sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
13594dc3c29004f76da8e54f24c6ad4dbdae0640ebfcd760b9dadb413f7ee65a | Go | 5,222 | 153 | package align
import (
"fmt"
"math"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/fasta"
)
func fastaListToIndividualGroups(records []fasta.Fasta) [][]fasta.Fasta {
answer := make([][]fasta.Fasta, len(records))
for i := range answer {
answer[i] = make([]fasta.Fasta, 1)
answer[i][0] =... |
3d645a77bbbccb54e034f96a5dddeed2e1a5781ba2ecdb78744df885dfecd0b6 | Go | 5,225 | 152 | package main
import (
"flag"
"fmt"
"github.com/vertgenlab/gonomics/bed"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fasta"
"github.com/vertgenlab/gonomics/fileio"
"log"
"strings"
)
type restrictionEnzyme struct {
name string
cutStrin... |
ca728f4270a748e199c6a3a113216cfbc58b446737d98da9c7d933f531460bbe | Go | 5,271 | 234 | package fileio
import (
"bytes"
"fmt"
"io"
"os"
"strings"
"testing"
"github.com/klauspost/pgzip"
"github.com/vertgenlab/gonomics/exception"
)
// example going straight to file.
func writeDnaFile(file *os.File) {
var fakeDna string = "ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT"
var err error
_, err = fmt.Fpr... |
64895be8be3434e6bbfce8611a2c278fc90002f86a03da993a2e3e2f4f847b61 | Go | 5,323 | 172 | package main
import (
"math"
"os"
"testing"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
)
var FaFindFastTests = []struct {
InFile string
OutFile string
ExpectedFile string
FirstQueryName string
SecondQueryName string
WindowSize int
RefChrom... |
1030bc80835f798bfee3f406685936f0907f17e428765f4ab7082edb5f0958fa | Go | 5,353 | 96 | package main
import (
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/numbers"
"github.com/vertgenlab/gonomics/vcf"
"os"
"strings"
"testing"
)
var VcfFilterTests = []struct {
inputFile string
tmpOutFile string
expectedOutputFile ... |
6480e11058353c752275fda4fa355316646e8a93bd72eb3382d5d40d7d2e5cd0 | Go | 5,355 | 181 | // Package bed provides functions for reading, writing, and manipulating Browser Extensible Data (BED) format files.
// More information on the BED file format can be found at https://genome.ucsc.edu/FAQ/FAQformat.html#format1
package bed
import (
"fmt"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgen... |
4a15452a79485d8d8454734fbead70665d81a84698c9ea1edb88f91340af3492 | Go | 5,363 | 263 | package vcf
import (
"testing"
)
var expectedFormat = map[string]interface{}{
"FormatF": [][]int{{1}, {2}},
"FormatJ": [][]rune{{'F', 'E'}, {'D', 'A'}},
"FormatK": [][]string{{"the,quick,brown,fox"}, {"jumps,over,the,lazy,dog"}},
}
var expectedInfo = map[string]interface{}{
"InfoA": [][]int{{10}},
"InfoB"... |
fcdf8784122618643098c49cfbbd37b9b661077fbe2d757ef46f5c392642eb5d | Go | 5,403 | 155 | // package psl defines the Psl struct containing alignment data as well as functions and methods that operate on the Psl struct
package psl
import (
"github.com/vertgenlab/gonomics/fileio"
"github.com/vertgenlab/gonomics/numbers/parse"
"log"
"strings"
)
// Psl struct declares data fields and types for Psl struct.... |
fa120d8de08ff31e32968d32d73224ea27f795e338820ef01128f808ad8d9b1a | Go | 5,420 | 148 | package sam
import (
"io"
"log"
"sort"
"github.com/vertgenlab/gonomics/chromInfo"
"github.com/vertgenlab/gonomics/exception"
)
// SeekBamRegion returns a slice of reads that overlap the input region. SeekBamRegion will advance the
// reader as necessary so beware continuing linear reading after a call to SeekBa... |
dc5abea5b0ee2f4744a51305031f36134fceaf5811d52ca249698d171ee5a529 | Go | 5,428 | 153 | // Command Group: "Data Simulation"
// Simulates Vcf data, partitioned by divergence-based ascertainment
package main
import (
"flag"
"fmt"
"log"
"math/rand"
"sort"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
"github.com/vertgenlab/gonomics/simulate"
"github.com/vertge... |
9a75ac4ca52d8fc7988665bbe3acd10abff68e000ed032357d20fd09b052062c | Go | 5,430 | 147 | package fastq
import (
"fmt"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
"log"
"strings"
"sync"
)
// PairedEnd is a struct that contains two paired Fastq structs, marked Fwd and Rev.
type PairedEnd struct {
Fwd Fastq
Rev Fastq
}
// ... |
a2eca262ba52f3269018162558ec232772a042edf422d92c49394c7d16b45acb | Go | 5,457 | 196 | package genomeGraph
import (
"log"
"github.com/vertgenlab/gonomics/cigar"
"github.com/vertgenlab/gonomics/dna"
)
var HumanChimpTwoScoreMatrixNoGap = [][]int64{
{90, -330, -236, -356},
{-330, 100, -318, -236},
{-236, -318, 100, -330},
{-356, -236, -330, 90},
}
func swMatrixSetup(size int64) ([][]int64, [][]by... |
ecb52f2f2fe903d3a6af19048f93dc3bc337a7ab9fdbbb5d70186a18b0a63e80 | Go | 5,550 | 119 | package dna
import "testing"
var revCompTests = []struct {
input []Base // input
expected []Base // after applying reverseComplement
}{
{[]Base{A, C, G, T, N, LowerA, LowerC, LowerG, LowerT, LowerN}, []Base{LowerN, LowerA, LowerC, LowerG, LowerT, N, A, C, G, T}},
{[]Base{A, C, G, T, N, A, C, G, T, N}, []Base{N... |
aa1b4fa62cb330ac368e0a44da5af802f29272ee9a0561acff74fbf5a86e3dff | Go | 5,578 | 170 | package vcf
import (
"log"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/variant"
)
// SmallVariantChans wraps channels for all of the small variants that
// are valid variant.Mutators and variant.Effectors. All channels except
// for Records sends a parsed version of a given Vcf record tha... |
9acda5995d4576b303c174deeec2be84953735d387885b300fbb85f93aef60d7 | Go | 5,585 | 190 | // Package cigar contains functions to manipulate cigar data in the SAM file format.
// More information on cigars can be found in http://samtools.github.io/hts-specs/SAMv1.pdf
package cigar
import (
"log"
"strconv"
"strings"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/numbers/pars... |
7eb783996e347c5643431c86e3268417ad9688cf6226e5bd2c66c616059956a4 | Go | 5,610 | 183 | package dna
// CompareBases returns an integer related to the lexographical order of nucleotides.
// i.e. A < C < a < c < Dot < Gap.
func CompareBases(alpha Base, beta Base, ignoreCase bool) int {
if ignoreCase {
alpha = ToUpper(alpha)
beta = ToUpper(beta)
}
if alpha < beta {
return -1
} else if alpha > beta... |
fc7dba167e910b09ddcd57efad5e06c093cb9f272ff78a289f5abd1a873e2bb1 | Go | 5,612 | 131 | package simulate
import (
"github.com/vertgenlab/gonomics/bed"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fasta"
"github.com/vertgenlab/gonomics/fileio"
"github.com/vertgenlab/gonomics/numbers"
"github.com/vertgenlab/gonomics/popgen"
"github.... |
0b63ba7cd41b5b38b910aa37bff95c9c266f5b52077af87eb6bdb524027bb87a | Go | 5,613 | 166 | package lastZWriter
import (
"log"
"os"
"strings"
"testing"
"github.com/vertgenlab/gonomics/fileio"
)
var parClose = []string{"O=600", "E=150", "H=2000", "T=2", "M=254", "K=4500", "L=3000", "Y=15000"}
var parDefault = []string{"O=400", "E=30", "H=2000", "T=1", "M=254", "K=3000", "L=3000", "Y=9400"}
var parFar =... |
a4efd3e2a3ec9d7fff8c15c656392d1329286523154faeb78f9abcda2de44720 | Go | 5,627 | 134 | package bigWig
import (
"encoding/binary"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
"log"
)
// Read parses a BigWig struct from an input filename.
func Read(filename string) BigWig {
var err error
var answer = BigWig{}
file := fileio.EasyOpen(filename)
answer.BbiHeader... |
389248a9938e6d93e8c7bab180257826ba7ab86e2a36f5cf08d5cd58e427760d | Go | 5,628 | 168 | package reconstruct
import (
"github.com/vertgenlab/gonomics/fasta"
"github.com/vertgenlab/gonomics/genePred"
"github.com/vertgenlab/gonomics/simulate"
"log"
)
// ReconAccuracy returns the percentage accuracy by base returned by reconstruct of each node and of all reconstructed nodes combined.
// If calcBaseAcc =... |
58c6e7e4f60dbd074b166e7f72bb17981a566c540967b857b101cd82cdc4c3e8 | Go | 5,651 | 173 | package obo
import (
"fmt"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
"log"
)
// buildTree is a helper function of Read that takes a map of string to *Obo structs and builds a tree, setting
// the Parents and Children fields to point to related nodes.
// If 'force' is true,... |
d6046ac1e5b8fa006400e172fb6c2f7a0c23001b0a3de5cfb6f4cc0d72697847 | Go | 5,652 | 171 | package interval
import (
"fmt"
"github.com/vertgenlab/gonomics/bed"
"github.com/vertgenlab/gonomics/numbers"
"log"
"sort"
"strings"
)
// CoordsToString takes in a interval and returns a string in the format of chr:start-end
func CoordsToString(i Interval) string {
return fmt.Sprintf("%s:%v-%v", i.GetChrom(), ... |
e3f353567a282cbebccb5ff7e67992c980f7067c2c7bba821e5b72239677ecd2 | Go | 5,654 | 232 | package main
import (
"fmt"
"io"
"log"
"strconv"
"strings"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/vcf"
)
func writeTableHeader(outfile io.Writer, header vcf.Header, maxAlts int) (infoOrder []vcf.InfoHeader, formatOrder []vcf.FormatHeader) {
s := new(strings.Builder)
if le... |
1c45f40f11bcbc0915c0f3ceefecd3c23f5260b3abfb0040ee9fd493ffddf753 | Go | 5,659 | 140 | // Command Group: "Sequence Evolution & Reconstruction"
// Command Usage: "Simulate evolution along a tree and perform ancestral reconstruction"
// Simulates evolution from the root of a newick tree to the extant species of the trees and then uses the leaf nodes to reconstruct the ancestral nodes and compares the answ... |
81afdab494c09875614ed56bf37cae4ba23f893abe38b55aa5724e4231cd5009 | Go | 5,661 | 151 | // Command Group: "General Tools"
// Produces a binary matrix for accessibility breadth analysis
package main
import (
"flag"
"fmt"
"log"
"sort"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
"github.com/vertgenlab/gonomics/interval"
)
func intervalSubsetMatrix(unionFile s... |
6f2f28c27178f99b751a21cac49ac1f65d64af66887f4f132c4aef78212ab061 | Go | 5,714 | 137 | package dnaThreeBit
import (
"log"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/numbers"
)
// ThreeBit is a struct to represent long DNA sequences in a memory efficient format
// Seq holds the encoded DNA sequence. The left-most three bits of Seq[0] hold the
// first base. The first base... |
3e16b30caf44db1754b64049082fb928a6ecf1cbef620c0f7c831b46a39f1614 | Go | 5,810 | 217 | // Package numbers provides a variety of functions related to statistics
package numbers
import (
"log"
"math"
"github.com/vertgenlab/gonomics/numbers/logspace"
)
// carefulMultDivFloat tries to gracefully handle the case when you have a
// bunch of numbers being multiplied together in a numerator (numer)
// and ... |
bdd6be1b5dfae4d9f14a5ccd5dbddb56ff62a5cd3f1031f2929a0e5d272e4885 | Go | 5,827 | 220 | // Package fileio provides wrappers of the builtin golang Reader/Writer utilities for ease of use and automatic gzip handling.
package fileio
import (
"bufio"
"errors"
"fmt"
"io"
"log"
"os"
"sort"
"strings"
"github.com/vertgenlab/gonomics/exception"
)
// MustCreate creates a file with the input name.
// Fat... |
c6a056a1098b75d73793cd80f306db2cbf07eb4c154a81d223ca6a2af6e72597 | Go | 5,830 | 174 | // Command Group: "SAM Tools"
//TODO: Input-normalization.
// Generate count matrix from single-cell sequencing data
package main
import (
"flag"
"fmt"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
"github.com/vertgenlab/gonomics/gtf"
"... |
80c672d5da8e8069eee7f20b8a41178ec76fb1ce9358f197363cfa2b301a5e6c | Go | 5,861 | 186 | // Package genePred is a package for reading, writing, and manipulating genePred structs
package genePred
import (
"fmt"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/numbers/parse"
"io"
"log"
"strings"
"github.com/vertgenlab/gonomics/fileio"
)
// GenePred is a data struct which d... |
17f8dab3542de79123328b6f66a2199de6cacfa473bfb3043df3ebf86b5f8614 | Go | 5,868 | 157 | package genomeGraph
import (
"fmt"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/dna/dnaTwoBit"
"github.com/vertgenlab/gonomics/fastq"
"github.com/vertgenlab/gonomics/numbers"
"github.com/vertgenlab/gonomics/numbers/parse"
"log"
)
func RandomPairedReads(genome *GenomeGraph, readLength in... |
443d7e28f594e247470737b2da1a4f7cf5d2f1c9d46f2469124442ae08978ece | Go | 5,879 | 240 | package dna
import (
"log"
"strings"
"testing"
"unicode/utf8"
)
var equalStringsAndBases = []struct {
characters string // first input
bases []Base // second input
}{
{"ACGTNacgtn", []Base{A, C, G, T, N, LowerA, LowerC, LowerG, LowerT, LowerN}},
{"ACACGGGGNNNNNN", []Base{A, C, A, C, G, G, G, G, N, N, N, ... |
ca96176a985158e152bf099678276caee11c7c0f619412b47ba8135e6d6b417e | Go | 5,898 | 191 | // Package bedpe provides functions for handling Bed Paired End format files, used for
// handling pairs of genomic regions.
package bedpe
import (
"fmt"
"github.com/vertgenlab/gonomics/bed"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
"github.com/vertgenlab/gonomics/numbers... |
615493ddbad38333f5704f66b8ca4d6f57d6f9cac40e7048e38b28308b5bd69e | Go | 5,899 | 178 | // Package axt provides the struct and functions that operate on alignments in Axt format.
package axt
import (
"fmt"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
"github.com/vertgenlab/gonomics/numbers/parse"
"io"
"log"
"strings"
)
//... |
81c507d7b2f8595b9c0b86879aff06fe29691d71f88fe6332dcac4d578c8d309 | Go | 5,939 | 190 | // Command Group: "General Tools"
// Finds values in a file and replaces them, processes the input as a string
package main
import (
"flag"
"fmt"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
"log"
"regexp"
"strings"
)
func readFindReplacePairs(filename string, delim strin... |
b9af70e1d7a0bba93d8ad59f9c4c9a9fa34be8784a66820f15221cee5e85b5b2 | Go | 5,943 | 196 | package main
import (
"os"
"testing"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fasta"
"github.com/vertgenlab/gonomics/fileio"
)
var FaFormatTests = []struct {
InputFile string
OutputFile string
ExpectedFile string
LineLength ... |
68a79ebe562000423c18d82cc72bb9e07121581e4e610f43c1e786b6787c4309 | Go | 5,954 | 186 | // Command Group: "BED Tools"
// Returns bed file with entries annotated based on the values corresponding to the region in a wig file
package main
import (
"flag"
"fmt"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
"log"
"math"
"github.com/vertgenlab/gonomics/bed"
"githu... |
867cf3f7793549fd93edca948f5a5e4eedea06ce4f82c5d6464e002fb3d64561 | Go | 5,978 | 229 | package genomeGraph
import (
"bytes"
"fmt"
"strings"
"github.com/vertgenlab/gonomics/cigar"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/giraf"
"github.com/vertgenlab/gonomics/numbers/parse"
"github.com/vertgenlab/gonomics/sam"
)
func PathToSeq(p giraf.Path, genome *GenomeGraph) []dna... |
eaed7983e171943a47c0c1fe8f17e074566c4b549d86507abc7fffc53a19bcfd | Go | 6,009 | 150 | // Command Group: "Sequence Evolution & Reconstruction"
// For two pFasta sequences, calculate a score at each base for the divergence between the two pDNA bases, convert the score to a binary substitution/non-substitution call, and return the calculations over a given window size
package main
import (
"flag"
"fmt"... |
24649931abffb473f3a07ae558b808532c5859ee465e77576ff0a77492bc4d1e | Go | 6,087 | 165 | package popgen
import (
"fmt"
"log"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
)
// PlotAfsF writes the Allele Frequency F function (AfsSampleDensity) to an output file for downstream visualization.
func PlotAfsF(alpha float64, n int, outFile string, integralError float64)... |
448764e0161afdad50e7d5b275210b63232e6a878377d53fc7602b412add6f48 | Go | 6,087 | 191 | package sam
import (
"log"
"strconv"
"strings"
"github.com/vertgenlab/gonomics/chromInfo"
)
// Metadata stores semi-parsed header data with several explicitly
// parsed fields (e.g. Version) and the rest of the header encoded in
// the AllTags field as a HeaderTagMap.
type Metadata struct {
Version string ... |
64f0a8e7c02959a54e1468cb479e35ed64d3d2bd4769fbd6658cdac0061b1cce | Go | 6,129 | 239 | package gene
import (
"testing"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/fasta"
"github.com/vertgenlab/gonomics/gtf"
)
func TestPointMutation(t *testing.T) {
g := gtf.Read("testdata/test.gtf")
f := fasta.Read("testdata/test.fasta")
var answerPos, answerNeg EffectPrediction
var er... |
db59ebfb42b036ae878cc3cc92c1a0bdd16f7fe88e023f7a2f827c85551c94ef | Go | 6,177 | 149 | package main
import (
"log"
"math/rand"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/numbers"
"github.com/vertgenlab/gonomics/sam"
)
// diploidInsertion performs insertion variant calling on an input pile. If an insertion is found, it is added to
// the answer structs, ans and mlt.
// Th... |
380c6e9eb853f90970f53831d09d045683729b87c46f8c10935e3a9c98de424b | Go | 6,220 | 184 | // Package motif provides functions for reading, writing, and manipulating position matrices for transcription factor binding site motif analysis.
package motif
import (
"fmt"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
"github.com/vertgenlab/gonomics/numbers/parse"
"log"
"... |
a1253c4688ca687e3b11d6977f52b72f238a510e86e1530069fd23456190713f | Go | 6,232 | 193 | package bed
import (
"testing"
)
var CompareDistanceTests = []struct {
A Bed
B Bed
expectedDistance int
expectedError bool
}{
{A: Bed{Chrom: "chr1", ChromStart: 10, ChromEnd: 20, Name: ""}, B: Bed{Chrom: "chr2", ChromStart: 21, ChromEnd: 30, Name: ""}, expectedDistance: -1, expe... |
f3dc0c2ad1c7dc0a9003ef9d545f62d47ba4b12b33a3a79197b43c136bc32d86 | Go | 6,259 | 192 | package genomeGraph
import (
"fmt"
"github.com/vertgenlab/gonomics/cigar"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/fastq"
"github.com/vertgenlab/gonomics/sam"
)
func GraphSmithWatermanMemPool(gg *GenomeGraph, read fastq.FastqBig, seedHash map[uint64][]uint64, seedLen int, stepSize in... |
644da4ae7486e819ebeaf634b391d3c88db08fb67428854a57d8f0c81e11d5b3 | Go | 6,272 | 107 | // Command Group: "FASTA and Multi-FASTA Tools"
// Takes pairwise alignment maf and finds insertions in species_ins not present in species_del but flanked by continuous alignments
package main
import (
"flag"
"fmt"
"log"
"github.com/vertgenlab/gonomics/bed"
"github.com/vertgenlab/gonomics/fileio"
"github.com/v... |
0866e295dde55703b4108c7dd452989a5b8c023aa88528b16abedd2d212db6c4 | Go | 6,274 | 143 | package gtf
import (
"github.com/vertgenlab/gonomics/bed"
"github.com/vertgenlab/gonomics/chromInfo"
"github.com/vertgenlab/gonomics/numbers"
)
// GeneToTssBed returns the positions of all TSSs from a Gene as a slice of single base-pair bed entries.
func GeneToTssBed(g Gene, c map[string]chromInfo.ChromInfo) []bed... |
112bdfdc50de0688c3af0cb15dde024fb937fa78e9b0cabaf35163647aabb623 | Go | 6,287 | 256 | package main
import (
"log"
"strconv"
"strings"
"github.com/vertgenlab/gonomics/vcf"
)
type operator string
const (
equal operator = "="
notEqual operator = "!="
greater operator = ">"
less operator = "<"
greaterEqual operator = ">="
lessEqual operator = "<="
present opera... |
9ad62f2c80b896ddb3b256b5ff956a8b7c9c51a6af13e87cbb0e21af7a1b8dd8 | Go | 6,312 | 140 | package main
import (
"flag"
"fmt"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/expandedTree"
"github.com/vertgenlab/gonomics/fasta"
"github.com/vertgenlab/gonomics/fileio"
"github.com/vertgenlab/gonomics/numbers"
"github.com/vertgenlab/gonomics/simulate"
"log"
"math/rand"
"os"... |
472a039fa4871847a91c8860b5ee999926a2797773f104ba5d2039dab56a7145 | Go | 6,316 | 198 | // Package matrix provides tools for operations on matrices. This package relies heavily on
// the gonum mat package, which implements high performance linear algebra operations.
package matrix
import (
"github.com/vertgenlab/gonomics/exception"
"gonum.org/v1/gonum/mat"
"log"
"math"
)
// FractionalSymmetricMatri... |
aaa294f8ef84cbb28007f91b39ddfcc105ff01799e84deee2674a8657bd090ca | Go | 6,329 | 102 | package bigWig
// Note that package bigWig is written to parse bigWig format version 4.
// specs for version 4 are found in this file: https://github.com/ucscGenomeBrowser/kent/blob/master/src/inc/bbiFile.h
// the official documentation for the bigWig file format (version 3)
// can be found in the supplementary materi... |
3627d439545d96b80b02b8a04e4fbd1db3664a8877471a8139e6a9ba36d7c1ce | Go | 6,330 | 189 | // Command Group: "FASTA and Multi-FASTA Tools"
// Reformat the sequences in a fasta file
package main
import (
"flag"
"fmt"
"log"
"strings"
"github.com/vertgenlab/gonomics/bed"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fasta"
"github.com/vertgenlab/gonomics/fileio"
)
type S... |
53c59454820cb61851fed6f5f909abe84e3a0f0a0bddac3a17289d56e9bd071b | Go | 6,336 | 210 | package main
import (
"flag"
"fmt"
"log"
"os"
"strings"
"github.com/vertgenlab/gonomics/axt"
"github.com/vertgenlab/gonomics/bed"
"github.com/vertgenlab/gonomics/chain"
"github.com/vertgenlab/gonomics/fasta"
"github.com/vertgenlab/gonomics/fileio"
"github.com/vertgenlab/gonomics/genomeGraph"
"github.com/v... |
ccfcb24a6c2f11d42935db3988fb217659de4c632e25af2a4afd9207183fad5b | Go | 6,353 | 203 | package dnaTwoBit
import (
"testing"
"github.com/vertgenlab/gonomics/dna"
)
type seedTest struct {
SeqA []dna.Base
SmallA *TwoBit
SeqB []dna.Base
SmallB *TwoBit
StartA int
StartB int
TrueMatchesLeft int
TrueMatchesRight int
}
var longDnaOne ... |
497c64badbd893d6b883edad79ba98bdc442fc4b14d15fb46e603157e2b8a611 | Go | 6,368 | 268 | package sam
import (
"runtime"
"testing"
"time"
"github.com/vertgenlab/gonomics/chromInfo"
"github.com/vertgenlab/gonomics/cigar"
"github.com/vertgenlab/gonomics/dna"
)
func BenchmarkPileupLinkedList(b *testing.B) {
for i := 0; i < b.N; i++ {
b.StopTimer()
reads, header := GoReadToChan("testdata/peak.bam"... |
f6cb5368fb0cae82a71fd04fbfb9a6054efbfa4807948a0367bb203121f23188 | Go | 6,374 | 221 | package vcf
import (
"fmt"
"io"
"log"
"strconv"
"strings"
"sync"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
)
// Read parses a slice of VCF structs from an input filename. Does not store or return the header.
func Read(filename string) ([]Vcf, Header) {
var answer []... |
89ef2e596f8f415c35fb7a0e4d43c2e34452a69d3f37ce7c0fcef61f1e6b0ef9 | Go | 6,392 | 179 | package fasta
import (
"testing"
"github.com/vertgenlab/gonomics/dna"
)
var seqThreeA = dna.StringToBases("ACGTacgTCATCATCATTACTACTAC")
var seqThreeB = dna.StringToBases("acgtACGTACGT")
var seqThreeC = dna.StringToBases("ACGTACGTACGTT")
var rcSeqThreeA = dna.StringToBases("GTAGTAGTAATGATGATGAcgtACGT")
var rcSeqThr... |
e978416791c65d0cd3c881799d4136718b4f6926f878465b0e04c97445badbc3 | Go | 6,422 | 204 | package vcf
import (
"log"
"math/rand"
"github.com/vertgenlab/gonomics/dna"
)
// IsHeterozygous returns true if more than 1 allele is present in the sample.
func IsHeterozygous(s Sample) bool {
if len(s.Alleles) == 0 {
return false
}
alleleBase := s.Alleles[0]
for i := 1; i < len(s.Alleles); i++ {
if s.Al... |
2eb10ff6fdcb0e5cce0220ae3c0cb10074d45fd90820be1599f51a221a5ad09b | Go | 6,438 | 200 | // Command Group: "General Tools"
// Utilities for axt alignments
package main
import (
"flag"
"fmt"
"github.com/vertgenlab/gonomics/bed"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/interval"
"github.com/vertgenlab/gonomics/interval/lift"
"log"
"github.com/vertgenlab/gonomics/a... |
6f4affd75bac42c57b2e3c045c11897e8f5efdabfc9d4c868c3297f5d60766ab | Go | 6,480 | 196 | package main
import (
"math"
"os"
"testing"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
"github.com/vertgenlab/gonomics/numbers"
)
var BedFilterTests = []struct {
InFile string
OutFile string
ExpectedFile string
MinScore ... |
f956863f7c69b1ad9086f8afba82482ff8d6491dfdf02025361a8b26c0be8977 | Go | 6,491 | 190 | // Package genomeGraph has structs and tools for reading, writing, editing and aligning graph representations of genomes
package genomeGraph
import (
"fmt"
"io"
"log"
"strings"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/dna/dnaTwoBit"
"github.com/vertgenlab/gonomics/exception"
"githu... |
e02eab2c07956e138cf93675144ee69282d70fdd2430e52e7c02ee19f0597f09 | Go | 6,502 | 163 | package sam
import "testing"
var DiploidIndelCallFromPileTests = []struct {
P Pile
Delta float64
Epsilon float64
Kappa float64
ExpectedInsertion DiploidInsertion
ExpectedDeletion DiploidDeletion
}{
{P: Pile{CountF: [13]int{30, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ... |
25404d7a8453b9c8067962419427e143763b8104decfa24c921cac658f3f1206 | Go | 6,621 | 203 | package dnaThreeBit
import (
"testing"
"github.com/vertgenlab/gonomics/dna"
)
type seedTest struct {
SeqA []dna.Base
SmallA *ThreeBit
SeqB []dna.Base
SmallB *ThreeBit
StartA int
StartB int
TrueMatchesLeft int
TrueMatchesRight int
}
var longD... |
d00e69ba7ebd84b514727272badb5c70e23472872463aba908229e36b9892a4f | Go | 6,624 | 139 | // Command Group: "Linear Alignment Tools"
// Align two FASTA files, each with only 1 sequence
package main
import (
"flag"
"fmt"
"log"
"os" //raven added this line for MSA Fasta output
"strings" //raven added this line for CountSeqIdx
"github.com/vertgenlab/gonomics/align"
"github.com/vertgenlab/gonomic... |
c46b7c161b255cf5452cf4de501b6b65008abc1185cb51a0cda315f9f38d75cd | Go | 6,654 | 210 | // Package fasta provides functions for reading, writing, and manipulating fasta files.
package fasta
import (
"bytes"
"errors"
"fmt"
"io"
"log"
"strings"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
)
// Fasta stores the name and se... |
f2abecab361e1434fe831b2031941ee2a5838b5617dce1d2b9399e4019f5ebdd | Go | 6,691 | 209 | package main
//TODO : add check for self-overlap bed files
//TODO: add enrichment calculations
import (
"flag"
"fmt"
"github.com/vertgenlab/gonomics/bed"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
"github.com/vertgenlab/gonomics/interval"
"log"
"strings"
)
type setting... |
a38d637bb5a7ed884fe7c8f245ddfb98590d45b81bdf25288450f5e55bde014c | Go | 6,697 | 224 | package net
import (
"fmt"
"github.com/vertgenlab/gonomics/chromInfo"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
"github.com/vertgenlab/gonomics/numbers/parse"
"strconv"
"strings"
"sync"
)
// Net represents an alignment block built off of chains, it represents the UCSC ... |
7fa8a8528b4e837b2aa8c4e29629974e2d471c204b61b7d14773f1a8bc11f46d | Go | 6,831 | 191 | package motif
import (
"log"
"math"
"math/rand"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/fasta"
)
// PfmToPpm creates a position probability matrix from an input position frequency matrix.
// Pseudocounts may be applied for Laplace smoothing. The input float represents the value adde... |
35e4ccb751be68f8633b523a1ce499dfbf20ede9bf2ad821f4e810630e40766d | Go | 6,899 | 245 | // A collection of tools that use the gonomics core library
package main
import (
_ "embed"
"flag"
"io/fs"
"io/ioutil"
"log"
"os"
"os/exec"
"path/filepath"
"strings"
"github.com/vertgenlab/gonomics/exception"
)
//go:embed command_cache.txt
var cache string
// getBin returns the path to binary executables ... |
ef15b794466a3e9804aaa600e8b5fc315ac8f5306503776b9682d190d0712b90 | Go | 6,915 | 239 | // Package sort holds structs and functions for sorting genomic data types
package sort
import (
"container/heap"
"fmt"
"github.com/vertgenlab/gonomics/exception"
"log"
"os"
"sort"
"strconv"
"sync"
"github.com/vertgenlab/gonomics/fileio"
"github.com/vertgenlab/gonomics/giraf"
)
const (
maxTmpFilesAllowed ... |
db9dc683d99c7872d0e762a9446843cb456a5d3617bd938459cd4303740a0e90 | Go | 7,056 | 169 | package sam
import (
"math"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/numbers"
"github.com/vertgenlab/gonomics/numbers/logspace"
)
// HaploidCall is a struct to represent the data of a haploid genotype called
// from a Pileup from a haploid genome.
type HaploidCall struct {
Base ... |
2bd31f9a927cedfccf74d8e82d2c8ef7b98a5168e558a29352bc2b164bc45317 | Go | 7,067 | 209 | package main
import (
"os"
"testing"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
)
var BedFormatTests = []struct {
InFile string
OutFile string
CoordName bool
ExpectedFile string
UCSCToEnsembl boo... |
5209217a7c19730f90a2d9de9a8e19aa6c2e1ae2969a00aa82aa0b30af88f116 | Go | 7,112 | 211 | // Package gaf provides functions for reading, writing, and manipulating GO Annotation File (GAF) format files.
// This package uses the GAF 2.2 file format as specified at the following URL: http://geneontology.org/docs/go-annotation-file-gaf-format-2.2/
// Files in this format can be downloaded after fileting for des... |
995b199479f29e3c1234acbe48de61dfe496e21068d6221033daafa4076901af | Go | 7,130 | 317 | package sam
import (
"os"
"reflect"
"sync"
"testing"
"github.com/vertgenlab/gonomics/cigar"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/fileio"
)
var r001 = Sam{
QName: "r001",
Flag: 99,
MapQ: 30,
RName: "ref",
Pos: 7,
Cigar: cigar.FromString("8M2I4M1D3M"),
RNext: "=",
PNe... |
da2a183575e2700ef12727b8ac0beb57972dafed63f88df85939515a7f10cbf0 | Go | 7,136 | 218 | package convert
import (
"os"
"strings"
"testing"
"github.com/vertgenlab/gonomics/bed"
"github.com/vertgenlab/gonomics/sam"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fasta"
"github.com/vertgenlab/gonomics/fileio"
"github.com/vertgenlab/g... |
7aa1272901d427b963edfb7b285d4a2f4c2e0e8e5ac3cdbfa63d06f77cea1bf4 | Go | 7,145 | 193 | package dna
import (
"testing"
)
var expected []Codon = []Codon{{A, A, G}, {T, G, A}, {A, A, C}}
var testSeq = StringToBases("AAGTGAAAC")
var test2DNA = StringToBases("atgcagatttttgtgaaaaccctgaccggcaaaacctga")
var expectedShortProtein string = "MQIFVKTLTGKT*"
var expectedProtein string = "MetGlnIlePheValLysThrLeuTh... |
53bce33a90b7316b4f2bb0130f12c0d664f67c92b10174c4fe426e4ab6211153 | Go | 7,149 | 266 | package pDna
import (
"github.com/vertgenlab/gonomics/dna"
"log"
"math"
"math/rand"
)
// Float32Base encodes a DNA base as a probability vector using float32 precision.
// Note that gap probabilities can be stored implicitly as 1 - (A + C + G + T).
type Float32Base struct {
A float32
C float32
G float32
T flo... |
e6c8e7cb4fd16aa691414d7c3e654d08d243e24d7ff52d6f030ac8bd77b88f8b | Go | 7,170 | 134 | package popgen
import (
"log"
"math"
"github.com/vertgenlab/gonomics/numbers"
"github.com/vertgenlab/gonomics/numbers/logspace"
)
// BuildFCache builds a slice of len(n) where each index i contains log(F(i | n, alpha)), where F is popgen.AFSSampleDensity.
func BuildFCache(n int, alpha float64, binomCache [][]flo... |
1c0cc7be8a8a76146cc5d1353e953db1b4b9cd49c44fcd02b54271f4dfeafb71 | Go | 7,227 | 198 | package numbers
import (
"log"
"math"
"math/rand"
)
// SampleInverseNormal returns a simulated value from a normal distribution.
func SampleInverseNormal(mu float64, sigma float64) float64 {
return rand.NormFloat64()*sigma + mu
}
// InitializeFastRejectionSampler takes in the parameters of a rejection sampler an... |
2fd535f75394963f9a9ebefeb0156d9cfa0018ed8d9ae1a503ddfa35cdf6606d | Go | 7,235 | 177 | // Package lastZWriter takes in alignment information and creates a file that contains all necessary lastz jobs with all required parameters for any species listed, as well as creating all the directories where data will be stored when those jobs are run.
package lastZWriter
import (
"github.com/vertgenlab/gonomics/f... |
80f70638e0c2584c7a6c1e4ff388a5ed81ca8777bac3266638d6d141b500ce9d | Go | 7,281 | 125 | package sam
import (
"math"
"testing"
)
var AncientBaseLikelihoodTests = []struct {
aCount int
cCount int
gCount int
tCount int
epsilon float64
lambda float64
ExpectedValues []float64
}{
{
aCount: 13,
cCount: 5,
gCount: 0,
tCount... |
cdb3a6957d87d975253fbdcd355c3cd2664400b7094f0a9e08be82c5e939827b | Go | 7,281 | 255 | package interval
import (
"bytes"
"fmt"
"log"
"os"
"strings"
"testing"
"github.com/vertgenlab/gonomics/axt"
"github.com/vertgenlab/gonomics/bed"
"github.com/vertgenlab/gonomics/chain"
"github.com/vertgenlab/gonomics/cigar"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/fileio"
"gith... |
740ade9fe7c3654d8c34b6e87fee2f7ccb4d68bd4395e64dfdff8d3d241b873e | Go | 7,298 | 192 | package graphReconstruct
import (
"log"
"testing"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/dna/dnaTwoBit"
"github.com/vertgenlab/gonomics/expandedTree"
"github.com/vertgenlab/gonomics/genomeGraph"
)
var (
allAlign []graphColumn
humanGraph = genomeGraph.EmptyGraph()
humanNode1 =... |
2204ba9f6e4341fe437b67461c4c7e27809994f4fb0ce799ef6797e68767d9a6 | Go | 7,405 | 511 | package pFasta
import (
"fmt"
"github.com/vertgenlab/gonomics/bed"
"github.com/vertgenlab/gonomics/dna/pDna"
"testing"
)
// ExtractTests tests a valid input to Extract
var ExtractTests = []struct {
Input []PFasta
Start int
End int
OutputName string
Chrom string
TakeCoords bool
Expecte... |
49cb515a5bbcb4bca10f90afc3894b17aecfeb4543a0db2f41d78e9e3a432f89 | Go | 7,413 | 229 | // Command Group: "Data Conversion"
// Convert a pairwise multiFa format alignment to a chain file. First species is the target by default
package main
import (
"flag"
"fmt"
"log"
"github.com/vertgenlab/gonomics/chain"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/fasta"
)
type State by... |
8ef52300223ac99c6816a5fe2211ca670c74ee77554438aee32c093097aace5f | Go | 7,434 | 286 | //# GONOMICS: testse
package main
import (
"fmt"
"log"
"os"
"os/exec"
"runtime"
"sort"
"strings"
"text/tabwriter"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
"golang.org/x/exp/slices"
)
var Reset = "\033[0m"
var Red = "\033[31m"
var Green = "\033[32m"
var Yellow = "... |
691d122ae813aebcf5142bf6cd61297d49285a4b5489ff501294a5712346e333 | Go | 7,494 | 211 | // Command Group: "Data Simulation"
// Simulate alignments to a reference sequence
package main
import (
"flag"
"fmt"
"log"
"math/rand"
"sort"
"strings"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fasta"
"github.com/vertgenlab/gonomics/fileio"
"github.com/vertgenlab/gonomics/... |
e02656544220e00d65f95232019da52a2ffd904ed763fa8250cfc56de44cd612 | Go | 7,508 | 201 | // Command Group: "BED Tools"
// Output a subset of a bed file using score, name, position, and length
package main
import (
"flag"
"fmt"
"log"
"math"
"math/rand"
"github.com/vertgenlab/gonomics/bed"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
"github.com/vertgenlab/go... |
2aaf6719cc6cba24e08074173acdb43e6549b6ed33712338faeb1ff0c34e1830 | Go | 7,585 | 196 | package gene
import (
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/fasta"
"github.com/vertgenlab/gonomics/gtf"
)
// GtfToGene converts a gtf record into a Gene data structure.
// If multiple isoforms are present, only the isoform with the longest CDS is used.
func GtfToGene(g *gtf.Gene, ref... |
9fafeb6cf2fcfb05b573aef90eeedd3d816e7094b582bb07241c7f71ca5dad36 | Go | 7,594 | 220 | package sam
import (
"fmt"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/numbers"
)
// consensusType represents the possible types of consensus variants in a Pile,
// which includes Bases, INDELs, or undefined (in the case where the Pile contains no data).
type consensusType byte
const (
... |
dc818f2ac111f60de21ea81bb42f116decc45568dfd414dc586644b0c9d2a37e | Go | 7,638 | 211 | package align
import (
"fmt"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fasta"
"testing"
)
var affineAlignTests = []struct {
seqOne string
seqTwo string
aln string
}{
{"ACGT", "ACGT", "ACGT\nACGT\n"},
{"ACGT", "CGT", "ACGT\n-CGT\n"},
{... |
15e408676b0a5394a8549705e395d6bd091ea3f33211a09c6a59345b8f71838a | Go | 7,655 | 215 | package numbers
import (
"fmt"
"math"
"testing"
)
//All expected values are calculated from online calculator tools or in the R programming language.
func ExplicitBinomialDist(n int, k int, p float64) float64 {
return float64(BinomCoefficient(n, k)) * math.Pow(p, float64(k)) * math.Pow(1-p, float64(n-k))
}
func... |
20b85963600fe751f7261b58861a9ebfaedf5c95d3976f17e7bf9695cdf6ac2d | Go | 7,668 | 192 | package main
import (
"flag"
"fmt"
"log"
"math"
"math/rand"
"os"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fasta"
"github.com/vertgenlab/gonomics/fileio"
"github.com/vertgenlab/gonomics/wig"
)
// ToTrainingSetSettings defines the usage ... |
f6e54c68534a8561494936946d03e2d2071e8d88c9319abad6edcfd26dd489f7 | Go | 7,689 | 250 | package fasta
import (
"log"
"github.com/vertgenlab/gonomics/dna"
)
// BinGenomeNoBreaks takes in an entire genome which is sorted largest to smallest contig and breaks up the fasta so
// that smaller contigs get combined into a single fasta, while large contigs become a single fasta on their own. The user
// must... |
e886ff5d3c53a20026ba7a5d01dda2b205d25d11d642fb9a36c511f74fb6e802 | Go | 7,735 | 260 | // Package tree provides a struct and functions that allow for creating binary trees
// modifying them, and doing calculations on them.
package tree
import (
"bytes"
"errors"
"fmt"
"github.com/vertgenlab/gonomics/exception"
"log"
"os"
"strconv"
"strings"
"github.com/vertgenlab/gonomics/fileio"
)
// A Tree i... |
671e69cd5d201c6cb6814d75b3f0715ea3ba39303de82f2b5b6017d097ca9963 | Go | 7,767 | 251 | // Command Group: "FASTQ Tools"
// Returns a filtered fastq based on option parameters
package main
import (
"flag"
"fmt"
"log"
"math/rand"
"sync"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fastq"
"github.com/vertgenlab/gonomics/fileio"
"... |
96972c2afb345360d2d7d00f1da293bd7308ce6405552de1fe4fcae65a2d60de | Go | 7,769 | 267 | // Command Group: "Data Simulation"
// Predict amplicon products generated from PCR
package main
import (
"flag"
"fmt"
"log"
"math"
"runtime"
"sort"
"strings"
"sync"
"github.com/vertgenlab/gonomics/bed"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab... |
737663117f7d4db684899158e646b9f6e3d33ea13c8b43ffd0016ba315193fa8 | Go | 7,782 | 234 | package main
import (
"os"
"testing"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
)
var ancoraBuildTests = []struct {
SamFileName string
RefFile string
OutFileA string
OutFileB string
MultiFaDir string
qNameA... |
684f629f601ba82badf8a6ecb18a276b3d2acd1a10c9beeb3cda8b9f93d408da | Go | 7,861 | 310 | package cigar
import (
"bytes"
"log"
"os"
"strings"
"testing"
)
var c1 Cigar = Cigar{RunLength: 35, Op: Match}
var c2 Cigar = Cigar{RunLength: 2, Op: Insertion}
var c3 Cigar = Cigar{RunLength: 16, Op: Deletion}
var c4 Cigar = Cigar{RunLength: 5, Op: Match}
var c5 Cigar = Cigar{RunLength: 2, Op: Mismatch}
var c6 ... |
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