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‎CONTRIBUTING.md

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@@ -60,11 +60,11 @@ As one final guideline please be welcoming to newcomers and encourage new contri
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Unsure where to begin contributing to Poly? You can start by looking through these beginner and help-wanted issues:
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[Good first issues](https://github.com/TimothyStiles/poly/contribute) - issues which are good for first time contributors.
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[Good first issues](https://github.com/bebop/poly/contribute) - issues which are good for first time contributors.
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[Help wanted issues](https://github.com/TimothyStiles/poly/issues?q=is%3Aissue+is%3Aopen+label%3A%22help+wanted%22+) - issues which should be a bit more involved than beginner issues.
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[Help wanted issues](https://github.com/bebop/poly/issues?q=is%3Aissue+is%3Aopen+label%3A%22help+wanted%22+) - issues which should be a bit more involved than beginner issues.
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[Feature requests](https://github.com/TimothyStiles/poly/labels/enhancement) - before requesting a new feature search through previous feature requests to see if it's already been requested. If not then feel free to submit a request and tag it with the enhancement tag!
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[Feature requests](https://github.com/bebop/poly/labels/enhancement) - before requesting a new feature search through previous feature requests to see if it's already been requested. If not then feel free to submit a request and tag it with the enhancement tag!
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### Working on your first Pull Request?
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### Non-security related bugs
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For non-security bug reports please [submit it using this template!](https://github.com/TimothyStiles/poly/issues/new?assignees=&labels=&template=bug_report.md&title=)
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For non-security bug reports please [submit it using this template!](https://github.com/bebop/poly/issues/new?assignees=&labels=&template=bug_report.md&title=)
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# How to suggest a feature or enhancement
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If you want to suggest a feature it's as easy as filling out this [issue template](https://github.com/TimothyStiles/poly/issues/new?assignees=&labels=&template=feature_request.md&title=), but before you do please [check to see if it's already been suggested!](https://github.com/TimothyStiles/poly/labels/enhancement)
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If you want to suggest a feature it's as easy as filling out this [issue template](https://github.com/bebop/poly/issues/new?assignees=&labels=&template=feature_request.md&title=), but before you do please [check to see if it's already been suggested!](https://github.com/bebop/poly/labels/enhancement)
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# How add a recommended VSCode Plugin
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‎README.md

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# (Poly)merase <img align="right" src="https://cdn.discordapp.com/attachments/766785755305213953/777596834734145546/ProfileFrameArtboard_1.png" width="100">
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[![PkgGoDev](https://pkg.go.dev/badge/github.com/TimothyStiles/poly)](https://pkg.go.dev/github.com/TimothyStiles/poly)
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[![GitHub license](https://img.shields.io/badge/license-MIT-blue.svg)](https://github.com/TimothyStiles/poly/blob/main/LICENSE)
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![Tests](https://github.com/TimothyStiles/poly/workflows/Test/badge.svg)
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[![PkgGoDev](https://pkg.go.dev/badge/github.com/bebop/poly)](https://pkg.go.dev/github.com/bebop/poly)
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[![GitHub license](https://img.shields.io/badge/license-MIT-blue.svg)](https://github.com/bebop/poly/blob/main/LICENSE)
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![Tests](https://github.com/bebop/poly/workflows/Test/badge.svg)
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![Test Coverage](https://img.shields.io/endpoint?url=https://gist.githubusercontent.com/TimothyStiles/e58f265655ac0acacdd1a38376ccd32a/raw/coverage.json)
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Poly is a Go package for engineering organisms.
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## Install
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`go get github.com/TimothyStiles/poly@latest`
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`go get github.com/bebop/poly@latest`
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## Documentation
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* **[Library](https://pkg.go.dev/github.com/TimothyStiles/poly#pkg-examples)**
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* **[Library](https://pkg.go.dev/github.com/bebop/poly#pkg-examples)**
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* **[Tutorials](https://github.com/TimothyStiles/poly/tree/main/tutorials)**
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* **[Tutorials](https://github.com/bebop/poly/tree/main/tutorials)**
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* **[Learning Synbio](https://github.com/TimothyStiles/how-to-synbio)**
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‎align/align.go

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package align
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import (
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"github.com/TimothyStiles/poly/align/matrix"
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"github.com/bebop/poly/align/matrix"
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)
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// Scoring is a struct that holds the scoring matrix for match, mismatch, and gap penalties.

‎align/align_test.go

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import (
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"testing"
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"github.com/TimothyStiles/poly/align"
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"github.com/TimothyStiles/poly/align/matrix"
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"github.com/TimothyStiles/poly/alphabet"
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"github.com/bebop/poly/align"
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"github.com/bebop/poly/align/matrix"
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"github.com/bebop/poly/alphabet"
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)
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func TestNeedlemanWunsch(t *testing.T) {

‎align/example_test.go

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import (
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"fmt"
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"github.com/TimothyStiles/poly/align"
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"github.com/TimothyStiles/poly/align/matrix"
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"github.com/TimothyStiles/poly/alphabet"
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"github.com/bebop/poly/align"
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"github.com/bebop/poly/align/matrix"
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"github.com/bebop/poly/alphabet"
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)
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func ExampleNeedlemanWunsch() {

‎align/matrix/matrix.go

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import (
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"fmt"
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"github.com/TimothyStiles/poly/alphabet"
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"github.com/bebop/poly/alphabet"
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)
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// SubstitutionMatrix is a struct that holds a substitution matrix and the two alphabets that the matrix is defined over.

‎align/matrix/matrix_test.go

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import (
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"testing"
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"github.com/TimothyStiles/poly/align/matrix"
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"github.com/TimothyStiles/poly/alphabet"
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"github.com/bebop/poly/align/matrix"
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"github.com/bebop/poly/alphabet"
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"github.com/stretchr/testify/assert"
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)
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‎alphabet/alphabet_test.go

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"reflect"
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"testing"
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"github.com/TimothyStiles/poly/alphabet"
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"github.com/bebop/poly/alphabet"
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)
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func TestAlphabet(t *testing.T) {

‎checks/checks.go

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import (
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"strings"
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"github.com/TimothyStiles/poly/transform"
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"github.com/bebop/poly/transform"
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)
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// IsPalindromic accepts a sequence of even length and returns if it is

‎checks/checks_test.go

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import (
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"testing"
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"github.com/TimothyStiles/poly/checks"
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"github.com/bebop/poly/checks"
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)
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// This also needs an example test.

‎clone/clone.go

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"sort"
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"strings"
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"github.com/TimothyStiles/poly/checks"
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"github.com/TimothyStiles/poly/seqhash"
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"github.com/TimothyStiles/poly/transform"
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"github.com/bebop/poly/checks"
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"github.com/bebop/poly/seqhash"
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"github.com/bebop/poly/transform"
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// Part is a simple struct that can carry a circular or linear DNA sequence.

‎clone/example_test.go

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"fmt"
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"log"
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"github.com/TimothyStiles/poly/clone"
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"github.com/TimothyStiles/poly/seqhash"
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"github.com/bebop/poly/clone"
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"github.com/bebop/poly/seqhash"
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func ExampleGoldenGate() {

‎doc.go

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https://github.com/sponsors/TimothyStiles
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Browse our subpackages to find the functionality and documentation you need:
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https://pkg.go.dev/github.com/TimothyStiles/poly#section-directories
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https://pkg.go.dev/github.com/bebop/poly#section-directories
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*/
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package poly

‎fold/dna.go

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package fold
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import "github.com/TimothyStiles/poly/transform"
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import "github.com/bebop/poly/transform"
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var dnaComplement = transform.ComplementBase
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‎fold/example_test.go

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import (
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"fmt"
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"github.com/TimothyStiles/poly/fold"
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"github.com/bebop/poly/fold"
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func ExampleZuker() {

‎fold/fold.go

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"math"
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"github.com/TimothyStiles/poly/transform"
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"github.com/bebop/poly/transform"
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// Zuker folds the DNA sequence and return the lowest free energy score.

‎fold/rna.go

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package fold
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import "github.com/TimothyStiles/poly/transform"
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import "github.com/bebop/poly/transform"
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‎fold/seqfold.go

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"math"
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"strings"
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"github.com/TimothyStiles/poly/checks"
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"github.com/bebop/poly/checks"
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)
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const (

‎go.mod

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module github.com/TimothyStiles/poly
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module github.com/bebop/poly
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go 1.18
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‎io/example_test.go

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package io_test
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import (
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"github.com/TimothyStiles/poly/io/fasta"
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"github.com/TimothyStiles/poly/io/genbank"
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"github.com/TimothyStiles/poly/io/gff"
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"github.com/TimothyStiles/poly/io/polyjson"
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"github.com/bebop/poly/io/fasta"
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"github.com/bebop/poly/io/genbank"
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"github.com/bebop/poly/io/gff"
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"github.com/bebop/poly/io/polyjson"
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// This is where the integration tests that make effed up cyclic dependencies go.

‎io/fasta/example_test.go

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"strings"
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"github.com/TimothyStiles/poly/io/fasta"
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"github.com/bebop/poly/io/fasta"
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)
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//go:embed data/base.fasta

‎io/fastq/example_test.go

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"os"
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"strings"
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"github.com/TimothyStiles/poly/io/fastq"
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"github.com/bebop/poly/io/fastq"
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//go:embed data/nanosavseq.fastq

‎io/genbank/example_test.go

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"os"
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"path/filepath"
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"github.com/TimothyStiles/poly/io/genbank"
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"github.com/bebop/poly/io/genbank"
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// This example shows how to open a genbank file and search for a gene given

‎io/genbank/genbank.go

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"strconv"
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"strings"
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"github.com/TimothyStiles/poly/transform"
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"github.com/bebop/poly/transform"
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"github.com/lunny/log"
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"github.com/mitchellh/go-wordwrap"
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‎io/genbank/genbank_test.go

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"reflect"
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"github.com/TimothyStiles/poly/transform"
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"github.com/bebop/poly/transform"
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"github.com/google/go-cmp/cmp"
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"github.com/google/go-cmp/cmp/cmpopts"
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"github.com/stretchr/testify/assert"

‎io/gff/example_test.go

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"path/filepath"
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"testing"
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"github.com/TimothyStiles/poly/io/gff"
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"github.com/TimothyStiles/poly/transform"
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"github.com/bebop/poly/io/gff"
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"github.com/bebop/poly/transform"
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// This example shows how to open a gff file and search for a gene given its

‎io/gff/gff.go

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"lukechampine.com/blake3"
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"github.com/TimothyStiles/poly/transform"
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"github.com/bebop/poly/transform"
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var (

‎io/polyjson/example_test.go

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"path/filepath"
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"time"
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"github.com/TimothyStiles/poly/io/polyjson"
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"github.com/TimothyStiles/poly/seqhash"
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"github.com/bebop/poly/io/polyjson"
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"github.com/bebop/poly/seqhash"
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func Example() {

‎io/polyjson/polyjson.go

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"os"
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"time"
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"github.com/TimothyStiles/poly/transform"
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"github.com/bebop/poly/transform"
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/******************************************************************************

‎io/polyjson/polyjson_test.go

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"strings"
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"testing"
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"github.com/TimothyStiles/poly/transform"
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"github.com/bebop/poly/transform"
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"github.com/stretchr/testify/assert"
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‎io/rebase/example_test.go

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"fmt"
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"github.com/TimothyStiles/poly/io/rebase"
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"github.com/bebop/poly/io/rebase"
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)
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// This example reads rebase into an enzymeMap and returns the AarI recognition

‎io/slow5/example_test.go

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"fmt"
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"os"
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"github.com/TimothyStiles/poly/io/slow5"
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"github.com/bebop/poly/io/slow5"
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func ExampleNewParser() {

‎io/slow5/slow5.go

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newRead.ChannelNumber = values[valueIndex]
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default:
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newRead.Error = fmt.Errorf("Unknown field to parser '%s' found on line %d. Please report to github.com/TimothyStiles/poly", fieldValue, parser.line)
303+
newRead.Error = fmt.Errorf("Unknown field to parser '%s' found on line %d. Please report to github.com/bebop/poly", fieldValue, parser.line)
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}
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}
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return newRead, nil

‎io/uniprot/example_test.go

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"github.com/TimothyStiles/poly/io/uniprot"
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"github.com/bebop/poly/io/uniprot"
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)
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// This example shows how to open a uniprot data dump file and read the results

‎mash/example_test.go

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import (
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"fmt"
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"github.com/TimothyStiles/poly/mash"
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"github.com/bebop/poly/mash"
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func ExampleMash() {

‎mash/mash_test.go

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"testing"
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"github.com/TimothyStiles/poly/mash"
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"github.com/bebop/poly/mash"
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func TestMash(t *testing.T) {

‎primers/pcr/example_test.go

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"fmt"
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"github.com/TimothyStiles/poly/primers/pcr"
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"github.com/bebop/poly/primers/pcr"
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)
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// This example shows how to design a sequence.

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