Documentation
¶
Overview ¶
Package simulate contains functions for simulation of genomic data, including generating random sequences, variants, reads, or regions.
Index ¶
- Variables
- func BaseExtToBases(seq []BaseExt) []dna.Base
- func CheckExon(gene genePred.GenePred, position int) (bool, int)
- func CheckStart(gene genePred.GenePred, codon CodonExt) bool
- func CheckStop(gene genePred.GenePred, codon CodonExt) bool
- func ChooseRandomBase(GCcontent float64) dna.Base
- func CodonExtToCodon(cE CodonExt) dna.Codon
- func CodonExtsToCodons(cE []CodonExt) []dna.Codon
- func ETree(numNodes int, gammaAlpha float64, gammaBeta float64) *expandedTree.ETree
- func GoSimulateBed(searchSpace []bed.Bed, regionCount int, regionLength int) <-chan bed.Bed
- func IlluminaPairedSam(refName string, ref []dna.Base, numPairs, readLen, avgFragmentSize int, ...)
- func MutateGene(inputSeq []dna.Base, branchLength float64, geneFile string, deletions bool) []dna.Base
- func NonCoding(root *expandedTree.ETree, substitutionMatrixFile string, ...) *expandedTree.ETree
- func OrderBaseExtBySeqPos(unordered []BaseExt) []dna.Base
- func ParseSubstitutionMatrix(filename string) [][]float64
- func RandGene(name string, length int, GCcontent float64) []fasta.Fasta
- func RandIntergenicSeq(GcContent float64, lenSeq int) []dna.Base
- func RemoveAncestors(filename string, tree *expandedTree.ETree, outputFilename string)
- func Simulate(randSeqFilename string, root *expandedTree.ETree, gene string, deletions bool)
- func SingleVcf(alpha float64, numAlleles int, boundAlpha float64, boundBeta float64, ...) vcf.Vcf
- func VcfToFile(alpha float64, numAlleles int, numSites int, outFile string, ...)
- func WithIndels(fastaFile string, branchLength float64, propIndel float64, lambda float64, ...) []fasta.Fasta
- type BaseExt
- type CodonExt
Constants ¶
This section is empty.
Variables ¶
var BLOSUM = [][]float64{{0.288590604, 0.03087248322, 0.03087248322, 0.02953020134, 0.02147651007, 0.0255033557, 0.04026845638, 0.07785234899, 0.01476510067, 0.04295302013, 0.05906040268, 0.04429530201, 0.01744966443, 0.02147651007, 0.02953020134, 0.08456375839, 0.04966442953, 0.005369127517, 0.01744966443, 0.06845637584, 0.0},
{0.04457364341, 0.3449612403, 0.03875968992, 0.03100775194, 0.007751937984, 0.0484496124, 0.0523255814, 0.03294573643, 0.02325581395, 0.02325581395, 0.04651162791, 0.1201550388, 0.01550387597, 0.01744186047, 0.01937984496, 0.04457364341, 0.03488372093, 0.005813953488, 0.01744186047, 0.03100775194, 0.0},
{0.05122494432, 0.04454342984, 0.3140311804, 0.08240534521, 0.008908685969, 0.03340757238, 0.04899777283, 0.06458797327, 0.03118040089, 0.02227171492, 0.03118040089, 0.05345211581, 0.01113585746, 0.01781737194, 0.02004454343, 0.06904231626, 0.04899777283, 0.004454342984, 0.01559020045, 0.02672605791, 0.0},
{0.04104477612, 0.02985074627, 0.06902985075, 0.3973880597, 0.007462686567, 0.02985074627, 0.09141791045, 0.04664179104, 0.01865671642, 0.0223880597, 0.02798507463, 0.0447761194, 0.009328358209, 0.01492537313, 0.0223880597, 0.05223880597, 0.03544776119, 0.003731343284, 0.01119402985, 0.02425373134, 0.0},
{0.06504065041, 0.0162601626, 0.0162601626, 0.0162601626, 0.4837398374, 0.01219512195, 0.0162601626, 0.0325203252, 0.008130081301, 0.04471544715, 0.06504065041, 0.02032520325, 0.0162601626, 0.02032520325, 0.0162601626, 0.0406504065, 0.03658536585, 0.00406504065, 0.01219512195, 0.05691056911, 0.0},
{0.05588235294, 0.07352941176, 0.04411764706, 0.04705882353, 0.008823529412, 0.2147058824, 0.1029411765, 0.04117647059, 0.02941176471, 0.02647058824, 0.04705882353, 0.09117647059, 0.02058823529, 0.01470588235, 0.02352941176, 0.05588235294, 0.04117647059, 0.005882352941, 0.02058823529, 0.03529411765, 0.0},
{0.05524861878, 0.04972375691, 0.04051565378, 0.09023941068, 0.007366482505, 0.06445672192, 0.2965009208, 0.0349907919, 0.02578268877, 0.02209944751, 0.03683241252, 0.07550644567, 0.01289134438, 0.01657458564, 0.02578268877, 0.05524861878, 0.03683241252, 0.005524861878, 0.01657458564, 0.03130755064, 0.0},
{0.07827260459, 0.02294197031, 0.03913630229, 0.03373819163, 0.01079622132, 0.01889338731, 0.02564102564, 0.5101214575, 0.01349527665, 0.01889338731, 0.02834008097, 0.03373819163, 0.009446693657, 0.01619433198, 0.01889338731, 0.05128205128, 0.02968960864, 0.005398110661, 0.01079622132, 0.02429149798, 0.0},
{0.04198473282, 0.04580152672, 0.0534351145, 0.03816793893, 0.007633587786, 0.03816793893, 0.0534351145, 0.03816793893, 0.3549618321, 0.02290076336, 0.03816793893, 0.04580152672, 0.01526717557, 0.03053435115, 0.01908396947, 0.04198473282, 0.02671755725, 0.007633587786, 0.0572519084, 0.02290076336, 0.0},
{0.0471281296, 0.0176730486, 0.0147275405, 0.0176730486, 0.01620029455, 0.01325478645, 0.0176730486, 0.0206185567, 0.0088365243, 0.2709867452, 0.1678939617, 0.0235640648, 0.03681885125, 0.0441826215, 0.0147275405, 0.02503681885, 0.03976435935, 0.0058910162, 0.0206185567, 0.176730486, 0.0},
{0.04453441296, 0.02429149798, 0.01417004049, 0.01518218623, 0.01619433198, 0.01619433198, 0.02024291498, 0.02125506073, 0.01012145749, 0.1153846154, 0.3755060729, 0.02530364372, 0.0495951417, 0.05465587045, 0.01417004049, 0.02429149798, 0.03340080972, 0.007085020243, 0.02226720648, 0.09615384615, 0.0},
{0.05699481865, 0.1070811744, 0.0414507772, 0.0414507772, 0.008635578584, 0.05354058722, 0.07081174439, 0.04317789292, 0.0207253886, 0.02763385147, 0.04317789292, 0.2780656304, 0.01554404145, 0.01554404145, 0.02763385147, 0.05354058722, 0.03972366149, 0.00518134715, 0.01727115717, 0.03281519862, 0.0},
{0.05220883534, 0.03212851406, 0.02008032129, 0.02008032129, 0.01606425703, 0.0281124498, 0.0281124498, 0.0281124498, 0.01606425703, 0.1004016064, 0.1967871486, 0.03614457831, 0.1606425703, 0.04819277108, 0.01606425703, 0.03614457831, 0.04016064257, 0.008032128514, 0.02409638554, 0.09236947791, 0.0},
{0.03382663848, 0.01902748414, 0.01691331924, 0.01691331924, 0.01057082452, 0.01057082452, 0.01902748414, 0.02536997886, 0.01691331924, 0.06342494715, 0.1141649049, 0.01902748414, 0.02536997886, 0.3868921776, 0.01057082452, 0.02536997886, 0.02536997886, 0.01691331924, 0.088794926, 0.05496828753, 0.0},
{0.05684754522, 0.02583979328, 0.02325581395, 0.03100775194, 0.01033591731, 0.02067183463, 0.03617571059, 0.03617571059, 0.01291989664, 0.02583979328, 0.03617571059, 0.04134366925, 0.01033591731, 0.01291989664, 0.4935400517, 0.04392764858, 0.03617571059, 0.002583979328, 0.01291989664, 0.03100775194, 0.0},
{0.109947644, 0.04013961606, 0.05410122164, 0.04886561955, 0.01745200698, 0.03315881326, 0.05235602094, 0.06631762653, 0.01919720768, 0.02966841187, 0.04188481675, 0.05410122164, 0.01570680628, 0.02094240838, 0.02966841187, 0.219895288, 0.08202443281, 0.005235602094, 0.01745200698, 0.04188481675, 0.0},
{0.07297830375, 0.03550295858, 0.04339250493, 0.03747534517, 0.01775147929, 0.02761341223, 0.03944773176, 0.04339250493, 0.01380670611, 0.05325443787, 0.0650887574, 0.04536489152, 0.01972386588, 0.02366863905, 0.02761341223, 0.09270216963, 0.2465483235, 0.005917159763, 0.01775147929, 0.07100591716, 0.0},
{0.0303030303, 0.02272727273, 0.01515151515, 0.01515151515, 0.007575757576, 0.01515151515, 0.02272727273, 0.0303030303, 0.01515151515, 0.0303030303, 0.05303030303, 0.02272727273, 0.01515151515, 0.06060606061, 0.007575757576, 0.02272727273, 0.02272727273, 0.4924242424, 0.06818181818, 0.0303030303, 0.0},
{0.04049844237, 0.02803738318, 0.02180685358, 0.01869158879, 0.009345794393, 0.02180685358, 0.02803738318, 0.02492211838, 0.04672897196, 0.04361370717, 0.06853582555, 0.03115264798, 0.01869158879, 0.1308411215, 0.01557632399, 0.03115264798, 0.02803738318, 0.02803738318, 0.3177570093, 0.04672897196, 0.0},
{0.06995884774, 0.0219478738, 0.01646090535, 0.01783264746, 0.01920438957, 0.01646090535, 0.02331961591, 0.02469135802, 0.008230452675, 0.1646090535, 0.1303155007, 0.02606310014, 0.03155006859, 0.03566529492, 0.01646090535, 0.0329218107, 0.04938271605, 0.00548696845, 0.02057613169, 0.268861454, 0.0},
{0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0}}
BLOSUM matrix for amino acid switching probabilities normalized to 0-1.
var GC float64 = 0.42
GC is the expected GC-content
Functions ¶
func BaseExtToBases ¶
BaseExtToBases converts a slice of BaseExt to a slice of dna.Base.
func CheckExon ¶
CheckExon takes in a genePred and a position and determines if the base at that position is in an exon. It returns a bool and the int that refers to the exon the base is in.
func CheckStart ¶
CheckStart determines if a base is the beginning of a start codon by comparing it to the start position of the genePred CDS.
func CheckStop ¶
CheckStop determines if a base is the beginning of a stop codon by comparing it to the end position of the genePred CDS.
func ChooseRandomBase ¶
ChooseRandomBase chooses one of the four bases according to the GC content provided.
func CodonExtToCodon ¶
CodonExtToCodon converts a since CodonExt to a single dna.Codon.
func CodonExtsToCodons ¶
CodonExtsToCodons converts a slice of CodonExt to a slice of dna.Codon.
func ETree ¶ added in v1.0.1
func ETree(numNodes int, gammaAlpha float64, gammaBeta float64) *expandedTree.ETree
ETree produces a phylogenetic tree with a user-specified number of nodes and random gamma-distributed branch lengths, determined by a user-specific alpha and beta parameter.
func GoSimulateBed ¶
GoSimulateBed takes a searchSpace (represented by a noGap.bed input file, here as a parsed struct) and generates a number of regions (regionCount) of a specified length (regionLength) and sends the simulated regions to an output chan.
func IlluminaPairedSam ¶
func IlluminaPairedSam(refName string, ref []dna.Base, numPairs, readLen, avgFragmentSize int, avgFragmentStdDev float64, flatErrorRate float64, ancientErrorRate float64, flatBinomialAlias numbers.BinomialAlias, ancientBinomialAlias numbers.BinomialAlias, geometricParam float64, out *fileio.EasyWriter, bw *sam.BamWriter, bamOutput bool, deaminationDistributionSlice []int)
IlluminaPairedSam generates pairs of sam reads randomly distributed across the input DNA sequence. The inputs are the name of the input DNA sequence, the sequence itself, the number of read pairs to generate, the length of each read, the average fragment size, the standard deviation of fragment sizes, the error rate where a base in the read will not match the input DNA, a numbers.binomialAlias that is used to speed up calculations, and output file handles for sam, bam, and a bool denoting if bam (or sam) should be the output. Whichever handle (sam or bam) is not being used can be nil.
func MutateGene ¶
func MutateGene(inputSeq []dna.Base, branchLength float64, geneFile string, deletions bool) []dna.Base
MutateGene takes a starting sequence, a branch length, and the gene structure of the starting sequence in the form of a genePred file, along with a flag for if deletions should be allowed along with substitutions. The function returns the evolved sequence.
func NonCoding ¶ added in v1.0.1
func NonCoding(root *expandedTree.ETree, substitutionMatrixFile string, unitBranchLength float64) *expandedTree.ETree
func OrderBaseExtBySeqPos ¶
OrderBaseExtBySeqPos orders a string of BaseExt by seq position.
func ParseSubstitutionMatrix ¶ added in v1.0.1
ParseSubstitutionMatrix reads a substitution matrix from an input file and returns it as a [][]float64
func RandGene ¶
RandGene takes a gene name, length (in bp) and expected GC content and makes a random gene with start and stop codons. Length must be a multiple of 3 and it returns the gene as a slice of fasta.Fasta with a single entry that is the gene.
func RandIntergenicSeq ¶
RandIntergenicSeq makes a randomly generated DNA sequence by drawing from a distribution with a specified GC content. Unlike RandGene, it does not have to be divisible by 3. The inputs are the expected GC content and the desired length of the output sequence.
func RemoveAncestors ¶
func RemoveAncestors(filename string, tree *expandedTree.ETree, outputFilename string)
RemoveAncestors takes a an input fasta filename and a pointer to a tree, along with an output file. All sequences in the input file that match the name of a leaf node in the tree will be written to the output file.
func Simulate ¶
func Simulate(randSeqFilename string, root *expandedTree.ETree, gene string, deletions bool)
Simulate takes a filename of a fasta file that will be the starting sequence at the root nodes, a pointer to a phylogenetic tree, a genePred filename related to the starting sequence, and if deletions should be allowed along with substitutions. The starting sequence will then be evolved according to the neutral tree provided and each node in the tree will be assigned a DNA sequence.
func SingleVcf ¶
func SingleVcf(alpha float64, numAlleles int, boundAlpha float64, boundBeta float64, boundMultiplier float64, pos int) vcf.Vcf
SingleVcf returns a single simulated Vcf record for a user-specified selection parameter alpha and genomic position. There also needs to be parameters for the bounding function, where alpha, beta, and multiplier parameters of 0.001, 0.001, and 10000 are good for most applications.
func VcfToFile ¶
func VcfToFile(alpha float64, numAlleles int, numSites int, outFile string, boundAlpha float64, boundBeta float64, boundMultiplier float64)
VcfToFile generates simulated VCF data. The inputs are alpha (the selection parameter), the number of sites, the output filename, along with parameters for the bounding function for sampling. Reasonable parameters choices for boundAlpha, boundBeta, and boundMultiplier are 0.001, 0.001, and 10000.
func WithIndels ¶ added in v1.0.1
func WithIndels(fastaFile string, branchLength float64, propIndel float64, lambda float64, gcContent float64, transitionBias float64, vcfOutFile string, qName string) []fasta.Fasta
WithIndels takes an input fastaFile, which must contain a single fasta entry, and simulates a mutated sequence. The output sequence is provided in a multiFa alignment, aligned to the initial sequence. branchLength (a float from 0 to 1) specifies the expected value of the proportion of sites in the input sequence that will be mutated. propIndel (a float from 0 to 1) specifies the expected value of the proportion of indels in the output sequence. lambda specifies the rate parameter for an exponential distribution, from which INDEL sizes will be sampled. gcContent specifies the expected value of GC content for inserted sequences. vcfOutFile specifies an optional (empty string disables this option) return that records all variants made during the simulated mutation process. transitionBias specifies the expected value of the ratio of transitions to transversions in the output sequence. qName sets the suffix for the output query fasta name.
Types ¶
type BaseExt ¶
BaseExt holds the original position of a base in the starting Seq and the base at that position.
func BasesToBaseExt ¶
BasesToBaseExt converts a slice of dna.Base to a slice of BaseExt.
func CodonExtToBaseExt ¶
CodonExtToBaseExt converts a slice of CodonExt to a slice of BaseExt.
type CodonExt ¶
type CodonExt struct {
Seq []BaseExt
}
CodonExt holds a slice of 3 bases and their original positions.
func CreateCodons ¶
CreateCodons takes a sequence and it's gene structure in genePred format, compensates for non-zero exon frame and returns all codons that correspond to a single exon.
Source Files