sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
e570b69ad43fe03ff60024bb2a81eaea7092297e39bd1eae383aea34ae5f1224 | Go | 1,381 | 42 | // Command Group: "Statistics & Population Genetics"
// Provides information about the number of scaffolds, including the N50, number of scaffolds, and distribution of lengths of assembled scaffolds.
package main
import (
"flag"
"fmt"
"log"
"github.com/vertgenlab/gonomics/fasta"
)
func assemblyStats(infile stri... |
b1a961a15bfe855f6cbc182d7fbcee3c222db0eb869183ba78bef02678122652 | Go | 1,389 | 53 | package main
import (
"github.com/vertgenlab/gonomics/axt"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fasta"
"github.com/vertgenlab/gonomics/fileio"
"github.com/vertgenlab/gonomics/genomeGraph"
"github.com/vertgenlab/gonomics/vcf"
)
func convertAxt(axtFile, format, targetFa, outp... |
6074b0d8f8bd2e100d69be876fec957b60794bcaf1797c230f56dee91eabd75c | Go | 1,390 | 53 | package genomeGraph
import (
"bytes"
"github.com/vertgenlab/gonomics/cigar"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/numbers/parse"
"github.com/vertgenlab/gonomics/sam"
"strings"
)
func calcExtension(seq []dna.Base) int64 {
var maxScore int64 = 0
for bases := 0; bases < len(seq); b... |
711f2c8b72e2861da395ec647004209774707ead45a53711088bc142bd5f7f66 | Go | 1,390 | 40 | package main
import (
"os"
"testing"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
)
var MultFaVisualizerTests = []struct {
Infile string
Outfile string
ExpectedFile string
Start int
End int
NoMask bool
Linelength int
E... |
c08834b8376a4e668cef8a11411c7b1579e73f89ff322d07459c0971cfee37a3 | Go | 1,397 | 44 | package pFasta
import (
"github.com/vertgenlab/gonomics/dna/pDna"
"strings"
)
// AllAreEqual returns true if two []pFasta data structures are determined
// to be equal, false otherwise.
// Two []pFasta data structures are said to be equal if: (1) they are of the same
// length. (2) Each component pFasta struct in '... |
3caf403e7febd046482b1444908ff77742abc77bf954c0693ee61e01fba184c1 | Go | 1,398 | 50 | // Command Group: "BED Tools"
// Converts bedGraph to wig. Wig scores will be equal to the bedGraph dataValue field across the range of the bedGraph entry
package main
import (
"flag"
"fmt"
"log"
"github.com/vertgenlab/gonomics/chromInfo"
"github.com/vertgenlab/gonomics/convert"
"github.com/vertgenlab/gonomics... |
7d03cc7e60786a1795875ba96a25d2aa2b521c53ac09721aef9f2f08492124d3 | Go | 1,400 | 47 | // Command Group: "Data Conversion"
// Reference-based diploid assembly of aligned short reads
package main
import (
"flag"
"fmt"
"log"
)
const bufferSize = 10_000_000
func usage() {
fmt.Print(
"ANCoRA - Ancient-DNA Nucleotide-damage Correction and Reference-guided Assembly.\n" +
"This program builds refer... |
9447f75f2c5ce9162aae6d8f581871a7d081831475029fe285fcfaf2245cd32a | Go | 1,404 | 60 | package main
import (
"os"
"testing"
"github.com/vertgenlab/gonomics/bed"
"github.com/vertgenlab/gonomics/exception"
)
var PeaksTests = []struct {
InWig string
ChromSizes string
OutBed string
ExpectedBed string
Threshold float64
FindMinima bool
DefaultValue float64
}{
{InWig: "testda... |
fd4f681a42dd4b76873981a8647a3bb6ead8797b99aae561603987a2845a5e8c | Go | 1,405 | 50 | package numbers
import (
"log"
"math"
)
// AverageFloat64 returns the mean value of type float64 from a slice of type float64.
func AverageFloat64(f []float64) float64 {
answer := 0.0
for i := range f {
answer = answer + f[i]
}
return answer / float64(len(f))
}
// VarianceFloat64 returns the variance (type f... |
cac45c670af13ca019e511244adc95b1a5afb699e1a9555d5253084567ba092c | Go | 1,407 | 61 | // Command Group: "FASTA and Multi-FASTA Tools"
// A collection of tools for manipulating pFasta files
package main
import (
"flag"
"fmt"
"log"
)
func usage() {
fmt.Printf(
"pFaTools - a collection of tools for manipulating pFasta files.\n" +
"Usage:\n" +
"\tpFaTools entropyTrack in.pfa out.wig\n" +
"... |
a087a176efd392802da06e2f550900842792f0368132f0f797c2bf61799aa45d | Go | 1,408 | 40 | package wig
// Smooth performs moving average smoothing on an input Wig struct using a user-specified windowSize and a value that represents missing data in the Wig.
func Smooth(w Wig, windowSize int, missing float64) Wig {
var j, k, midPoint int
var sum float64
var missingFound bool = false
//first we make a fres... |
1bf382eb8d846b849ad07cc26859994cb78cc3c377843b1ec760e58d7444b625 | Go | 1,413 | 38 | package genomeGraph
/*
import (
"github.com/vertgenlab/gonomics/fastq"
"github.com/vertgenlab/gonomics/sam"
"log"
"sync"
"time"
)
func GswSingleReadWrap(ref *SimpleGraph, readOne string, output string, threads int, seedLen int, stepSize int, scoreMatrix [][]int64, header *sam.SamHeader) {
log.SetFlags(log.Ldate... |
9d0fd35a080e51e4cbe6afcc244f5a19651454f8613190373ccb7472b78c418f | Go | 1,420 | 50 | package genePred
import (
"testing"
"github.com/vertgenlab/gonomics/fileio"
)
var genePred1 = GenePred{Id: "test", Chrom: "0", Strand: '+', TxStart: 0, TxEnd: 1001, CdsStart: 0, CdsEnd: 901, ExonNum: 4, ExonStarts: []int{0, 18, 500, 800}, ExonEnds: []int{3, 21, 503, 803}}
var genePred2 = GenePred{Id: "test", Chrom... |
1526ae567f036eb082954364098ca878603354c708aff087dbf5cb3bc9085c67 | Go | 1,428 | 74 | // Command Group: "Ontology Tools"
// Filter gaf file.
package main
import (
"flag"
"fmt"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
"github.com/vertgenlab/gonomics/ontology/gaf"
"log"
"strings"
)
type Settings struct {
InFile string
OutFile string
RemoveNot boo... |
84aa5a016e5b6ef5682385744a14b558eb1072ad631c75bcaa6954db81ab506a | Go | 1,439 | 52 | // Copyright 2020 Google Inc.
// Licensed under the Apache License, Version 2.0 (the "License");
// you may not use this file except in compliance with the License.
// You may obtain a copy of the License at
//
// http://www.apache.org/licenses/LICENSE-2.0
//
// Unless required by applicable law or agreed to in wr... |
19d2575d8c2157d25e3e24f860249cccff87647ef877e4724fe2af130802025b | Go | 1,443 | 65 | package main
import (
"os"
"testing"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
)
var VcfAfsTests = []struct {
inputFile string
outputFile string
expectedFile string
unPolarized bool
plotSelectionLikelihood string
lef... |
da86d481f0b28e2ccb2c16c89f993055573357e73ed67e9c96ec553e7fbd17ee | Go | 1,443 | 42 | package main
import (
"github.com/vertgenlab/gonomics/bed"
"github.com/vertgenlab/gonomics/bed/bedpe"
"os"
"testing"
)
var s = []struct {
truth []bedpe.BedPe
test []bed.Bed
expectedFreq float64
expectedBedMatches []bed.Bed
expectedNonMatches []bed.Bed
}{
{truth: bedpe.Read("... |
105e94619768014e13a9b3f1a8f969697e8865291356e37ed70a884c3d6c472d | Go | 1,449 | 61 | package numbers
import (
"math"
"testing"
)
var NegativeBinomialCdfTests = []struct {
X float64
R float64
P float64
Expected float64
}{
{X: 3,
R: 4,
P: 0.9,
Expected: 0.99727,
},
}
func TestNegativeBinomialCdf(t *testing.T) {
var currAnswer float64
for _, v := range... |
9bbdb5cca26521e040dc02a96de0f6e9471b852af0ef765980917c315b26ba1c | Go | 1,465 | 54 | package binaryGiraf
import (
"reflect"
"sync"
"testing"
"github.com/vertgenlab/gonomics/giraf"
)
const (
TestGiraf = "testdata/test.giraf"
TestGraph = "testdata/test.gg"
TestGiraffe = "testdata/test.giraf.fe"
)
func TestReadToSlice(t *testing.T) {
data := Read(TestGiraffe, TestGraph)
correct := giraf.R... |
fdf60c75a8e65d90808cc69612e5486ed76dbc60cdee10c433e2371a1661c228 | Go | 1,466 | 43 | package dnaTwoBit
import (
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/numbers"
)
func NewTwoBitRainbow(inSeq []dna.Base) []*TwoBit {
var start, end, sliceLenNeeded int = 0, 0, 0
clone := make([]dna.Base, len(inSeq))
copy(clone, inSeq)
answer := make([]*TwoBit, 32)
for startOffset := 0... |
8d1d798cba2b02c2b4b82f7cfd4e3a1817883acde10a9e590d24fb1a96655e89 | Go | 1,473 | 52 | package fasta
import (
"sort"
"github.com/vertgenlab/gonomics/dna"
)
// IsEqual returns true if two input Fasta structs have an equal name and sequence.
func IsEqual(alpha Fasta, beta Fasta) bool {
if alpha.Name == beta.Name && dna.CompareSeqsCaseSensitive(alpha.Seq, beta.Seq) == 0 {
return true
}
return fals... |
6a8bad6c3f91c20d27e7d63024bd1d79efc7fc53ef1848c10d29faba5d31db85 | Go | 1,479 | 57 | package numbers
import (
"log"
"math"
)
// NegativeBinomialCdf returns the CDF of the negative binomial distribution for an input score x for a distribution
// defined by parameters R and P.
func NegativeBinomialCdf(x float64, R float64, P float64) float64 {
return RegularizedIncompleteBeta(R, x+1, P)
}
// Regula... |
b52d9c7b9377e2cec6f78df963b92fe06cadd9f0102a4ad9fc7ff7ea57aa1e8e | Go | 1,486 | 49 | package gene
import (
"testing"
"github.com/vertgenlab/gonomics/dna"
)
var isEqualTest Gene = Gene{
id: "test_gene_id",
startPos: 0,
posStrand: true,
cdsStarts: []int{2, 7, 11},
cdsEnds: []int{4, 9, 13},
genomeSeq: dna.StringToBases("ACATGCACCGTTAACG"),
cdnaSeq: dna.StringTo... |
e1eccecbfc4bc634fa6809b44cd0d255c6c85f3b768d3426da43209e26ae9e61 | Go | 1,487 | 50 | package numbers
import (
"github.com/vertgenlab/gonomics/fileio"
"github.com/vertgenlab/gonomics/numbers/parse"
"os"
"strings"
"testing"
)
var PlotTests = []struct {
f func(float64) float64
left float64
right float64
bins int
outFile string
answerX []float64
answerFofX []fl... |
841031c7080594cde80bc9499c1e9bdec8639ae40a627654510b3311f1011af0 | Go | 1,491 | 66 | package main
import (
"os"
"testing"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
)
var MultiFaToChainTests = []struct {
InFile string
tName string
qName string
OutFile string
SwapTandQ bool
ExpectedFile string
QuerySeqName string
}{
{InFi... |
89aeac43b557521374298ca87878e7d22b8430425ab8749a683be338403b0c11 | Go | 1,505 | 57 | package numbers
import (
"testing"
)
func negativeNormalClosure(mu float64, sigma float64) func(float64) float64 {
return func(x float64) float64 {
return -1 * NormalDist(x, mu, sigma)
}
}
func negativeGammaClosure(alpha float64, beta float64) func(float64) float64 {
return func(x float64) float64 {
return -... |
6a10f1691f09318c168745012617ec38281629bf9a7179ca472ea9ba92889bad | Go | 1,508 | 49 | // Command Group: "Sorting"
// External sort of giraf records based on topological ordering of nodes in input graph
package main
import (
"flag"
"fmt"
"log"
"github.com/vertgenlab/gonomics/genomeGraph"
"github.com/vertgenlab/gonomics/sort"
)
func usage() {
fmt.Print(
"girafSort - External sort of giraf reco... |
32eb90edb903722cff85f0c2c118a03cdac4c0d1df1e8c1bee1fb4087541af73 | Go | 1,512 | 47 | package fileio
import (
"testing"
)
var httpTestingLookUp = []struct {
local string
internet string
}{
{"testdata/humanGenomeAbstract.txt", "https://raw.githubusercontent.com/vertgenlab/gonomics/main/fileio/testdata/humanGenomeAbstract.txt"},
}
// TestHttpReader will parse a local text file and a file uploade... |
1ebc1db10959614999ea95c2678fcd2ac0eeb1b4409a676138bdcc2d0240ff08 | Go | 1,513 | 67 | // Command Group: "FASTA and Multi-FASTA Tools"
// Pull unique sequences from a fasta file
package main
import (
"flag"
"fmt"
"log"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/fasta"
)
func faUniq(inFile string, outFile string) {
allSeqs := fasta.Read(inFile)
seqsSeen := make(map[st... |
1c2c92925375fa5e1c8eb75c91880252892e68b3863c5fbc0d4633a13256fc77 | Go | 1,521 | 54 | package dnaThreeBit
import (
"testing"
)
//func Append(fragment *ThreeBit, b ThreeBitBase) *ThreeBit { // too confusing to have Append and append (from std lib) in this package?
//func Cat(a *ThreeBit, b *ThreeBit) { // I was tempted to call this ligate
//func Copy(a *ThreeBit) *ThreeBit {
var dnaSeqs = []string{
... |
3f6edf54185383fc505a2f538617e1116ac325bbd729076a44a95038d5461e4a | Go | 1,523 | 49 | package pFasta
import (
"fmt"
"github.com/vertgenlab/gonomics/bed"
"github.com/vertgenlab/gonomics/dna/pDna"
"log"
)
// Extract returns a new pFa that is a subsequence of the input pFa, defined by a
// start (inclusive) and end (exclusive) position, like in bed; makes memory copy
func Extract(input []PFasta, star... |
00536a7a6cd724cf96ea15d187b2a86ece00569b065359cc575990ed7cd466ee | Go | 1,533 | 65 | package numbers
import (
"math"
"testing"
)
var Float64Tests = []struct {
Input []float64
Average float64
Variance float64
StdDev float64
}{
{
Input: []float64{5, 8, 8, 3, 9, 7, 6, 7, 12, 9, 3, 1},
Average: 6.5,
Variance: 9.545454545454545,
StdDev: 3.089571903266623,
},
}
func TestFloat64... |
3ca80111acfaaedeb8c36e1a80b2699b8e0b04d3e0c20e000b4c938d74619511 | Go | 1,533 | 46 | package bed
import (
"log"
"strings"
)
// negatePrevBed is a helper function to get regions as a bed that comes prev this bed.
func negatePrevBed(curr Bed, prev int) (int, Bed) {
if curr.ChromStart == 0 {
log.Fatalf("Error: this helper function does not deal with the 0th base...\n")
return 0, Bed{}
} else {
... |
575c8800f4ac4b4473b0b64f21e68203c0b6443232eadeaf3e5dc7e660ae7524 | Go | 1,533 | 56 | package main
import (
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
"log"
"os"
"testing"
"github.com/vertgenlab/gonomics/axt"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/fasta"
)
var axtStatsTests = []struct {
inAXT string
outStats string... |
470815b34d0494ef868d79ab799547d294a104001757a24a02477fdbce8223df | Go | 1,534 | 51 | // Command Group: "Data Simulation"
// Returns pseudorandomly generated DNA sequences in fasta format
package main
import (
"flag"
"fmt"
"log"
"math/rand"
"github.com/vertgenlab/gonomics/fasta"
"github.com/vertgenlab/gonomics/fileio"
"github.com/vertgenlab/gonomics/simulate"
)
func randSeq(outFile string, GC... |
d13798a72b17cd2ecfb5c600450fa95aa19b78726ac9d0098a2f23928945e19e | Go | 1,538 | 62 | // Command Group: "Data Conversion"
// Convert a maf alignment into a multiple fasta alignment
package main
import (
"flag"
"fmt"
"log"
"github.com/vertgenlab/gonomics/fasta"
"github.com/vertgenlab/gonomics/fileio"
"github.com/vertgenlab/gonomics/maf"
)
func mafToMultiFa(inMaf string, inFa string, inSpeciesLi... |
0d9f9cafba50fce6bf81d5c60b76b90ad21e623628ef8b42ad72fffa4ca8659f | Go | 1,555 | 46 | package genomeGraph
import (
"log"
"sort"
)
func printSeedDev(a []*SeedDev) {
for i := range a {
log.Printf("tId:%d\ttStart:%d\tqStart:%d\tLen:%d\ttotalLen:%d\tposStrand:%t\n", a[i].TargetId, a[i].TargetStart, a[i].QueryStart, a[i].Length, a[i].TotalLength, a[i].PosStrand)
}
}
func SortSeedDevByLen(seeds []*Se... |
a1d67f3c3782695c0a987741b9cc9c37f81387c921684b5efd0015f7fe246fb8 | Go | 1,586 | 60 | // Command Group: "Variant Calling & Annotation"
// Adds ancestral allele to the INFO column of entries in a VCF file
package main
import (
"flag"
"fmt"
"log"
"github.com/vertgenlab/gonomics/fasta"
"github.com/vertgenlab/gonomics/fileio"
"github.com/vertgenlab/gonomics/vcf"
)
func vcfAncestorAnnotation(inFile... |
d72ebfe238e38ae2f472955590bca6b7f0f7edca6279ff8198d471f61fb5e10d | Go | 1,589 | 56 | package popgen
import (
"testing"
"github.com/vertgenlab/gonomics/exception"
)
var MaximumLikelihoodTests = []struct {
VcfFile string
Left float64
Right float64
Error float64
UnPolarized bool
DivergenceAscertainment bool
D ... |
dc76f33a0d5fc40b8c45fd757551343b6a07279f144317308cd30637b4a24a18 | Go | 1,593 | 68 | package fasta
import (
"strings"
"github.com/vertgenlab/gonomics/dna"
)
// Remove fasta record with index i from slice of fasta.
func Remove(slice []Fasta, i int) []Fasta {
return append(slice[:i], slice[i+1:]...)
}
// RemoveGaps from all fasta records in a slice.
func RemoveGaps(records []Fasta) []Fasta {
for ... |
10bcc73cd7524bc6c3c3670448c8f5a4e01151cdea199793569f3e98774e3aa0 | Go | 1,601 | 39 | package main
import (
"os"
"testing"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
)
var MultiFaToVcfTests = []struct {
inputFa string
chromName string
outputVcf string
expectedVcf string
substitutionsOnlyFlag bool
retainN... |
3ed79ddf2b7f4d7b1805df642163155d3145cad0de066965e1aa921de1facd0b | Go | 1,611 | 62 | // Package exception provides globally available functions to simplify exit after unrecoverable errors are encountered.
package exception
import (
"log"
"math/rand"
"os"
"strings"
)
// init is run as the exception package is imported and modifies the GODEBUG variable to contain
// randautoseed=0 so that functions... |
d10e9bc5124c235d6793482afe4ca082626cef5a268e64ebc1b0502bcd6ee20b | Go | 1,612 | 62 | package main
import (
"os"
"testing"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
)
var SubsequenceSwapTestCases = []struct {
InFile string
BackgroundName string
ForegroundName string
SwapRegions string
ChromName string
OutFile string
ExpectedFi... |
e5214e991e9130c45221296c1e22f3e991b408de4240a4042729294f2b3ad81d | Go | 1,615 | 48 | package motif
import (
"github.com/vertgenlab/gonomics/fileio"
"github.com/vertgenlab/gonomics/numbers"
"github.com/vertgenlab/gonomics/numbers/parse"
"strings"
)
// AlmostEquals determines if floating-point numbers within two files are equal within a specified epsilon level.
func ApproxEquals(alpha, beta string,... |
2d7c5b3917eaa504f24f6d902043fbfc943c1c21ab35ab8b9b480c0db5fc54f5 | Go | 1,618 | 56 | package interval
type AggregateInterval struct {
chr string
start int
end int
tree map[string]*IntervalNode
}
func (a *AggregateInterval) GetChrom() string {
return a.chr
}
func (a *AggregateInterval) GetChromStart() int {
return a.start
}
func (a *AggregateInterval) GetChromEnd() int {
return a.end
}
//... |
62bf1e3507a3103f032587e96599dae95ac12e2539a03786340221d1ce147d4e | Go | 1,618 | 64 | package main
import (
"flag"
"fmt"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
"github.com/vertgenlab/gonomics/ontology/obo"
"log"
"os"
)
type MappingSettings struct {
InFile string
OutFile string
Force bool
}
func mappingUsage(mappingFlags *flag.FlagSet) {
fmt.Pr... |
60f3d16ef0a2f20b5056e1da446308c69cc3987c9c18443f962e0e73ddc662cb | Go | 1,619 | 104 | package parse
import (
"testing"
"golang.org/x/exp/constraints"
"golang.org/x/exp/slices"
)
func intContains(s []int, v int) bool {
for i := range s {
if s[i] == v {
return true
}
}
return false
}
func genericContains[E comparable](s []E, v E) bool {
for i := range s {
if s[i] == v {
return true
... |
580f15bfd686e43276efc46426d5b8c101f0fabc0a783ee761cf818e65e227a1 | Go | 1,620 | 54 | package bedGraph
import (
"os"
"testing"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
)
var b1 BedGraph = BedGraph{Chrom: "chr1", ChromStart: 100, ChromEnd: 200, DataValue: 40.5}
var b2 BedGraph = BedGraph{Chrom: "chr2", ChromStart: 400, ChromEnd: 900, DataValue: 10.2}
var b... |
27126038dbc8b84d9adcf8f0a241354965dd9d7c0e3cf99e7d66eb2f25b184fb | Go | 1,622 | 58 | package chain
import (
"log"
)
// TPosToQPos converts a target position in a chain to the corresponding query position.
// The bool returns true if the returned TPos was found in a (Size) section of a Chain, and
// false otherwise, as in when the TPos fell in TBases.
func TPosToQPos(c Chain, TPos int) (int, bool) {
... |
deb2f338cb13ed4225c41fcae3396490592567afefc413fbc56f1f283b965bfa | Go | 1,626 | 58 | // Command Group: "FASTA and Multi-FASTA Tools"
// Align two or more sequences by "chunks" of bases instead of by single bases. Each sequence must
// have a length that is divisible by the chunk size
package main
import (
"flag"
"fmt"
"github.com/vertgenlab/gonomics/align"
"github.com/vertgenlab/gonomics/exceptio... |
6d2bcacbb9014ec75c4f3f8462e3ced915bed39b721d74d33ac551ba72778bf9 | Go | 1,630 | 65 | package interval
import (
"fmt"
"path"
"github.com/vertgenlab/gonomics/axt"
"github.com/vertgenlab/gonomics/bed"
"github.com/vertgenlab/gonomics/chain"
"github.com/vertgenlab/gonomics/sam"
"github.com/vertgenlab/gonomics/vcf"
)
// GoReadToChan reads Interval interfaces to a channel from an input file (bed, ax... |
5eddcf4675b32f6d94fb21100e8bb74cb370d4c44eaac10f0a5007a284b7c468 | Go | 1,631 | 51 | package vcf
import (
"strings"
"github.com/vertgenlab/gonomics/dna"
)
// FixAllVcf runs FixVcf on each element in a slice of vcf structs.
// Along with the slice of vcfs, it also needs the reference genome
// in the form of chromosome names mapping to DNA sequences.
func FixAllVcf(query []Vcf, ref map[string][]dna... |
ad3aaf4b8bf2c42a28fe1c03bf5a6a7745e6fab2406dbe9aefb52688eab474cf | Go | 1,638 | 68 | // Command Group: "Genome Graph Tools"
// GIRAF <-> GIRAF.FE conversion, for more information, see the giraf package
package main
import (
"flag"
"fmt"
"log"
"path/filepath"
"strings"
"github.com/vertgenlab/gonomics/genomeGraph"
"github.com/vertgenlab/gonomics/giraf/binaryGiraf"
)
func usage() {
fmt.Print(
... |
fb288774a72e22bedbf53df1e081c6dcd14fc5e667198528f1b92aa5c83f590b | Go | 1,642 | 71 | package main
import (
"os"
"testing"
"github.com/vertgenlab/gonomics/exception"
//"github.com/vertgenlab/gonomics/exception".
"github.com/vertgenlab/gonomics/fileio"
"github.com/vertgenlab/gonomics/popgen"
)
var SelectionMleTests = []struct {
inputFile string
outFile string
exp... |
627e786508d6e1302c1d1ad1df5a7786394b5144a280591fd1f6e873babe7c82 | Go | 1,645 | 80 | package vcf
import (
"os"
"testing"
)
var readWriteTests = []struct {
filename string // input
}{
{"testdata/test.vcf"},
{"testdata/GP_DP_Samples.vcf"},
{"testdata/SingleHapData.vcf"},
}
func TestReadToChan(t *testing.T) {
alpha, _ := Read("testdata/test.vcf")
var beta []Vcf
vcfPipe, _ := GoReadToChan("test... |
c1d913c8d6d2224e73b1a08fab1335fa9aabd6e539a78fd57105cc22ff41d536 | Go | 1,647 | 54 | // Command Group: "FASTA and Multi-FASTA Tools"
// Provides human-readable multiple alignment from a given multiFa
package main
import (
"flag"
"fmt"
"github.com/vertgenlab/gonomics/browser"
"github.com/vertgenlab/gonomics/numbers/parse"
"log"
)
func multFaVisualizer(infile string, outfile string, start int, en... |
86fa639f6bb9491b681cb2e7ab2fa7a0d81df02112ee2669d5f82d6ef15cfe6e | Go | 1,653 | 61 | // Command Group: "Data Conversion"
// Extracts sequences from a fasta file from regions specified by an input bed
package main
import (
"flag"
"fmt"
"log"
"github.com/vertgenlab/gonomics/bed"
"github.com/vertgenlab/gonomics/convert"
"github.com/vertgenlab/gonomics/fasta"
)
func bedToFasta(fastaFile string, b... |
993a04695d1e17c3c5e84840fd3d4c80961ca6c884e3d38c4b50843597ea18d3 | Go | 1,655 | 87 | package pFasta
import (
"github.com/vertgenlab/gonomics/dna/pDna"
"github.com/vertgenlab/gonomics/fileio"
"testing"
)
var WriteTests = []struct {
OutFile string
Records []PFasta
Precision float32
}{
{OutFile: "testdata/out.test.pFa",
Records: []PFasta{
{Name: "chr1",
Seq: []pDna.Float32Base{
... |
22fcd82cfb1a6e1214a22c3f1d04c751d001cfbbbf3f1e93488f7df8094a32c9 | Go | 1,693 | 82 | package fasta
import (
"testing"
"github.com/vertgenlab/gonomics/dna"
)
func TestSeek(t *testing.T) {
sr := NewSeeker("testdata/cornerCases.fa", "")
ans, err := SeekByName(sr, "beta", 0, 2)
if err != nil {
t.Error(err)
}
if dna.BasesToString(ans) != "AG" {
t.Error("problem with fasta seek")
}
ans, err ... |
6136d9cc933df827eedc1288e510e2896518543164c88d0875957d7f9ea4bb3f | Go | 1,702 | 64 | package main
import (
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
"os"
"testing"
)
var FastqFormatTests = []struct {
InFile string
OutFile string
ExpectedOutFile string
R1InFile string
R2InFile string
R1OutFile string
R... |
dd4bc930dbc2e373a0e5d80bdd3123dbd5562754f02032661744c2d21cc50be5 | Go | 1,705 | 58 | package numbers
import (
"math"
)
// GoldenSectionMaxSearch returns returns a local maximum for the input range a to b from an input function f with a user specified error epsilon.
// For unimodal functions, we are guaranteed to find the maximum if it is contained within the interval a to b. For polymodal functions,... |
44f7fa2312e39c4ad00dd7d3127e9068142f29be0e96ed84f89b9df88e596677 | Go | 1,708 | 58 | package gtf
import "sort"
// CdnaLength returns the length of the cDNA in nucleotides.
func CdnaLength(t *Transcript) int {
var answer int = 0
for i := 0; i < len(t.Exons); i++ {
answer += t.Exons[i].End - t.Exons[i].Start + 1
}
return answer
}
// CdsLength returns the length of the Cds in nucleotides (after s... |
16d56f78fc48b343a069912a8d2d950a91b94878e329688d616398c1a708cea1 | Go | 1,720 | 79 | package fit
import (
"math"
"testing"
)
var ZeroTruncatedNegativeBinomialTests = []struct {
R float64
P float64
}{
{
R: 1.0,
P: 0.4,
},
{
R: 2,
P: 0.1,
},
{
R: 2,
P: 0.4,
},
{
R: 6,
P: 0.4,
},
{
R: 6,
P: 0.4,
},
}
func TestZeroTruncatedNegativeBinomial(t *testing.T) {
var currR, cu... |
e84306ce44875082c2add4021a9d494131ff934c4b5aaa10ed63ce3a3f9c020f | Go | 1,722 | 57 | package binaryGiraf
import (
"io"
"reflect"
"testing"
"github.com/vertgenlab/gonomics/cigar"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/dna/dnaThreeBit"
"github.com/vertgenlab/gonomics/fileio"
"github.com/vertgenlab/gonomics/giraf"
)
var TestQual = []uint8{40, 5, 5, 5, 5, 5, 5, 5, 3... |
72ecaabc6050b4618e62428865ed22adc20b94bedd190953f405eca1296464f3 | Go | 1,733 | 61 | package fit
import (
"fmt"
"math"
"math/rand"
"testing"
"golang.org/x/exp/slices"
)
func TestRunMixtureModel(t *testing.T) {
maxIterations := 200
maxResets := 10
countPerComponent := 300
acceptableError := 0.05
var meanA, meanB, stdA, stdB float64
mm := new(MixtureModel)
var converged bool
data := make(... |
d5e66f569d33974d8cf118ea15063317e3bab663d68c6483896ea71f4989cc76 | Go | 1,733 | 53 | package numbers
import (
"math"
"math/rand"
)
// RandGeometric returns a geometrically-distributed random variate using the inverse transform.
// Note the geometric distribution has CDF: F(x) = 1 - (1-p)^x.
// The inverse transform is derived as (1-p)^x = 1 - F(x) -> x*log(1-p) = log(1 - F(x)) -> x = log(1 - F(x)) ... |
240c49addfeff73b3262a6a158bcd5ea71189b3f46ef40a065a5a8dbb1652375 | Go | 1,737 | 44 | package main
import (
"github.com/vertgenlab/gonomics/exception"
"os"
"testing"
"github.com/vertgenlab/gonomics/fileio"
)
var VcfToFaTests = []struct {
inputVcfFile string
inputFaFile string
actualOutputFile string
expectedOutputFile string
useAlt bool
useSamples bool
ha... |
b86ac75ae58f42df9381293feb3e3b4d4e8cc96c9ac5b9b513c201e7d37345be | Go | 1,740 | 84 | package bedpe
import (
"os"
"testing"
"github.com/vertgenlab/gonomics/bed"
"github.com/vertgenlab/gonomics/exception"
)
var b1 BedPe = BedPe{
A: bed.Bed{
Chrom: "chr2",
ChromStart: 200,
ChromEnd: 240,
Name: "First",
Score: 40,
Strand: '... |
6705890a434d23af588a9922e403e1b2d8a7a6c1150fb5153a7e64a239874e5f | Go | 1,741 | 65 | package sam
import (
"fmt"
"testing"
"github.com/vertgenlab/gonomics/chromInfo"
"github.com/vertgenlab/gonomics/fileio"
)
func TestReadHeaderBytes(t *testing.T) {
br := fileio.EasyOpen("testdata/small.sam")
header := ReadHeader(br)
expectedChrom := chromInfo.ChromInfo{Name: "ref", Size: 45, Order: 0}
if len... |
995a56b67af7ae4f7fc2c335a11b4955dff5aa53f44e5e1aa8d4eb12f442916d | Go | 1,751 | 70 | package genePred
import (
"strings"
)
// AllAreEqual examines if two genePred files are the same entry by entry. The first unequal record will be returned with a slice of ints that refer to which fields are unequal.
func AllAreEqual(a []GenePred, b []GenePred) (bool, []int) {
var fields []int
var equal bool
if l... |
751e04a8bcb546a642bcda3d6eb3a1ed41c2ab689b4d7d818ea627fef929d0cf | Go | 1,759 | 48 | package main
import (
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
"os"
"testing"
)
var BedMergeTests = []struct {
InFile string
ExpectedFile string
OutFile string
MergeAdjacent bool
Pad int
LowMem bool
KeepAllNames bool
}{
{"testdata/t... |
9581f2fb176d21e43399ad52cac3395a482d104268d76ea358d548c7bba25969 | Go | 1,776 | 40 | package main
import (
"os"
"testing"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
)
var BedPeOverlapTests = []struct {
selectFile string
inBedPe string
outBedPe string
bedSelect bool
overlapBoth bool
overlapThreshold float64
keepName... |
c4cd68d1c9dbcfe66775b7b4b8b4726df74058dd84e8bbf1c786a8d7c338305c | Go | 1,777 | 35 | // Package vcf contains functions for reading, writing, and manipulating VCF format files. More information on the VCF file format can be found
// in its official documentation at https://samtools.github.io/hts-specs/VCFv4.3.pdf. This file is parsed into a struct containing header information
// as well as a Vcf struct... |
0fe5bf10265d55a3e51c21a35fd7035d72bc2af4a25026f29b3749d7d64f90d0 | Go | 1,784 | 56 | // Package sketch provides utilities and color palettes for plotting graphs and images
package sketch
import (
"image"
"image/color"
"golang.org/x/image/font"
"golang.org/x/image/font/basicfont"
"golang.org/x/image/math/fixed"
)
// HLine draws a horizontal line on the given image between the xStart and xEnd coo... |
d17f190d63bd7c45dacce094f0069fabc48cd440c5f31e8c519b605cab5929e8 | Go | 1,785 | 117 | package convert
import (
"log"
)
// EnsemblToUCSC converts ensembl-style human chromosome names to the standard UCSC format chromosome names.
func EnsemblToUCSC(in string) string {
switch in {
case "1":
return "chr1"
case "2":
return "chr2"
case "3":
return "chr3"
case "4":
return "chr4"
case "5":
re... |
0db30858afb9b006414622d2d63f9f47bfd2424015b3c489bea185ca2c52ef6d | Go | 1,786 | 33 | package popgen
import (
"github.com/vertgenlab/gonomics/numbers"
)
// MleSettings delineates the experimental parameters for running maximum likelihood estimation on a set of variants using selectionMLE.
type MleSettings struct {
Left float64 //left bound of MLE search space
Right ... |
c362f47f026b18c18165c9f1c68559e5c7185fa3ce600f1a8152428f6b3059f9 | Go | 1,808 | 79 | package main
import (
"os"
"testing"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
)
var SimulateDivergentWindowsVcfTests = []struct {
ExpectedUpper string
ExpectedLower string
TmpUpper string
TmpLower string
Alpha float64
NumAlleles int... |
5f72665e71e8a9683787773d5bd7ff0f598a93a8ad48248d45341a7c96dc9b2a | Go | 1,812 | 71 | package main
import (
"os"
"testing"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
)
var WithIndelsTests = []struct {
InputFastaFile string
OutFile string
BranchLength float64
Lambda float64
PropIndels float64
GcContent float64
SetSeed ... |
2a4c1e2d7296362c13dc120634df06dff33346c544abaf8fa2f4258b4917b1ca | Go | 1,826 | 58 | package phylo
import (
"fmt"
"testing"
)
var BranchLengthsAlternatingLeastSquaresTests = []struct {
D AccelDistancesAndWeights
AllowNegative bool
Epsilon float64
ExpectedBranchLengths AccelBranchLengths
CavalliSforzaQ bool
}{
{AccelDistancesAndWeights{ //This p... |
d4e9390b39f83dabd82b619bc80bc32a23507c592a29b1f4bea2a30ab9cf2a8e | Go | 1,830 | 63 | package fasta
import (
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
"os"
"sort"
"testing"
"github.com/vertgenlab/gonomics/dna"
)
var contigOneSeq = dna.StringToBases("ACGTGAGTGAGTAGGACCACGATGACACGANNTGA")
var contigTwoSeq = dna.StringToBases("GgtAC")
var contigThreeSeq = d... |
dc2d7ad79c5ea4757e08f2e114928a2089a4034acd4276bff90cc0f50933cd7e | Go | 1,830 | 54 | package gene
import "github.com/vertgenlab/gonomics/dna"
// Reset reverts all mutations done to a Gene.
func Reset(g *Gene) {
var hasIndel bool
var err error
for _, val := range g.changeLog {
if len(val.added) != 1 || len(val.removed) != 1 {
hasIndel = true
break
}
}
if !hasIndel { // Point mutations ... |
664a549dee78d090c6a10e0489bbc368d00278afc4b6dbcfa96fe5d920bb7dcb | Go | 1,831 | 59 | // Command Group: "VCF Tools"
// Returns a sample from a VCF file with a specified number of results
package main
import (
"flag"
"fmt"
"log"
"math/rand"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
"github.com/vertgenlab/gonomics/vcf"
)
// sampleVcf takes a VCF file and... |
632ab2fee75d222ab2ba99572ff74a4d0826a6a38386a356911d592d8c8e4be2 | Go | 1,841 | 101 | package main
import (
"os"
"testing"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
"github.com/vertgenlab/gonomics/popgen"
)
var SimulateWFTests = []struct {
OutFile string
ExpectedFile string
PopSize int
MutRate float64
NumGen int
GenomeSize ... |
d303e09cc3e8a0bdeee0e7f7f0b421c18bba2033ec993e0f32b097286f23f866 | Go | 1,846 | 72 | package main
import (
"flag"
"fmt"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
"github.com/vertgenlab/gonomics/sam"
"log"
"os"
)
type ReadLengthSettings struct {
InFile string
OutFile string
}
func readLengthUsage(readLengthFlags *flag.FlagSet) {
fmt.Printf("samInfo ... |
e2490a9f789e09ce235ef6472b819774b1ae042d70a086d5c06851c0db41d812 | Go | 1,848 | 28 | package tree
import (
"testing"
)
var treeTests = []struct {
treeText string
}{
{"(human,chimp)ancestor;"},
{"((human,chimp),rhesus);"},
{"(((human,chimp),(mouse,rat)),dog);"},
{"((platypus,(opossum,((((rat,mouse),rabbit),human),dog))),(lizard,bird));"},
{"(((((((((((((((((((hg19:0.006653,panTro2:0.006643):0.0... |
10726db08db286d2751da8a8028b93f27851f9ed8d0265c4fc09fb58077b8770 | Go | 1,853 | 73 | package main
import (
"flag"
"fmt"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fasta"
"github.com/vertgenlab/gonomics/fastq"
"github.com/vertgenlab/gonomics/fileio"
"log"
"sort"
)
func longReadLibStats(inFq string, outfile string, readLengths string) {
var lens []int
var tot i... |
ccde6eb758b94dbe83701875be13935e682fd712db079c604b808e5fc42e3d16 | Go | 1,853 | 72 | // Command Group: "General Tools"
// Returns all regions that contact input genomic regions
package main
import (
"flag"
"fmt"
"log"
"github.com/vertgenlab/gonomics/bed"
"github.com/vertgenlab/gonomics/bed/bedpe"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
"github.com/v... |
efcaf811076bc6092094144edce03192a228a765a75f71bb79b66e8d4939d187 | Go | 1,855 | 60 | // Command Group: "FASTA and Multi-FASTA Tools"
// Align two or more sequences by "chunks" of bases instead of by single bases. Each sequence must
// have a length that is divisible by the chunk size
package main
import (
"flag"
"fmt"
"github.com/vertgenlab/gonomics/align"
"github.com/vertgenlab/gonomics/exceptio... |
e935a4c4b61365dbcd2f263c1a12ba6975893ace27ac2d5283ab0c53e5675541 | Go | 1,886 | 72 | // Command Group: "Sequence Evolution & Reconstruction"
// Command Usage: "Create PNG of Newick tree"
// Reads a newick format text file to a png for tree visualization
package main
import (
"flag"
"fmt"
"image"
"image/png"
"log"
"os"
"github.com/vertgenlab/gonomics/tree"
)
// drawNewickTree takes in a newic... |
c396e2107f7d4c08ba38eb11b9f3429c06e8b6ddac3db38eed81de45e0aa05d9 | Go | 1,889 | 73 | package main
import (
"flag"
"fmt"
"github.com/vertgenlab/gonomics/bed"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
"github.com/vertgenlab/gonomics/interval"
"log"
"math"
)
func bedTrim(trimPercent int, inBed string, outBed string) {
var size, toRemoveInt int
var toRem... |
cec38522b3cba997ff9f3a496cca89040e68de17577fa8196d7757572f180e4c | Go | 1,889 | 66 | package fastq
import (
"github.com/vertgenlab/gonomics/exception"
"math"
"strings"
)
// SAM format uses ascii offset of 33 to make everything start with individual characters
// without adding 33 you get values like spaces and newlines.
const asciiOffset uint8 = 33
// ToQualUint8 converts a slice of runes to uint... |
9433bd3fac7bfd4051677bd8048fc7e6e133fd6b8446c91b5f4e711cd631376d | Go | 1,908 | 73 | package main
import (
"flag"
"fmt"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/wig"
"log"
"os"
)
// FilterSettings defines the usage settings for the wigTools filter subcommand.
type FilterSettings struct {
InFile string
ChromSizes string
OutFile string
Chrom ... |
681135b8fe0e15903b521eb0538de340a9bc511248822a6846062c256dd3c2fd | Go | 1,914 | 62 | package main
import (
"os"
"testing"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
)
var VcfInfoTests = []struct {
InFile string
TypesOutFile string
DivergenceOutFile string
TypesExpectedFile string
DivergenceExpectedFile string
}{
{"... |
b7b98bc895a8a78290eb604ec11919e0eb8c2e065be6d29b3423d8feedb8f257 | Go | 1,915 | 75 | package main
import (
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
"os"
"testing"
)
var SamToWigTests = []struct {
InFile string
Reference string
OutFile string
ExpectedFile string
FragLength int
DefaultValue float64
Deletions bool
}{
{InFile: "test... |
2f750fc8993fcfba9263942917d8aa288c4eed7d5f9842a307c42541cc0b035b | Go | 1,919 | 66 | package main
import (
"os"
"testing"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
)
var haplotypeGeneratorTests = []struct {
InputFaFile string
InputVcfFile string
InputBedFile string
OutDir string
IncludeRef bool
LineLength int
Verbose int
Out... |
fa1259818ad04a0fe8496310d4d19ed110be06c3f593d39ccf2e0ee3ba37546e | Go | 1,921 | 70 | // Package chromInfo provides function to read and manipulate chromInfo files
package chromInfo
import (
"log"
"strconv"
"strings"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
)
// ChromInfo stores the chromosome name and size of each chromosome as well as the order they ap... |
a72f1585b001571b6733bd93f3482057bea5d2826ec446ea5a6509d9b09457a3 | Go | 1,926 | 85 | package fileio
import (
"errors"
"log"
)
// Close the receiving EasyReader.
func (er *EasyReader) Close() error {
var gzErr, fileErr error
if er.internalGzip != nil {
gzErr = er.internalGzip.Close()
}
if er.File != nil {
fileErr = er.File.Close()
} else {
return errors.New("no file found")
}
switch { ... |
06a39cdf78caf43adcb9a2156d2e32052833c717550f0c998f91cf8e2b97a7b4 | Go | 1,927 | 83 | package vcf
import (
"testing"
)
func TestSamplesToString(t *testing.T) {
tests := []struct {
name string
samples []Sample
expected string
}{
{
name: "Single sample",
samples: []Sample{
{Alleles: []int16{0, 1}, Phase: []bool{false, false}, FormatData: []string{""}},
},
expected: "0/1",... |
e8a6c3c10aa9ab3be7f716073097cb966ef51d5ae6bdb4d8f9107bd55f79d08a | Go | 1,929 | 81 | package main
import (
"flag"
"fmt"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
"github.com/vertgenlab/gonomics/ontology"
"github.com/vertgenlab/gonomics/ontology/gaf"
"github.com/vertgenlab/gonomics/ontology/obo"
"log"
"sort"
)
func ontologyHistogram(oboFile string, gaf... |
5a6b01becb91d25a8299eeb9f27d8949b6c9c25020c9d1224487b92c8be267ad | Go | 1,946 | 75 | package main
import (
"flag"
"fmt"
"github.com/vertgenlab/gonomics/bed"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
"github.com/vertgenlab/gonomics/numbers"
"github.com/vertgenlab/gonomics/sam"
"log"
)
type settings struct {
inBam string
inBed string
outFile strin... |
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