TASSELpy.net.maizegenetics.dna.map package

Submodules

TASSELpy.net.maizegenetics.dna.map.Chromosome module

class TASSELpy.net.maizegenetics.dna.map.Chromosome.Chromosome(*args, **kwargs)

Bases: TASSELpy.net.maizegenetics.dna.map.Chromosome.MetaChromosome

Defines the chromosome structure and length. The name and length recorded for each chromosome

Methods

castTo(pyType)	Casts this object to another java/python type
clone(*args)	Creates and returns a copy of this object
compareTo(*args)	Compares this object with the specified object for order.
equals(*args)	Indicates whether some other object is “equal to” this one
getAllAnnotationEntries(*args)	Returns all annotation Map.Entries
getAnnotation(*args)	Returns all annotation value for a given annotation key
getAnnotationAsMap(*args)	Returns all annotations in TreeMap
getArray(size)	Gets an empty wrapped java array that can accept the type of the wrapped
getAverageAnnotation(*args)	Returns average annotation for a given annotation key
getCanonicalChromosome(*args)	signature:getCanonicalChromosome (Chromosome chr)
getChromosomeNumber(*args)	Returns the integer value of the chromosome (if name is not a number
getClass(*args)	Returns the runtime class of this Object.
getConsensusAnnotation(*args)	Returns consensus value for given annotation key
getDblArray(rows[, cols])	Gets an empty wrapped java array that can accept the type of other wrapped java arrays: i.e.
getLength(*args)	Gets the length of the chromosome in base pairs
getName(*args)	Gets the name of the chromosome
getQuantAnnotation(*args)	Returns all annotation value for given annotation key
getTextAnnotation(*args)	Returns all annotation values for a given annotation key
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

__init__(*args, **kwargs)

Instantiates a Chromosome object

Signature:

Chromosome (String name, int length, GeneralAnnotation features)

Signature:

Chromosome (String name)

Parameters:

• name (String) – Name of the chromosome
• length (int) – Length of chromosome in base pairs
• features (GeneralAnnotation) – Map of features about the chromosome

static getCanonicalChromosome(*args)

Signature:getCanonicalChromosome (Chromosome chr)

getChromosomeNumber(*args)

Returns the integer value of the chromosome (if name is not a number then Integer.MAX_VALUE is returned

Signature:getChromosomeNumber () Returns:The integer value of the chromosome Return type:int

getLength(*args)

Gets the length of the chromosome in base pairs

Signature:getLength () Returns:The length of the chromosome in base pairs Return type:int

getName(*args)

Gets the name of the chromosome

Signature:getName () Returns:The name of the chromosome Return type:String

class TASSELpy.net.maizegenetics.dna.map.Chromosome.MetaChromosome(*args, **kwargs)

Bases: TASSELpy.java.lang.Comparable.Comparable, TASSELpy.net.maizegenetics.util.GeneralAnnotation.GeneralAnnotation

Methods

castTo(pyType)	Casts this object to another java/python type
clone(*args)	Creates and returns a copy of this object
compareTo(*args)	Compares this object with the specified object for order.
equals(*args)	Indicates whether some other object is “equal to” this one
getAllAnnotationEntries(*args)	Returns all annotation Map.Entries
getAnnotation(*args)	Returns all annotation value for a given annotation key
getAnnotationAsMap(*args)	Returns all annotations in TreeMap
getArray(size)	Gets an empty wrapped java array that can accept the type of the wrapped
getAverageAnnotation(*args)	Returns average annotation for a given annotation key
getClass(*args)	Returns the runtime class of this Object.
getConsensusAnnotation(*args)	Returns consensus value for given annotation key
getDblArray(rows[, cols])	Gets an empty wrapped java array that can accept the type of other wrapped java arrays: i.e.
getQuantAnnotation(*args)	Returns all annotation value for given annotation key
getTextAnnotation(*args)	Returns all annotation values for a given annotation key
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.map.Position module

class TASSELpy.net.maizegenetics.dna.map.Position.Position(*args, **kwargs)

Bases: TASSELpy.java.lang.Comparable.Comparable, TASSELpy.net.maizegenetics.util.GeneralAnnotation.GeneralAnnotation

Defines a genomic position and its known variants. Includes attributes of chromosome, position, strand, centiMorgans, name (or SNP ID), whether this position is a nucleotide, or includes an indel

Methods

castTo(pyType)	Casts this object to another java/python type
clone(*args)	Creates and returns a copy of this object
compareTo(*args)	Compares this object with the specified object for order.
equals(*args)	Indicates whether some other object is “equal to” this one
getAllAnnotationEntries(*args)	Returns all annotation Map.Entries
getAllele(*args)	Returns the allele specified by alleleType, if unkonwn Alignment.Unknown is returned
getAnnotation(*args)	Returns all annotation value for a given annotation key
getAnnotationAsMap(*args)	Returns all annotations in TreeMap
getArray(size)	Gets an empty wrapped java array that can accept the type of the wrapped
getAverageAnnotation(*args)	Returns average annotation for a given annotation key
getCM(*args)	Return the genetic position for a site definition
getChromosome(*args)	Return the locus (generally a chromosome) of a site
getClass(*args)	Returns the runtime class of this Object.
getConsensusAnnotation(*args)	Returns consensus value for given annotation key
getDblArray(rows[, cols])	Gets an empty wrapped java array that can accept the type of other wrapped java arrays: i.e.
getGlobalMAF(*args)	Return the minor allele frequency in a global scope
getGlobalSiteCoverage(*args)	Returns the proportion of genotypes scored at a given site
getKnownVariants(*args)	Returns the nature of the polymorphism (“ACTAT”, “-“} or {“A”,”C”,”G”} or {“100”,”103”,”106”}
getPosition(*args)	Return the physical position of a site
getQuantAnnotation(*args)	Returns all annotation value for given annotation key
getSNPID(*args)	Return the ID (name) for a site
getStrand(*args)	Return the strand for a site definition
getTextAnnotation(*args)	Returns all annotation values for a given annotation key
hashCode(*args)	Returns a hash code vlaue for the object
isIndel(*args)	Whether the position includes indels, which would be defined in the variants
isNucleotide(*args)	Whether the position is a nucleotide position or another marker type (SSR, AFLP, RAPD,
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)

getAllele(*args)

Returns the allele specified by alleleType, if unkonwn Alignment.Unknown is returned

Signature:getAllele (Allele alleleType) Parameters:alleleType (Allele) – An alleleType Returns:The allele specified by alleleType Return type:byte

getCM(*args)

Return the genetic position for a site definition

Signature:getCM () Returns:The genetic position for a site definition Return type:float

getChromosome(*args)

Return the locus (generally a chromosome) of a site

Signatures:

Chromosome getChromosome

Returns:

The locus of a site

getGlobalMAF(*args)

Return the minor allele frequency in a global scope

Signature:getGlobalMAF () Returns:the minor allele frequency in a global scope Return type:float

getGlobalSiteCoverage(*args)

Returns the proportion of genotypes scored at a given site

Signature:getGlobalSiteCoverage () Returns:The proportion of genotypes scored at a given site Return type:float

getKnownVariants(*args)

Returns the nature of the polymorphism (“ACTAT”, “-“} or {“A”,”C”,”G”} or {“100”,”103”,”106”}

Signature:getKnownVariants () Returns:The nature of the polymorphism Return type:String[]

getPosition(*args)

Return the physical position of a site

Signature:getPosition () Returns:The physical position of a site Return type:int

getSNPID(*args)

Return the ID (name) for a site

Signature:getSNPID () Returns:The ID (name) for a site Return type:String

getStrand(*args)

Return the strand for a site definition

Signature:getStrand () Returns:The strand for a site definition Return type:byte

isIndel(*args)

Whether the position includes indels, which would be defined in the variants

Signature:isIndel () Returns:Whether the position includes indels Return type:boolean

isNucleotide(*args)

Whether the position is a nucleotide position or another marker type (SSR, AFLP, RAPD, CNV, which are recorded with text states)

Signature:isNucleotide () Returns:Whether the position is a nucleotide position Return type:boolean

TASSELpy.net.maizegenetics.dna.map.PositionList module

class TASSELpy.net.maizegenetics.dna.map.PositionList.PositionList(*args, **kwargs)

Bases: TASSELpy.java.util.FilterList.FilterList

List of Positions in the genome. This type is used by every GenotypeTable, but it can also be used as list of GWAS results and other genomic annotations

Methods

add(*args)	Ensures that this collection contains the specified element.
addAll(*args)	Adds all of the elements in the specified collection to this collection.
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
clear(*args)	Removes all of the elements from this collection.
clone(*args)	Creates and returns a copy of this object
contains(*args)	Returns true if this collection contains the specified element.
containsAll(*args)	Returns true if this collection contains all of the elements in the specified collection
equals(*args)	Indicates whether some other object is “equal to” this one
filterEnumerator(filterFunc)	Enumerates the list, returning index and items for which a function
filterIterator(filterFunc)	Iterates through the list, but only returns items for which a function evaluates True.
genomeVersion(*args)	Gets the Genome Assembly
get(*args)	Returns the element at the specified position in this list
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.
hasReference(*args)	Returns whether this alignment has defined reference sequence.
hashCode(*args)	Returns a hash code vlaue for the object
indelSize(*args)	Returns size of indel at given site.
indexOf(*args)	Returns the index of the first occurrence of the specified element in this list, or -1 if this list does not contain the element.
isEmpty(*args)	Returns true if this collection contains no elements
isIndel(*args)	Returns whether given site is an indel
isPositiveStrand(*args)	Returns whether is positive strand at given site
iterator(*args)	Returns an iterator over a set of elements of type T
lastIndexOf(*args)	Returns the index of the last occurrence of the specified element in this list, or -1 if this list does not contain the element.
listIterator(*args)	Returns a list iterator over the elements in this list
numChromosomes(*args)	Return number of chromosomes
numberOfSites(*args)	Returns total number of sites of this genotype table
physicalPositions(*args)	Returns all physical positions
referenceGenotype(*args)	Return the reference diploid allele values at given site
referenceGenotypeForAllSites(*args)	Returns reference sequence of diploid allele values.
referenceGenotypes(*args)	Returns reference sequence of diploid allele values for given taxon in specified range (end site not included).
remove(*args)	Removes a single instance of the specified element from this collection, if it is present.
removeAll(*args)	Removes all of this collection’s elements that are also contained in the specified collection.
retainAll(*args)	Retains only the elements in this collection that are contained in the specified collection.
set(*args)	Replaces the element at the specified position in this list with
siteName(*args)	Get SNP ID for specified site
siteOfPhysicalPosition(*args)	Returns sites of given physical position/SNP ID in chromosome.
size(*args)	Returns the number of elements in this collection.
startAndEndOfChromosome(*args)	Get the first (inclusive) and last (exclusive) site of the specified
subList(*args)	REturns a view of the portion of this list between the specified fromIndex, inclusive, and toIndex, exclusive.
toArray(*args)	Returns an array containing all of the elements in this collection.
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)

chromosomalPosition(*args)

Returns the physical position at given site

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

chromosome(*args)

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)

Return chromosome name for given site

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

chromosomeSiteCount(*args)

Return number of sites for given chromosome

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

chromosomes(*args)

Return all chromosomes

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

chromosomesOffsets(*args)

Returns starting site for each chromosome

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

genomeVersion(*args)

Gets the Genome Assembly

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

hasReference(*args)

Returns whether this alignment has defined reference sequence.

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

indelSize(*args)

Returns size of indel at given site.

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

isIndel(*args)

Returns whether given site is an indel

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

isPositiveStrand(*args)

Returns whether is positive strand at given site

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

numChromosomes(*args)

Return number of chromosomes

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

numberOfSites(*args)

Returns total number of sites of this genotype table

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

physicalPositions(*args)

Returns all physical positions

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

referenceGenotype(*args)

Return the reference diploid allele values at given site

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

referenceGenotypeForAllSites(*args)

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

referenceGenotypes(*args)

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:

referenceGenotypes (int startSite, int endSite)

Parameters:

• startSite (int) – start site
• endSite (int) – end site

Returns:

Reference sequence of diploid allele values

Return type:

byte[]

siteName(*args)

Get SNP ID for specified site

Signature:

String siteName(int site)

Arguments:

site – site

Returns:

Site name

siteOfPhysicalPosition(*args)

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

startAndEndOfChromosome(*args)

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

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

Module contents