=None, taxaFilter=None)[source]¶

getBaseAlignment(*args)[source]¶

Signature:	getBaseAlignment ()

getBaseSitesShown(*args)[source]¶

Returns sites from original alignment that are viewable (not filtered) by this filter alignment

Signature:	getBaseSitesShown ()
Returns:	list of sites
Return type:	int[]

static getInstance(*args)[source]¶

This returns FilterGenotypeTable with only specified subTaxaList. Defaults to retain unknown taxa. If retainUnkownTaxa is true then Alignment will return unknown values for missing taxa

Signature:	getInstance (GenotypeTable a, TaxaList subTaxaList)
Signature:	getInstance (GenotypeTable a, TaxaList subTaxaList, boolean retainUnknownTaxa)
Signature:	getInstance (GenotypeTable a, int[] subSites)
Signature:	getInstance (GenotypeTable a, String[] siteNamesToKeep)
Signature:	getInstance (GenotypeTable a, String chromosome, int startPhysicalPos, int endPhysicalPos)
Signature:	getInstance (GenotypeTable a, Chromosome chromosome, int startPhysicalPos, int endPhysicalPos)
Signature:	getInstance (GenotypeTable a, Chromosome chromosome)
Signature:	getInstance (GenotypeTable a, int startSite, int endSite)
Parameters:	a (GenotypeTable) – alignment subTaxaList (TaxaList) – subset id group retainUnknownTaxa (boolean) – whether to retain unknown taxa subSites (int[]) – subset of sites you want siteNamesToKeep (String[]) – names of the sites to keep chromosome (Chromosome) – name of chromosome startPhysicalPos (int) – starting physical position endPhysicalPos (int) – ending physical position startSite (int) – start site (inclusive) endSite (int) – end site (inclusive)
Returns:	filter alignment
Return type:	GenotypeTable

static getInstanceRemoveIDs(*args)[source]¶

Removes specific IDs

Signature:	getInstanceRemoveIDs (GenotypeTable a, TaxaList subTaxaList)
Parameters:	a (GenotypeTable) – alignment to filter subTaxaList (TaxaList) – specified IDs
Returns:	Filtered Alignment
Return type:	GenotypeTable

static getInstanceRemoveSiteNames(*args)[source]¶

Removes specific named sites

Signature:	getInstanceRemoveSiteNames (GenotypeTable a, String[] siteNamesToRemove)
Parameters:	a (GenotypeTable) – alignment siteNamesToRemove (String[]) – names of the sites to remove
Returns:	Filtered Alignment
Return type:	FilterGenotypeTable

isSiteFilter(*args)[source]¶

Signature:	isSiteFilter ()

isSiteFilterByRange(*args)[source]¶

Signature:	isSiteFilterByRange ()

isTaxaFilter(*args)[source]¶

Signature:	isTaxaFilter ()

reverseTranslateSite(*args)[source]¶

Returns site of this FilterGenotypeTable based on given site from embedded Alignment

Signature:	reverseTranslateSite (int site)
Parameters:	site (int) – site
Returns:	site of this FilterGenotypeTable based on given site from embedded Alignment
Return type:	int

translateSite(*args)[source]¶

Signature:	translateSite (int site)
Parameters:	site (int) – site

translateTaxon(*args)[source]¶

Signature:	translateTaxon (int taxon)
Parameters:	taxon (int) – taxon

TASSELpy.net.maizegenetics.dna.snp.GenotypeTable module¶

class TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.GenotypeTable(*args, **kwargs)[source]¶

Bases: TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.MetaGenotypeTable

A representation of the SNP and indel variation for a set of taxa and genomic positions.

GenotypeTable always consists of a TaxaList, PositionList, and GenotypeCallTable. Additionally, as needed they also represent alleles in bit form, with sequencing depth, or other scores (e.g. quality scores).

Use GenotypeTableBuilder to create GenotypeTable

Methods

`alleleDefinitions`(*args)	For the first signature: Returns allele values as strings for all sites.
`allelePresenceForAllSites`(*args)	Returns sequence of true/false values indicating whether taxon at each site matches a specific allele (based on frequency).
`allelePresenceForAllTaxa`(*args)	Returns sequence of true/false values indicating whether site at
`allelePresenceForSitesBlock`(*args)	Returns sequence of true/false values indicating whether taxon at site
`alleles`(*args)	Returns all alleles at given site in order of frequency.
`allelesBySortType`(*args)	Returns all alleles at given site in order defined by scope
`allelesSortedByFrequency`(*args)	Return sorted list of alleles from highest frequency to lowest at given site in genotype table.
`bitStorage`(*args)	Returns BitStorage for this Genotype
`castTo`(pyType)	Casts this object to another java/python type
`chromosomalPosition`(*args)	Returns the physical position at given site
`chromosome`(*args)	Returns Chromosome for given site or with matching name
`chromosomeName`(*args)	Return chromosome name for given site
`chromosomeSiteCount`(*args)	Return number of sites for given chromosome
`chromosomes`(*args)	Return all chromosomes
`chromosomesOffsets`(*args)	Returns starting site for each chromosome
`clone`(*args)	Creates and returns a copy of this object
`compositeAlignments`(*args)	Returns individual genotype tables within this genotype table
`depth`(*args)	Returns allele depth object (null if not present)
`depthForAlleles`(*args)	Returns depth count for each diploid allele at the given taxon and site
`diploidAsString`(*args)	Returns String representation of diploid allele value at site.
`equals`(*args)	Indicates whether some other object is “equal to” this one
`firstLastSiteOfChromosome`(*args)	Get the first (inclusive) and last (exclusive) site of the specified
`genoCounts`(*args)	Returns counts of all diploid combinations from highest frequency to lowest for whole genotype table.
`genomeVersion`(*args)	Gets the Genome Assembly
`genosSortedByFrequency`(*args)	Returns sorted list of diploid values from highest frequency to lowest at given site in genotype table.
`genotype`(*args)	Returns diploid value (genotype) for a given taxon and site
`genotypeAllSites`(*args)	Returns sequence of diploid allele values for all taxa for given site.
`genotypeAllTaxa`(*args)	Returns sequence of diploid allele values for all taxa for given site.
`genotypeArray`(*args)	Returns diploid values for given taxon and site.
`genotypeAsString`(*args)	Returns string representation of diploid values returned by genotype() for given taxon and site.
`genotypeAsStringArray`(*args)	Returns string representation of diploid values returned by genotypeArray() for given taxon and site.
`genotypeAsStringRange`(*args)	Returns string representation of diploid alleles for given taxon in specified range (end site excluded).
`genotypeAsStringRow`(*args)	Returns string representation of diploid alleles for given taxon for all sites.
`genotypeMatrix`(*args)	Returns the immutable genotype matrix.
`genotypeRange`(*args)	Returns sequence of diploid allele values for given taxon in specified range (end site excluded).
`getArray`(size)	Gets an empty wrapped java array that can accept the type of the wrapped
`getClass`(*args)	Returns the runtime class of this Object.
`getDblArray`(rows[, cols])	Gets an empty wrapped java array that can accept the type of other wrapped java arrays: i.e.
`haplotypeAllelePresenceForAllSites`(*args)	Returns sequence of true/false values indicating whether taxon at each
`haplotypeAllelePresenceForAllTaxa`(*args)	Returns a sequence of true/false values indicating whether site at each taxon for given parent matches a specific allele (based on frequency).
`haplotypeAllelePresenceForSitesBlock`(*args)	Returns sequence of true/false values indicating whether taxon at sites (in given blocks, 64 sites per block including start block but excluding end block) for given parent matches a specific allele (based on frequency).
`hasAlleleProbabilities`(*args)	Returns true if this genotype table has allele probabilities
`hasDepth`(*args)	Returns true if this genotype table has sequencing depth
`hasReference`(*args)	Returns whether this genotype table has defined reference sequence.
`hashCode`(*args)	Returns a hash code vlaue for the object
`heterozygousCount`(*args)	Returns number of heterozygous taxa at given site
`heterozygousCountForTaxon`(*args)	Returns number of heterozygous sites at given taxon
`indelSize`(*args)	Returns size of indel at given site.
`isAllPolymorphic`(*args)	Returns whether all sites are polymorphic
`isHeterozygous`(*args)	Returns whether allele values at given taxon and site are heterozygous.
`isIndel`(*args)	Returns whether given site is an indel
`isPhased`(*args)	Returns whether this genotype table is phased
`isPolymorphic`(*args)	Returns whether given site is polymorphic
`isPositiveStrand`(*args)	Returns whether is positive strand at given site
`majorAllele`(*args)	Returns most common allele at given site.
`majorAlleleAsString`(*args)	Returns most common allele at given site.
`majorAlleleCount`(*args)	Returns the major allele count for given site
`majorAlleleFrequency`(*args)	Returns frequency for major allele at given site.
`majorMinorCounts`(*args)	Returns counts of all major/minor allele combinations from highest frequency to lowest for whole genotype table.
`maxNumAlleles`(*args)	Returns max number of alleles defined for any given site
`minorAllele`(*args)	Returns most common minor allele at given site.
`minorAlleleAsString`(*args)	Returns most common minor allele at given site.
`minorAlleleCount`(*args)	Returns the minor allele count for given site
`minorAlleleFrequency`(*args)	Returns frequency for most common minor allele at given site.
`minorAlleles`(*args)	Returns all minor alleles at given site.
`numChromosomes`(*args)	Return number of chromosomes
`numberOfSites`(*args)	Returns total number of sites of this genotype table
`numberOfTaxa`(*args)	Returns the number of taxa
`physicalPositions`(*args)	Returns all physical positions
`positions`(*args)	Return the position list for the gneotype table
`referenceAllele`(*args)	Returns reference diploid allele values at given site.
`referenceAlleleForAllSites`(*args)	Returns reference sequence of diploid allele values.
`referenceAlleles`(*args)	Returns reference sequence of diploid allele values for given taxon in specified range (end site not included).
`retainsRareAlleles`(*args)	Returns true if this genotype table retains rare alleles.
`siteName`(*args)	Get SNP ID for specified site
`siteOfPhysicalPosition`(*args)	Returns sites of given physical position/SNP ID in chromosome.
`siteScore`(*args)	Returns the site score of the given taxon and site
`siteScores`(*args)	Returns the site scores
`taxa`(*args)	Return taxa list of this genotype table
`taxaName`(*args)	Returns taxa name at given index
`toString`(*args)	Returns a string representation of the object
`totalGametesNonMissingForSite`(*args)	Returns total number of non-missing allele values for given site.
`totalGametesNonMissingForTaxon`(*args)	Returns total number of non-missing allele values for given taxon.
`totalNonMissingForSite`(*args)	Returns total number of non-missing taxa for given site.
`totalNonMissingForTaxon`(*args)	Returns total number of non-missing sites for given taxon.
`wrap_existing_array`(arr_instance)	Wraps a java array of this class’s type

ALLELE_SORT_TYPE = <Frequency: 0, Depth: 1, Global_Frequency: 2, Reference: 3>¶

SITE_SCORE_TYPE = <None: 0, QualityScore: 1, ReferenceProbablity: 2, Dosage: 3, DepthA: 4, DepthC: 5, DepthG: 6, DepthT: 7, DepthGap: 8, DepthInsertion: 9, ProbA: 10, ProbC: 11, ProbG: 12, ProbT: 13, ProbGap: 14, ProbInsertion: 15>¶

__init__(*args, **kwargs)[source]¶

alleleDefinitions(*args)[source]¶

For the first signature: Returns allele values as strings for all sites. The first dimension of this array indexes the sites. The second dimension indexes the allele values for the given site. The indices for the allele values are used as the codes to store data. These codes (indices) are returned by the genotype() methods. If only one array of allele values is returned, that is the encoding for all sites For the second signature: Same as alleleDefinitions() for only one site

Signature:	alleleDefinitions ()
Signature:	alleleDefinitions (int site)
Parameters:	site (int) – site
Returns:	String[][] alleleDefinitions() allele values for all sites String[] alleleDefinitions(int site) allele values for given site
Return type:	String[][]

allelePresenceForAllSites(*args)[source]¶

Returns sequence of true/false values indicating whether taxon at each site matches a specific allele (based on frequency). Allele number of value 0 would be the major allele. Allele number of value 1 would be the minor allele. Allele number of value 2 would be the third most frequent allele value and so on.

Signature:	allelePresenceForAllSites (int taxon, WHICH_ALLELE allele)
Parameters:	taxon (int) – taxon (int) allele (WHICH_ALLELE) – allele (WHICH_ALLELE)
Returns:	Sequence of true/false value (BitSet)
Return type:	BitSet

allelePresenceForAllTaxa(*args)[source]¶

Returns sequence of true/false values indicating whether site at each taxon matches a specific allele

Signature:	allelePresenceForAllTaxa (int site, WHICH_ALLELE allele)
Parameters:	site (int) – site allele (WHICH_ALLELE) – allele
Returns:	sequence of true/false values
Return type:	BitSet

allelePresenceForSitesBlock(*args)[source]¶

Returns sequence of true/false values indicating whether taxon at site (in given blocks, 64 sites per block including start block but excluding end block) matches a specific allele

Signature:	allelePresenceForSitesBlock (int taxon, WHICH_ALLELE allele, int startBlock, int endBlock)
Parameters:	taxon (int) – taxon (int) allele (WHICH_ALLELE) – allele (WHICH_ALLELE) startBlock (int) – starting block (int) endBlock (int) – end block (int)
Returns:	Sequence of true/false values (long[])
Return type:	long[]

alleles(*args)[source]¶

Returns all alleles at given site in order of frequency. Gap is included as state. Heterozygous count one for each allele value. Homozygous counts two for the allele value

Signature:	alleles (int site)
Parameters:	site (int) – site
Returns:	All alleles
Return type:	byte[]

allelesBySortType(*args)[source]¶

Returns all alleles at given site in order defined by scope

Signature:	allelesBySortType (GenotypeTable.ALLELE_SORT_TYPE scope, int site)
Parameters:	scope (GenotypeTable.ALLELE_SORT_TYPE) – scope site (int) – site
Returns:	alleles
Return type:	byte[]

allelesSortedByFrequency(*args)[source]¶

Return sorted list of alleles from highest frequency to lowest at given site in genotype table. Resulting double dimension array holds alleles (bytes) in result[0]. And the counts are in result[1]. Counts haploid values twice and diploid values once. Higher ploids are not supported

Signature:	allelesSortedByFrequency (int site)
Parameters:	site (int) – site
Returns:	sorted list of alleles and counts
Return type:	int[][]

bitStorage(*args)[source]¶

Returns BitStorage for this Genotype

Signature:	bitStorage (GenotypeTable.WHICH_ALLELE allele)
Parameters:	allele (GenotypeTable.WHICH_ALLELE) – allele
Returns:	BitStorage
Return type:	BitStorage

chromosomalPosition(*args)[source]¶

Returns the physical position at given site

Signature:	chromosomalPosition (int site)
Parameters:	site (int) – site
Returns:	physical position
Return type:	int

chromosome(*args)[source]¶

Returns Chromosome for given site or with matching name (first to match will be returned)

Signature:	chromosome (int site)
Signature:	chromosome (String name)
Parameters:	site (int) – site Chromosome chromosome(String name): name (String) – name
Returns:	Chromosome
Return type:	Chromosome

chromosomeName(*args)[source]¶

Return chromosome name for given site

Signature:	chromosomeName (int site)
Parameters:	site (int) – site
Returns:	Chromosome name
Return type:	String

chromosomeSiteCount(*args)[source]¶

Return number of sites for given chromosome

Signature:	chromosomeSiteCount (Chromosome chromosome)
Parameters:	chromosome (Chromosome) – chromosome
Returns:	Number of sites
Return type:	int

chromosomes(*args)[source]¶

Return all chromosomes

Signature:	chromosomes ()
Returns:	chromosomes
Return type:	Chromosome[]

chromosomesOffsets(*args)[source]¶

Returns starting site for each chromosome

Signature:	chromosomesOffsets ()
Returns:	Starting site for each chromosome
Return type:	int[]

compositeAlignments(*args)[source]¶

Returns individual genotype tables within this genotype table

Signature:	compositeAlignments ()
Returns:	list of genotype tables
Return type:	GenotypeTable[]

depth(*args)[source]¶

Returns allele depth object (null if not present)

Signature:	depth ()
Returns:	allele depth associated with genotypeTable
Return type:	AlleleDepth

depthForAlleles(*args)[source]¶

Returns depth count for each diploid allele at the given taxon and site

Signature:	depthForAlleles (int taxon, int site)
Parameters:	taxon (int) – taxon site (int) – site
Returns:	two counts
Return type:	int[]

diploidAsString(*args)[source]¶

Returns String representation of diploid allele value at site.

Signature:	diploidAsString (int site, byte value)
Parameters:	site (int) – site value (byte) – diploid allele value
Returns:	String representation
Return type:	String

firstLastSiteOfChromosome(*args)[source]¶

Get the first (inclusive) and last (exclusive) site of the specified chromosome in this genotype table

Signature:	firstLastSiteOfChromosome (Chromosome chromosome)
Parameters:	chromosome (Chromosome) – chromosome
Returns:	first and last site
Return type:	int[]

genoCounts(*args)[source]¶

Returns counts of all diploid combinations from highest frequency to lowest for whole genotype table. Resulting double dimension array holds diploids (Strings) in result[0]. And the counts are in result[1] (Longs)

Signature:	genoCounts ()
Returns:	diploid counts
Return type:	Object[][]

genomeVersion(*args)[source]¶

Gets the Genome Assembly

Signature:	genomeVersion ()
Returns:	The genome assembly
Return type:	String

genosSortedByFrequency(*args)[source]¶

Returns sorted list of diploid values from highest frequency to lowest at given site in genotype table. Resulting double dimension array holds diploids (Strings) in result[0]. And the counts are in result[1] (Integers).

Signature:	genosSortedByFrequency (int site)
Parameters:	site (int) – site
Returns:	Sorted list of diploids and counts
Return type:	Object[][]

genotype(*args)[source]¶

Returns diploid value (genotype) for a given taxon and site

Signature:	genotype (int taxon, int site)
Signature:	genotype (int taxon, Chromosome chromosome, int physicalPosition)
Parameters:	taxon (int) – taxon site (int) – site genotype(int taxon, Chromosome chromosome, int physicalPosition): chromosome (Chromosome) – chromosome physicalPosition (int) – physicalPosition
Returns:	High four bits generally encode more frequent allele and lower four bits encode the less frequent allele
Return type:	byte

genotypeAllSites(*args)[source]¶

Returns sequence of diploid allele values for all taxa for given site. Each value in array is what would be returned by genotype().

Signature:	genotypeAllSites (int taxon)
Parameters:	site – site
Returns:	Sequence of diploid allele values
Return type:	byte[]

genotypeAllTaxa(*args)[source]¶

Returns sequence of diploid allele values for all taxa for given site. Each value in array is what would be returned by genotype().

Signature:	genotypeAllTaxa (int site)
Parameters:	site (int) – site
Returns:	Sequence of diploid allele values
Return type:	byte[]

genotypeArray(*args)[source]¶

Returns diploid values for given taxon and site. Same values as genotype(), except two values are already separated into two bytes.

Signature:	genotypeArray (int taxon, int site)
Parameters:	taxon (int) – taxon site (int) – site
Returns:	First byte (index 0) holds first allele value in right-most four bits. Second byte (index 1) holds second allele value in right-most four bits
Return type:	byte[]

genotypeAsString(*args)[source]¶

Returns string representation of diploid values returned by genotype() for given taxon and site. The two allele values will be separated by a colon (:) delimiter.

Signature:	genotypeAsString (int taxon, int site)
Signature:	genotypeAsString (int site, byte value)
Parameters:	taxon (int) – taxon (int) site (int) – site (int) value (byte) – allele value
Returns:	string representation of diploid values
Return type:	String

genotypeAsStringArray(*args)[source]¶

Returns string representation of diploid values returned by genotypeArray() for given taxon and site. Same two allele values as genotypeAsString(), except already separated by two Strings.

Signature:	genotypeAsStringArray (int taxon, int site)
Parameters:	taxon (int) – taxon (int) site (int) – site (int)
Returns:	string representation of diploid values
Return type:	String[]

genotypeAsStringRange(*args)[source]¶

Returns string representation of diploid alleles for given taxon in specified range (end site excluded). Each value in string is what would be retuned by genotypeAsString()

Signature:	genotypeAsStringRange (int taxon, int startSite, int endSite)
Parameters:	taxon (int) – taxon (int) startSite (int) – start site (int) endSite (int) – end site (int)
Returns:	string representation of alleles in range
Return type:	String

genotypeAsStringRow(*args)[source]¶

Returns string representation of diploid alleles for given taxon for all sites. Each value in string is what would be returned by genotypeAsString()

Signature:	genotypeAsStringRow (int taxon)
Parameters:	taxon (int) – taxon (int)
Returns:	string representaiton of alleles
Return type:	String

genotypeMatrix(*args)[source]¶

Returns the immutable genotype matrix. Taxa and positions are not part of the matrix. This method is used for copying genotype tables, when either the taxa or positions have changed

Signature:	genotypeMatrix ()
Returns:	Genotype matrix
Return type:	GenotypeCallTable

genotypeRange(*args)[source]¶

Returns sequence of diploid allele values for given taxon in specified range (end site excluded). Each value in array is what would be returned by genotype()

Signature:	genotypeRange (int taxon, int startSite, int endSite)
Parameters:	taxon (int) – taxon startSite (int) – start site endSite (int) – end site
Returns:	Sequence of diploid allele values
Return type:	byte[]

haplotypeAllelePresenceForAllSites(*args)[source]¶

Returns sequence of true/false values indicating whether taxon at each site for given parent matches a specific allele

Signature:	haplotypeAllelePresenceForAllSites (int taxon, boolean firstParent, WHICH_ALLELE allele)
Parameters:	taxon (int) – taxon (int) firstParent (boolean) – true for first parent (false for second parent) allele (WHICH_ALLELE) – allele (WHICH_ALLELE)
Returns:	Sequence of true/false values (BitSet)
Return type:	BitSet

haplotypeAllelePresenceForAllTaxa(*args)[source]¶

Returns a sequence of true/false values indicating whether site at each taxon for given parent matches a specific allele (based on frequency). Allele number of value 0 would be the major allele. Allele number of value 1 would be the minor allele. Allele number of value 2 would be the third most frequent allele value and so on

Signature:	haplotypeAllelePresenceForAllTaxa (int site, boolean firstParent, WHICH_ALLELE allele)
Parameters:	site (int) – site (int) firstParent (boolean) – true for first parent (false for second parent) allele (WHICH_ALLELE) – allele (WHICH_ALLELE)
Returns:	Sequence of true/false values (BitSet)
Return type:	BitSet

haplotypeAllelePresenceForSitesBlock(*args)[source]¶

Returns sequence of true/false values indicating whether taxon at sites (in given blocks, 64 sites per block including start block but excluding end block) for given parent matches a specific allele (based on frequency). Allele number of value 0 would be the major allele. Allele number of value 1 would be the minor allele. Allele number of value 2 would be the third most frequent allele value and so on.

Signature:	haplotypeAllelePresenceForSitesBlock (int taxon, boolean firstParent, WHICH_ALLELE allele, int startBlock, int endBlock)
Parameters:	taxon (int) – taxon (int) firstParent (boolean) – true for first parent (false for second parent) allele (WHICH_ALLELE) – allele (WHICH_ALLELE) startBlock (int) – starting block (int) endBlock (int) – ending block (int)

hasAlleleProbabilities(*args)[source]¶

Returns true if this genotype table has allele probabilities

Signature:	hasAlleleProbabilities ()
Returns:	true if this genotype table has allele probabilities
Return type:	boolean

hasDepth(*args)[source]¶

Returns true if this genotype table has sequencing depth

Signature:	hasDepth ()
Returns:	True if this genotype table has sequencing depth
Return type:	boolean

hasReference(*args)[source]¶

Returns whether this genotype table has defined reference sequence.

Signature:	hasReference ()
Returns:	True if this genotype table has reference sequence
Return type:	boolean

heterozygousCount(*args)[source]¶

Returns number of heterozygous taxa at given site

Signature:	heterozygousCount (int site)
Parameters:	site (int) – site
Returns:	Number of heterozygous taxa
Return type:	int

heterozygousCountForTaxon(*args)[source]¶

Returns number of heterozygous sites at given taxon

Signature:	heterozygousCountForTaxon (int taxon)
Parameters:	taxon (int) – taxon
Returns:	number of heterozygous sites
Return type:	int

indelSize(*args)[source]¶

Returns size of indel at given site.

Signature:	indelSize (int site)
Parameters:	site (int) – site
Returns:	indel size
Return type:	int

isAllPolymorphic(*args)[source]¶

Returns whether all sites are polymorphic

Signature:	isAllPolymorphic ()
Returns:	true if all sites are polymorphic
Return type:	boolean

isHeterozygous(*args)[source]¶

Returns whether allele values at given taxon and site are heterozygous.

Signature:	isHeterozygous (int taxon, int site)
Parameters:	taxon (int) – taxon site (int) – site
Returns:	Whether heterozygous
Return type:	boolean

isIndel(*args)[source]¶

Returns whether given site is an indel

Signature:	isIndel (int site)
Parameters:	site (int) – site
Returns:	true if indel
Return type:	boolean

isPhased(*args)[source]¶

Returns whether this genotype table is phased

Signature:	isPhased ()
Returns:	true if phased
Return type:	boolean

isPolymorphic(*args)[source]¶

Returns whether given site is polymorphic

Signature:	isPolymorphic (int site)
Parameters:	site (int) – site
Returns:	true if given site is polymorphic
Return type:	boolean

isPositiveStrand(*args)[source]¶

Returns whether is positive strand at given site

Signature:	isPositiveStrand (int site)
Parameters:	site (int) – site
Returns:	whether is positive strand
Return type:	boolean

majorAllele(*args)[source]¶

Returns most common allele at given site. Gap is included as state. Heterozygous count one for each allele value. Homozygous counts two for the allele value

Signature:	majorAllele (int site)
Parameters:	site (int) – site
Returns:	most common allele
Return type:	byte

majorAlleleAsString(*args)[source]¶

Returns most common allele at given site. Gap is included as state. Heterozygous count one for each allele value. Homozygous counts two for allele value

Signature:	majorAlleleAsString (int site)
Parameters:	site (int) – site
Returns:	most common allele as String
Return type:	String

majorAlleleCount(*args)[source]¶

Returns the major allele count for given site

Signature:	majorAlleleCount (int site)
Parameters:	site (int) – site
Returns:	major allele count
Return type:	int

majorAlleleFrequency(*args)[source]¶

Returns frequency for major allele at given site. Gap is included as state. Heterozygous count one for each allele value. Homozygous counts two for the allele value

Signature:	majorAlleleFrequency (int site)
Parameters:	site (int) – site
Returns:	frequency
Return type:	double

majorMinorCounts(*args)[source]¶

Returns counts of all major/minor allele combinations from highest frequency to lowest for whole genotype table. Resulting double dimension array holds major/minor allele (Strings) in result[0]. And the counts are in result[1] (Longs)

Signature:	majorMinorCounts ()
Returns:	diploid counts
Return type:	Object[][]

maxNumAlleles(*args)[source]¶

Returns max number of alleles defined for any given site

Signature:	maxNumAlleles ()
Returns:	max number of alleles
Return type:	int

minorAllele(*args)[source]¶

Returns most common minor allele at given site. Gap is included as state. Heterozygous count one for each allele value. Homozygous counts two for the allele value

Signature:	minorAllele (int site)
Parameters:	site (int) – site
Returns:	most common minor allele
Return type:	byte

minorAlleleAsString(*args)[source]¶

Returns most common minor allele at given site. Gap is included as state. Heterozygous count one for each allele value. Homozygous counts two for allele value

Signature:	minorAlleleAsString (int site)
Parameters:	site (int) – site
Returns:	most common minor allele as String
Return type:	String

minorAlleleCount(*args)[source]¶

Returns the minor allele count for given site

Signature:	minorAlleleCount (int site)
Parameters:	site (int) – site
Returns:	minor allele count
Return type:	int

minorAlleleFrequency(*args)[source]¶

Returns frequency for most common minor allele at given site. Gap is included as state. Heterozygous count one for each allele value. Homozygous counts two for the allele value

Signature:	minorAlleleFrequency (int site)
Parameters:	site (int) – site
Returns:	frequency
Return type:	double

minorAlleles(*args)[source]¶

Returns all minor alleles at given site. Gap is included as state Heterozygous count one for each allele value. Homozygous counts two for the allele value

Signature:	minorAlleles (int site)
Parameters:	site (int) – site

numChromosomes(*args)[source]¶

Return number of chromosomes

Signature:	numChromosomes ()
Returns:	Number of chromosomes
Return type:	int

numberOfSites(*args)[source]¶

Returns total number of sites of this genotype table

Signature:	numberOfSites ()
Returns:	Number of sites
Return type:	int

numberOfTaxa(*args)[source]¶

Returns the number of taxa

Signature:	numberOfTaxa ()
Returns:	Number of taxa
Return type:	int

physicalPositions(*args)[source]¶

Returns all physical positions

Signature:	physicalPositions ()
Returns:	physical positions
Return type:	int[]

positions(*args)[source]¶

Return the position list for the gneotype table

Signature:	positions ()
Returns:	PositionList for all sites
Return type:	PositionList

referenceAllele(*args)[source]¶

Returns reference diploid allele values at given site.

Signature:	referenceAllele (int site)
Parameters:	site (int) – site
Returns:	First 4 bits are the first allele value and the second 4 bits are the second allele value.
Return type:	byte

referenceAlleleForAllSites(*args)[source]¶

Returns reference sequence of diploid allele values. Each value in array contains both diploid values. First 4 bits holds the first allele, and the second 4 bits holds the second allele

Signature:	referenceAlleleForAllSites ()
Returns:	Reference sequence of diploid allele values
Return type:	byte[]

referenceAlleles(*args)[source]¶

Returns reference sequence of diploid allele values for given taxon in specified range (end site not included). Each value in array contains both diploid values. First 4 bits holds the first allele, and the second 4 bits holds the second allele

Signature:	referenceAlleles (int startSite, int endSite)
Parameters:	startSite (int) – start site endSite (int) – end site
Returns:	Reference sequence of diploid allele values
Return type:	byte[]

retainsRareAlleles(*args)[source]¶

Returns true if this genotype table retains rare alleles. If false, rare alleles are recorded as unknown

Signature:	retainsRareAlleles ()
Returns:	Whether rare alleles are retained
Return type:	boolean

siteName(*args)[source]¶

Get SNP ID for specified site

Signature:

String siteName(int site)

Arguments:

site – site

Returns:

Site name

siteOfPhysicalPosition(*args)[source]¶

Returns sites of given physical position/SNP ID in chromosome. If the physical position doesn’t exist, (-(insertion point) -1) is returned. If chromosome is not found, an exception is thrown. This can support multiple sites with the same physical position but different SNP IDs

Signature:	siteOfPhysicalPosition (int physicalPosition, Chromosome chromosome)
Signature:	siteOfPhysicalPosition (int physicalPosition, Chromosome chromosome, String snpName)
Parameters:	physicalPosition (int) – physical position chromosome (Chromosome) – chromosome. If null, the first chromosome is used snpName (String) – SNP ID
Returns:	Index
Return type:	int

siteScore(*args)[source]¶

Returns the site score of the given taxon and site

Signature:	siteScore (int taxon, int site)
Parameters:	taxon (int) – taxon index site (int) – site
Returns:	site score
Return type:	float

siteScores(*args)[source]¶

Returns the site scores

Signature:	siteScores ()
Returns:	site scores
Return type:	float[][]

taxa(*args)[source]¶

Return taxa list of this genotype table

Signature:	taxa ()
Returns:	taxa list
Return type:	TaxaList

taxaName(*args)[source]¶

Returns taxa name at given index

Signature:	taxaName (int index)
Parameters:	index (int) – index
Returns:	taxa name
Return type:	String

totalGametesNonMissingForSite(*args)[source]¶

Returns total number of non-missing allele values for given site. This can be twice the number of taxa, as diploid values are supported

Signature:	totalGametesNonMissingForSite (int site)
Parameters:	site (int) – site
Returns:	Number of non-missing allele values
Return type:	int

totalGametesNonMissingForTaxon(*args)[source]¶

Returns total number of non-missing allele values for given taxon. This can be twice the number of sites, as diploid values are supported

Signature:	totalGametesNonMissingForTaxon (int taxon)
Parameters:	taxon (int) – taxon
Returns:	Number of non-missing allele values
Return type:	int

totalNonMissingForSite(*args)[source]¶

Returns total number of non-missing taxa for given site. Taxa are considered missing only if both allele values are Unknown (N).

Signature:	totalNonMissingForSite (int site)
Parameters:	site (int) – site
Returns:	Number of non-missing taxa
Return type:	int

totalNonMissingForTaxon(*args)[source]¶

Returns total number of non-missing sites for given taxon. Sites are considered missing only if both allele values are Unknown (N).

Signature:	totalNonMissingForTaxon (int taxon)
Parameters:	taxon (int) – taxon
Returns:	number of non-missing sites
Return type:	int

class TASSELpy.net.maizegenetics.dna.snp.GenotypeTable.MetaGenotypeTable(*args, **kwargs)[source]¶

Bases: TASSELpy.java.lang.Object.Object

Methods

`castTo`(pyType)	Casts this object to another java/python type
`clone`(*args)	Creates and returns a copy of this object
`equals`(*args)	Indicates whether some other object is “equal to” this one
`getArray`(size)	Gets an empty wrapped java array that can accept the type of the wrapped
`getClass`(*args)	Returns the runtime class of this Object.
`getDblArray`(rows[, cols])	Gets an empty wrapped java array that can accept the type of other wrapped java arrays: i.e.
`hashCode`(*args)	Returns a hash code vlaue for the object
`toString`(*args)	Returns a string representation of the object
`wrap_existing_array`(arr_instance)	Wraps a java array of this class’s type

TASSELpy.net.maizegenetics.dna.snp.GenotypeTableBuilder module¶

TASSELpy.net.maizegenetics.dna.snp.GenotypeTableUtils module¶

class TASSELpy.net.maizegenetics.dna.snp.GenotypeTableUtils.GenotypeTableUtils(*args, **kwargs)[source]¶

Bases: TASSELpy.java.lang.Object.Object

Utility methods for comparing, sorting, and counting genotypes

Methods

`calcBitPresenceFromGenotype`(*args)	Method for getting TBits rapidly from major and minor allele arrays
`castTo`(pyType)	Casts this object to another java/python type
`clone`(*args)	Creates and returns a copy of this object
`equals`(*args)	Indicates whether some other object is “equal to” this one
`getAlleleStates`(*args)	Gets the String states of alleles
`getAlleles`(*args)	Gets the alleles at a site
`getAllelesSortedByFrequency`(*args)	This sorts alleles by frequency.
`getArray`(size)	Gets an empty wrapped java array that can accept the type of the wrapped
`getClass`(*args)	Returns the runtime class of this Object.
`getDataBytes`(*args)	Gets the data as bytes
`getDblArray`(rows[, cols])	Gets an empty wrapped java array that can accept the type of other wrapped java arrays: i.e.
`getDiploidValue`(*args)	Combines 2 allele values into 1 diploid value.
`getDiploidValuePhased`(*args)	Combines 2 allele values into one diploid value.
`getDiploidValues`(*args)	Separates diploid allele value into its two values.
`getDiploidsSortedByFrequency`(*args)	Gets the diploids sorted by frequency
`getIncludedSitesBasedOnFreqIgnoreMissing`(*args)	Get sites to be included based on minimum frequency (the count
`getUnphasedDiploidValue`(*args)	Combines 2 allele values into 1 diploid value.
`getUnphasedDiploidValueNoHets`(*args)	Combines 2 genotype values into 1 diploid value.
`hashCode`(*args)	Returns a hash code vlaue for the object
`isEqual`(*args)	Returns whether two diploid allele values are equal, ignoring order
`isEqualOrUnknown`(*args)	Returns whether two diploid allele values are equal, ignoring order,
`isHeterozygous`(*args)	Returns whether diploid allele values are heterozygous.
`isPartiallyEqual`(*args)	Returns true if at least one allele agrees
`removeSitesBasedOnFreqIgnoreMissing`(*args)	Remove sites based on minimum frequency (the count of good bases,
`removeSitesOutsideRange`(*args)	Remove sites based on site position (excluded sites are <firstSite and
`toString`(*args)	Returns a string representation of the object
`wrap_existing_array`(arr_instance)	Wraps a java array of this class’s type

__init__(*args, **kwargs)[source]¶

static calcBitPresenceFromGenotype(*args)[source]¶

Method for getting TBits rapidly from major and minor allele arrays

Signature:	calcBitPresenceFromGenotype (byte[] genotype, byte[] mjA, byte[] mnA)
Signature:	calcBitPresenceFromGenotype (byte[] genotype, byte[] referenceValues)
Signature:	calcBitPresenceFromGenotype (byte[] genotype, byte mj, byte mn)
Signature:	calcBitPresenceFromGenotype (byte[] genotype, byte referenceValue)
Parameters:	genotype (byte[]) – genotype mjA (byte[]) – major alleles mnA (byte[]) – minor alleles referenceValues (byte[]) – reference mj (byte) – major byte mn (byte) – minor byte referenceValue (byte) – reference
Returns:	Tbits
Return type:	BitSet[]

static getAlleleStates(*args)[source]¶

Gets the String states of alleles

Signature:	getAlleleStates (String[][] data, int maxNumAlleles)
Parameters:	data (String[][]) – data maxNumAlleles (int) – maximum number of alleles
Returns:	The allele states at all loci
Return type:	String[][]

static getAlleles(*args)[source]¶

Gets the alleles at a site

Signature:	getAlleles (byte[][] data, int site)
Parameters:	data (byte[][]) – data site (int) – site
Returns:	Alleles at site
Return type:	byte[]

static getAllelesSortedByFrequency(*args)[source]¶

This sorts alleles by frequency. Each cell in the given array contains a diploid value which is separated and counted individually. Resulting double dimension array holds alleles (bytes) in result[0]. And the counts are in result[1]. Counts haploid values twice and diploid vlaues once. Higher ploidies are not supported

Signature:	getAllelesSortedByFrequency (byte[] data)
Signature:	getAllelesSortedByFrequency (byte[][] data, int site)
Signature:	getAllelesSortedByFrequency (String[][] data, int site)
Signature:	getAllelesSortedByFrequency (GenotypeTable alignment, int site)
Parameters:	data (String[][]) – data site (int) – site alignment (GenotypeTable) – an alignment
Returns:	alleles and counts
Return type:	int[][]

static getDataBytes(*args)[source]¶

Gets the data as bytes

Signature:	getDataBytes (String[] data)
Signature:	getDataBytes (String[][] data, String[][] alleleStates, int maxNumAlleles)
Parameters:	data (String[][]) – data alleleStates (String[][]) – allele states maxNumAlleles (int) – maximum number of alleles
Returns:	data as bytes
Return type:	byte[][]

static getDiploidValue(*args)[source]¶

Combines 2 allele values into 1 diploid value. Assumed phased

Signature:	getDiploidValue (byte a, byte b)
Parameters:	a (byte) – allele 1 b (byte) – allele 2
Returns:	diploid value
Return type:	byte

static getDiploidValuePhased(*args)[source]¶

Combines 2 allele values into one diploid value. Assumed phased

Signature:	getDiploidValuePhased (byte a, byte b)
Parameters:	a (byte) – allele 1 b (byte) – allele 2
Returns:	diploid value
Return type:	byte

static getDiploidValues(*args)[source]¶

Separates diploid allele value into its two values.

Signature:	getDiploidValues (byte genotype)
Parameters:	genotype (byte) – diploid value
Returns:	separated allele values
Return type:	byte[]

static getDiploidsSortedByFrequency(*args)[source]¶

Gets the diploids sorted by frequency

Signature:	getDiploidsSortedByFrequency (GenotypeTable alignment, int site)
Parameters:	alignment (GenotypeTable) – alignment site (int) – site
Returns:	Diploids, sorted by frequency
Return type:	Object[][]

static getIncludedSitesBasedOnFreqIgnoreMissing(*args)[source]¶

Get sites to be included based on minimum frequency (the count of good bases, INCLUDING GAPS) and based on the proportion of good sites (INCLUDING GAPS) different from consensus

Signature:	getIncludedSitesBasedOnFreqIgnoreMissing (GenotypeTable aa, double minimumProportion, double maximumProportion, int minimumCount)
Parameters:	aa (GenotypeTable) – the AnnotatedAlignment to filter minimumProportion (double) – minimum proportion of sites different from the consensus maximumProportion (double) – maximum proportion of sites different from the consensus minimumCount (int) – minimum number of sequences with a good base or a gap (but not N or ?)
Returns:	The sites to be included
Return type:	int[]

static getUnphasedDiploidValue(*args)[source]¶

Combines 2 allele values into 1 diploid value. In alphabetical order.

Signature:	getUnphasedDiploidValue (byte a, byte b)
Parameters:	a (byte) – allele 1 b (byte) – allele 2
Returns:	diploid value sorted by order A < C < G < T
Return type:	byte

static getUnphasedDiploidValueNoHets(*args)[source]¶

Combines 2 genotype values into 1 diploid value. Returns unknown if either parent is heterozygous or unknown, or alleles are swapped.

Signature:	getUnphasedDiploidValueNoHets (byte g1, byte g2)
Parameters:	g1 (byte) – genotype 1 g2 (byte) – genotype 2
Returns:	diploid value
Return type:	byte

static isEqual(*args)[source]¶

Returns whether two diploid allele values are equal, ignoring order

Signature:	isEqual (byte[] alleles1, byte[] alleles2)
Signature:	isEqual (byte diploidAllele1, byte diploidAllele2)
Parameters:	alleles1 (byte[]) – diploid alleles 1 alleles2 (byte[]) – diploid alleles 2 diploidAllele1 (byte) – diploid alleles 1 diploidAllele2 (byte) – diploid alleles 2
Returns:	true if equal
Return type:	boolean

static isEqualOrUnknown(*args)[source]¶

Returns whether two diploid allele values are equal, ignoring order, where unknown values equal anything

Signature:	isEqualOrUnknown (byte[] alleles1, byte[] alleles2)
Signature:	isEqualOrUnknown (byte diploidAllele1, byte diploidAllele2)
Parameters:	alleles1 (byte[]) – diploid alleles 1 alleles2 (byte[]) – diploid alleles 2 diploidAllele1 (byte) – diploid alleles 1 diploidAllele2 (byte) – diploid alleles 2
Returns:	true if equal
Return type:	boolean

static isHeterozygous(*args)[source]¶

Returns whether diploid allele values are heterozygous. First 4 bits in byte is one allele value. Second 4 bits is other allele value

Signature:	isHeterozygous (byte diploidAllele)
Parameters:	diploidAllele (byte) – alleles
Returns:	true if allele values different; false if values the same
Return type:	boolean

static isPartiallyEqual(*args)[source]¶

Returns true if at least one allele agrees

Signature:	isPartiallyEqual (byte genotype1, byte genotype2)
Parameters:	genotype1 (byte) – genotype 1 genotype2 (byte) – genotype 2
Returns:	true if at least 1 allele is equal
Return type:	boolean

static removeSitesBasedOnFreqIgnoreMissing(*args)[source]¶

Remove sites based on minimum frequency (the count of good bases, INCLUDING GAPS) and based on the proportion of good alleles (including gaps) different from consensus

Signatures:

static GenotypeTable removeSitesBasedOnFreqIgnoreMissing(GenotypeTable aa,: double minimumProportion, double maximumProportion, int minimumCount)

Arguments:

aa – the AnnotatedAlignment to filter minimumProportion – minimum proportion of sites different from the

consensus

maxmimumProportion – maximum proportion of sites different from the: consensus
minimumCount – minimum number of sequences with good bases (not N or ?),: where GAP IS CONSIDERED A GOOD BASE

Returns:

filtered GenotypeTable

static removeSitesOutsideRange(*args)[source]¶

Remove sites based on site position (excluded sites are <firstSite and > lastSite) This does not affect any prior exclusions

Signature:	removeSitesOutsideRange (GenotypeTable aa, int firstSite, int lastSite)
Parameters:	aa (GenotypeTable) – the AnnotatedAlignment to filter firstSite (int) – first site to keep in the range lastSite (int) – last site to keep in the range
Returns:	Filtered GenotypeTable
Return type:	GenotypeTable

TASSELpy.net.maizegenetics.dna.snp.ImportUtils module¶

class TASSELpy.net.maizegenetics.dna.snp.ImportUtils.ImportUtils(*args, **kwargs)[source]¶

Bases: TASSELpy.java.lang.Object.Object

Methods

`castTo`(pyType)	Casts this object to another java/python type
`clone`(*args)	Creates and returns a copy of this object
`equals`(*args)	Indicates whether some other object is “equal to” this one
`getArray`(size)	Gets an empty wrapped java array that can accept the type of the wrapped
`getClass`(*args)	Returns the runtime class of this Object.
`getDblArray`(rows[, cols])	Gets an empty wrapped java array that can accept the type of other wrapped java arrays: i.e.
`hashCode`(*args)	Returns a hash code vlaue for the object
`readFasta`(*args)	Read GenotypeTable from a fasta file
`readFromHapmap`(*args)	Read GenotypeTable from HapMap file
`readFromPLink`(*args)	Read GenotypeTable from PLink files
`readFromVCF`(*args)	Reads from a VCF file
`readGuessFormat`(*args)	Reads in a file after guessing its format
`toString`(*args)	Returns a string representation of the object
`wrap_existing_array`(arr_instance)	Wraps a java array of this class’s type

__init__(*args, **kwargs)[source]¶

static readFasta(*args)[source]¶

Read GenotypeTable from a fasta file

Signature:	readFasta (String filename)
Parameters:	filename (String) – The name of the file
Returns:	A GenotypeTable
Return type:	GenotypeTable

static readFromHapmap(*args)[source]¶

Read GenotypeTable from HapMap file

Signatures:

static GenotypeTable readFromHapmap(final String filename) static GenotypeTable readFromHapmap(final String filename, ProgressListener listener)

Arguments:

static GenotypeTable readFromHapmap(final String filename): filename – The name of the file
static GenotypeTable readFromHapmap(final String filename, ProgressListener listener): filename – The name of the file listener – A progresslistener (can be null)

Returns:

A GenotypeTable

static readFromPLink(*args)[source]¶

Read GenotypeTable from PLink files

Signatures:

static GenotypeTable readFromPLink(final String pedFilename,: final String mapFilename, ProgressListener listener)

Arguments:

static GenotypeTable readFromPLink(final String pedFilename,: final String mapFilename, ProgressListener listener)

pedFilename – The name of the ped file mapFilename – The name of the map file listener – A progresslistener (can be null)

Returns:

A GenotypeTable

static readFromVCF(*args)[source]¶

Reads from a VCF file

Signatures:

static GenotypeTable readFromVCF(final String filename, ProgressListener listener) static GenotypeTable readFromVCF(final String filename, ProgressListener listener,

boolean ignoreDepth)

Arguments:

static GenotypeTable readFromVCF(final String filename, ProgressListener listener): filename – The name of the file listener – A progresslistener (can be null)
static GenotypeTable readFromVCF(final String filename, ProgressListener listener,: boolean ignoreDepth)

filename – The name of the file listener – A progresslistener (can be null) ignoreDepth – Whether to ignore depth information

Returns:

A GenotypeTable

static readGuessFormat(*args)[source]¶

Reads in a file after guessing its format

Signature:	readGuessFormat (String fileName)
Parameters:	fileName (String) – The name of the file
Returns:	A GenotypeTable
Return type:	GenotypeTable

TASSELpy.net.maizegenetics.dna.snp package¶

Subpackages¶

Submodules¶

TASSELpy.net.maizegenetics.dna.snp.CoreGenotypeTable module¶

TASSELpy.net.maizegenetics.dna.snp.FilterGenotypeTable module¶

TASSELpy.net.maizegenetics.dna.snp.GenotypeTable module¶

TASSELpy.net.maizegenetics.dna.snp.GenotypeTableBuilder module¶

TASSELpy.net.maizegenetics.dna.snp.GenotypeTableUtils module¶

TASSELpy.net.maizegenetics.dna.snp.ImportUtils module¶

Module contents¶

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TASSELpy.net.maizegenetics.dna.snp package¶

Subpackages¶

Submodules¶

TASSELpy.net.maizegenetics.dna.snp.CoreGenotypeTable module¶

TASSELpy.net.maizegenetics.dna.snp.FilterGenotypeTable module¶

TASSELpy.net.maizegenetics.dna.snp.GenotypeTable module¶

TASSELpy.net.maizegenetics.dna.snp.GenotypeTableBuilder module¶

TASSELpy.net.maizegenetics.dna.snp.GenotypeTableUtils module¶

TASSELpy.net.maizegenetics.dna.snp.ImportUtils module¶

Module contents¶

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