variants

Documentation

Overview

Package variants implements functionality to annotate mutations relative to a reference sequence for all records in a multiple sequence alignment in fasta format.

Index

• func AggregateWriteVariants(w io.Writer, start, end int, appendSNP bool, threshold float64, refID string, ...)
• func FormatVariant(v Variant, appendSNP bool) (string, error)
• func GetMSAOffsets(refseq []byte) ([]int, []int)
• func Variants(msaIn io.Reader, stdin bool, refID string, annoIn io.Reader, annoSuffix string, ...) error
• func WriteVariants(w io.Writer, start, end int, firstmissing bool, appendSNP bool, refID string, ...)
• type AnnoStructs
  • func GetVariantsPair(ref, query []byte, refID, queryID string, idx int, cdsregions []Region, ...) (AnnoStructs, error)
• type Region
  • func CDSRegion2fromGFF(fs []gff.Feature, refSeqDegapped string) (Region, error)
  • func CDSRegion2fromGenbank(f genbank.GenbankFeature) (Region, error)
  • func RegionsFromGFF(anno gff.GFF, refSeqDegapped string) ([]Region, []int, error)
  • func RegionsFromGenbank(gb genbank.Genbank, refLength int) ([]Region, []int, error)
• type Variant

Functions

func AggregateWriteVariants

func AggregateWriteVariants(w io.Writer, start, end int, appendSNP bool, threshold float64, refID string, cVariants chan AnnoStructs, cWriteDone chan bool, cErr chan error)

AggregateWriteOutput aggregates the mutations that are present greater than or equal to threshold, and writes their frequencies to file or stdout

func FormatVariant

func FormatVariant(v Variant, appendSNP bool) (string, error)

FormatVariant returns a string representation of a single mutation, the format of which varies given its type (aa/nuc/indel)

func GetMSAOffsets

func GetMSAOffsets(refseq []byte) ([]int, []int)

GetMSAOffsets returns two arrays which contain coordinate shifting information that can be used to convert reference to msa coordinates, and vice versa

func Variants

func Variants(msaIn io.Reader, stdin bool, refID string, annoIn io.Reader, annoSuffix string, out io.Writer, start int, end int, aggregate bool, threshold float64, appendSNP bool, threads int) error

func WriteVariants

func WriteVariants(w io.Writer, start, end int, firstmissing bool, appendSNP bool, refID string, cVariants chan AnnoStructs, cWriteDone chan bool, cErr chan error)

WriteVariants writes each query's mutations to file or stdout

Types

type AnnoStructs

type AnnoStructs struct {
	Queryname string
	Vs        []Variant
	Idx       int
}

AnnoStructs is for passing groups of Variant structs around with an index which is used to retain input order in the output

func GetVariantsPair

func GetVariantsPair(ref, query []byte, refID, queryID string, idx int, cdsregions []Region, intregions []int, offsetRefCoord []int, offsetMSACoord []int) (AnnoStructs, error)

type Region

type Region struct {
	Whichtype   string // only "protein-coding" for now
	Name        string // name of feature, if it has one
	Start       int    // 1-based 5'-most position of region on the forward strand, inclusive
	Stop        int    // 1-based 3'-most position of region on the forward strand, inclusive
	Translation string // amino acid sequence of this region if it is CDS
	Strand      int    // values in the set {-1, +1} only (and "0" for a mixture?!)
	Positions   []int  // all the (1-based, unadjusted) positions in order, on the reverse strand if needs be
}

func CDSRegion2fromGFF

func CDSRegion2fromGFF(fs []gff.Feature, refSeqDegapped string) (Region, error)

func CDSRegion2fromGenbank

func CDSRegion2fromGenbank(f genbank.GenbankFeature) (Region, error)

func RegionsFromGFF

func RegionsFromGFF(anno gff.GFF, refSeqDegapped string) ([]Region, []int, error)

func RegionsFromGenbank

func RegionsFromGenbank(gb genbank.Genbank, refLength int) ([]Region, []int, error)

Parses a genbank flat format file of genome annotations to extract information about the the positions of CDS and intergenic regions, in order to annotate mutations within each

type Variant

type Variant struct {
	Queryname      string
	RefAl          string
	QueAl          string
	Position       int    // (1-based) genomic location (for an amino acid change, this is the first position of the codon)
	Residue        int    // (1-based) amino acid location
	Changetype     string // one of {nuc,aa,ins,del}
	Feature        string // this should be, for example, the name of the CDS that the thing is in
	Length         int    // for indels
	SNPs           string // if this is an amino acid change, what are the snps
	Representation string
}

A Variant is a struct that contains information about one mutation (nuc, amino acid, indel) between reference and query