cls.VCF2Dintegrator.CVCF2Dintegrator Class Reference

Conversion of VCF files to Data Integrator format. More...

Public Member Functions
def	__init__ (s, build, vcfReader, add, extract, noData, permissiveness)
	Constructor. More...
def	SNP (s, vcfChrom, vcfPos, vcfRef, vcfAlt)
	Returns the coordinate, ref, and alt field of a SNP in Dint format. More...
def	Deletion (s, vcfChrom, vcfPos, vcfRef, vcfAlt)
	Returns the coordinate, ref, and alt field of a Deletion in Dint format. More...
def	Insertion (s, vcfChrom, vcfPos, vcfRef, vcfAlt)
	Returns the coordinate, ref, and alt field of an Insertion in Dint format. More...
def	MNP (s, vcfChrom, vcfPos, vcfRef, vcfAlt)
	Returns the coordinate, ref, and alt field of an multi nucleotide polymorpthism (MNP) in Dint format. More...
def	WriteDintLine (s, vcfLine, coord, ref, alt, info)
	Prints one variant in Dintegrator format. More...
def	Vcf2Dint (s)
	Performs the conversion of the VCF file to the Dint file. More...

Detailed Description

Conversion of VCF files to Data Integrator format.

Constructor & Destructor Documentation

__init__()

def cls.VCF2Dintegrator.CVCF2Dintegrator.__init__	(		s,
			build,
			vcfReader,
			add,
			extract,
			noData,
			permissiveness
	)

Constructor.

    @param vcfReader Instance of cls.DefaultTable.CVcfTableReader.
    @param add @c boolean Indicates if the INFO column of the VCF file
    should be printed
    @param extract List of column names to extract.
    @param noData the Dintegrator empty cell value
    @param permissiveness Behavior for unexpected row.

Member Function Documentation

Deletion()

def cls.VCF2Dintegrator.CVCF2Dintegrator.Deletion	(		s,
			vcfChrom,
			vcfPos,
			vcfRef,
			vcfAlt
	)

Returns the coordinate, ref, and alt field of a Deletion in Dint format.

Converts the genomic coordinate, reference and alternative allele of a Deletion from VCF format to Dintegrator format.

Parameters

vcfChrom	The variant chromosome in VCF format.
vcfPos	The variant genomic position in VCF format.
vcfRef	The variant ref allele in VCF format.
vcfAlt	The variant alt allele in VCF format.

Insertion()

def cls.VCF2Dintegrator.CVCF2Dintegrator.Insertion	(		s,
			vcfChrom,
			vcfPos,
			vcfRef,
			vcfAlt
	)

Returns the coordinate, ref, and alt field of an Insertion in Dint format.

Converts the genomic coordinate, reference and alternative allele of an Insertion from VCF format to Dintegrator format.

Parameters

vcfChrom	The variant chromosome in VCF format.
vcfPos	The variant genomic position in VCF format.
vcfAlt	The variant alt allele in VCF format.

MNP()

def cls.VCF2Dintegrator.CVCF2Dintegrator.MNP	(		s,
			vcfChrom,
			vcfPos,
			vcfRef,
			vcfAlt
	)

Returns the coordinate, ref, and alt field of an multi nucleotide polymorpthism (MNP) in Dint format.

Converts the genomic coordinate, reference and alternative allele of a multi nucleotide polymorpthism (MNP) from VCF format to Dintegrator format.

Parameters

vcfChrom	The variant chromosome in VCF format.
vcfPos	The variant genomic position in VCF format.
vcfAlt	The variant alt allele in VCF format.

SNP()

def cls.VCF2Dintegrator.CVCF2Dintegrator.SNP	(		s,
			vcfChrom,
			vcfPos,
			vcfRef,
			vcfAlt
	)

Returns the coordinate, ref, and alt field of a SNP in Dint format.

    Converts the genomic coordinate, reference and alternative allele of a
    SNP from VCF format to Dintegrator format.
    @param vcfChrom The variant chromosome in VCF format.
    @param vcfPos The variant genomic position in VCF format.
    @param vcfRef The variant ref allele in VCF format.
    @param vcfAlt The variant alt allele in VCF format.

Vcf2Dint()

def cls.VCF2Dintegrator.CVCF2Dintegrator.Vcf2Dint

(

s

)

Performs the conversion of the VCF file to the Dint file.

WriteDintLine()

def cls.VCF2Dintegrator.CVCF2Dintegrator.WriteDintLine	(		s,
			vcfLine,
			coord,
			ref,
			alt,
			info
	)

Prints one variant in Dintegrator format.

Parameters

vcfLine	The VCF variant line.
coord	The coordinate in Dintegrator format.
ref	The reference allele in Dintegrator format.
alt	The alternative allele(s) in Dintegrator format.
info	The (refactored) info field for alt

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The documentation for this class was generated from the following file:

• cls/VCF2Dintegrator.py