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mandysullisammysheepnbx0samcwileySam Wiley
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Dev (#28)
* updating muts of int to include nucletoide differences in addition to aa differences with help from @samcwiley * add missing aa logic back in * updating to obtain partial codon info as well * Some refactoring ideas * updating seq same length logic to match seqs aligned logic * adding amino acid "X" handling * created a hamming distance package that measures hamm dist of all of the seqs within a fasta * creating a package that compares all of the seqs within a fasta file and give the positions and nucleotide diffs btw them all * updating documentation * adding in tail handlilng logic * updating docs * start containerization * improving Dockerfile * update docker compose * init GitHub Actions workflow for building binaries across multiple targets * refactor GitHub Actions workflow to use OS matrix for builds and rust nightly * bug * bug * Update GitHub Actions workflow to trigger on all branches except main * bug * Strip images to keep them small * Use multi-stage build with latest nightly alpine image * Add check_chemistry for Illumina and ONT to replace python scripts in MIRA-NF (#13) Adds module for argument parsing/handling and selecting proper configuration filepaths and IRMA modules. --------- Co-authored-by: Sam Wiley <dzw2@cdp-client-02.biotech.cdc.gov> * add check_chemistry * tweaking files for docker * updating output * changed package name * adding documentation for adding a package to the workspace * Updating docs * updating docs * restructing readme situation * fix picture * fixing link and finishing up * fix link * link test * fix link * fix typo * fix pic * fix format * arguments and subplots per segment * subplots and variant data * Add consistent color generation for segment names in plots * read flow Sankey diagram * Refactor subplot layout and enhance annotations for segment names in coverage plots * Update .gitignore to exclude lock files * Fix typo in README and update package addition steps for clarity * adding mutation_of_interest package * compress logic and sest up structs for Serde * Reading in info with serde and structs * Remove some clones * removing lock file and adding to .gitignore * Updating docs * updating docs * restructing readme situation * fix pic * fix format * update documentation * typo fixes and adding output structure * fix header size * created a hamming distance package that measures hamm dist of all of the seqs within a fasta * creating a package that compares all of the seqs within a fasta file and give the positions and nucleotide diffs btw them all * updating documentation * Some refactoring ideas * updating seq same length logic to match seqs aligned logic * adding in tail handlilng logic * updating docs * init GitHub Actions workflow for building binaries across multiple targets * refactor GitHub Actions workflow to use OS matrix for builds and rust nightly * bug * bug * Update GitHub Actions workflow to trigger on all branches except main * bug * Update .gitignore to exclude all lock files recursively * Refactor plot coverage segment function to remove unused variable and simplify fallback formulas * mira-oxide logo * smaller logo * Update Cargo.toml and main.rs: comment out file count increment and enhance filename formatting for Sankey plot * Enhance Sankey plot: add hover templates and update title for clarity * Update Cargo.toml and main.rs: switch plotly dependency to Git; enhance argument help descriptions; explicit node x,y * Remove unused Label import from plotly common * Update plotly dependency to use Git repository * Remove mutations_of_interest_table package and update workspace members * merge cleanup -- plots working * update docs * tweaking package to include subtype as a filter when filtering variants of interest (#24) --------- Co-authored-by: Samuel Shepard <vfn4@cdc.gov> Co-authored-by: Ben Rambo-Martin <nbx0@cdc.gov> Co-authored-by: Ben Rambo-Martin <39743838+nbx0@users.noreply.github.com> Co-authored-by: Samuel Wiley <26017589+samcwiley@users.noreply.github.com> Co-authored-by: Sam Wiley <dzw2@cdp-client-02.biotech.cdc.gov>
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‎.github/workflows/build-binaries.yml‎

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name: Build Binaries
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on:
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push:
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branches:
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- '**'
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- '!main'
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pull_request:
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branches:
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- '**'
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- '!main'
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jobs:
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build:
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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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include:
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- os: ubuntu-latest
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target: x86_64-unknown-linux-gnu
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- os: macos-latest
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target: aarch64-apple-darwin
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- os: windows-latest
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target: x86_64-pc-windows-msvc
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steps:
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- uses: actions/checkout@v4
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- name: Install Rust toolchain -- nightly
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run: |
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rustup update nightly
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rustup default nightly
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rustup target add ${{ matrix.target }}
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# - name: Install build dependencies
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# if: matrix.target == 'x86_64-unknown-linux-gnu'
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# run: |
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# sudo apt-get update
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# sudo apt-get install -y build-essential pkg-config libssl-dev
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- name: Build for ${{ matrix.target }}
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uses: actions-rs/cargo@v1
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with:
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command: build
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args: --release --target ${{ matrix.target }}
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- name: Upload artifacts
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uses: actions/upload-artifact@v4
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with:
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name: binaries-${{ matrix.target }}
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path: target/${{ matrix.target }}/release/
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name: Build Binaries
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on:
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push:
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branches:
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- '**'
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- '!main'
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pull_request:
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branches:
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- '**'
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- '!main'
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jobs:
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build:
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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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include:
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- os: ubuntu-latest
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target: x86_64-unknown-linux-gnu
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- os: macos-latest
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target: aarch64-apple-darwin
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- os: windows-latest
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target: x86_64-pc-windows-msvc
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steps:
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- uses: actions/checkout@v4
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- name: Install Rust toolchain -- nightly
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run: |
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rustup update nightly
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rustup default nightly
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rustup target add ${{ matrix.target }}
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# - name: Install build dependencies
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# if: matrix.target == 'x86_64-unknown-linux-gnu'
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# run: |
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# sudo apt-get update
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# sudo apt-get install -y build-essential pkg-config libssl-dev
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- name: Build for ${{ matrix.target }}
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uses: actions-rs/cargo@v1
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with:
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command: build
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args: --release --target ${{ matrix.target }}
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- name: Upload artifacts
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uses: actions/upload-artifact@v4
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with:
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name: binaries-${{ matrix.target }}
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path: target/${{ matrix.target }}/release/

‎.gitignore‎

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/test
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*test*
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*lock
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**/*lock
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*.crt

‎.vscode/settings.json‎

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"CFPB",
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"ISSO",
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"cybersecurity"
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]
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}
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],
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"[rust]": {
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"editor.defaultFormatter": "rust-lang.rust-analyzer",
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"editor.formatOnSave": true,
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},
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}
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‎Cargo.toml‎

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[workspace]
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members = [ "flu_prepare_irma_json",
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"mutations_of_interest_table", "plots",
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]
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members = [ "all_sample_hamming_dist", "all_sample_nt_diffs",
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"variants_of_interest_table", "plots", "check_chemistry", "add_flu_prepare_irma_json"]
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[workspace.dependencies]
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clap = { version = "4", features = ["derive"] }
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csv = "1.3.1"
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either = "1"
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serde = { version = "1.0.219", features = ["derive"] }
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serde_yaml = "0.9"
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glob = "0.3.2"
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ordered-float = "5.0.0"
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#plotly = "0.12.1"
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plotly = { git = "https://github.com/plotly/plotly.rs.git", branch = "main" }
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zoe = { git = "https://github.com/CDCgov/zoe.git", tag = "v0.0.18", default-features = false, features = [
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zoe = { version = "0.0.19", default-features = false, features = [
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"multiversion",
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] }
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[profile.release]
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strip = true

‎Dockerfile‎

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# Create an argument to pull a particular version of an image
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####################################################################################################
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# BASE IMAGE
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####################################################################################################
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FROM rustlang/rust:nightly-alpine AS builder
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# Required certs for apk update
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COPY ca.crt /root/ca.crt
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# Put certs in /etc/ssl/certs location
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RUN cat /root/ca.crt >> /etc/ssl/certs/ca-certificates.crt
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RUN apk update && apk add --no-cache build-base
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WORKDIR /app
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# Copy all scripts to docker images
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COPY . .
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# This build step will cache the dependencies
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RUN cargo build --release
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FROM alpine:latest as deploy
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WORKDIR /app
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COPY --from=builder \
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/app/target/release/mutations_of_interest_table \
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/app/target/release/all_sample_nt_diffs \
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/app/target/release/all_sample_hamming_dist \
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/app/target/release/plots \
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/app/target/release/check_chemistry /app/
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# Create working directory variable
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ENV WORKDIR=/data
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# Set up volume directory in docker
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VOLUME ${WORKDIR}
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# Export project directory to PATH
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ENV PATH "$PATH:/app"

‎README.md‎

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# MIRA-Oxide
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![](./assets/images/mira_logo_gemini_oxide_web_small.png)
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**General disclaimer** This repository was created for use by CDC programs to collaborate on public health related projects in support of the [CDC mission](https://www.cdc.gov/about/cdc/#cdc_about_cio_mission-our-mission). GitHub is not hosted by the CDC, but is a third party website used by CDC and its partners to share information and collaborate on software. CDC use of GitHub does not imply an endorsement of any one particular service, product, or enterprise.
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MIRA-Oxide is a RUST workspace that is utilized by [MIRA-NF](https://github.com/CDCgov/MIRA-NF) to perform assembly and annotation of Influenza genomes, SARS-CoV-2 genomes, the SARS-CoV-2 spike-gene and RSV genomes.
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## Adding New Package to the MIRA-Oxide Worksace
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## Adding New Package to the MIRA-Oxide Workspace
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Before starting be sure that you have rust nightly installed and set as default. You will also need to have Cargo installed. If you need more information about how to install those, [see here](https://rust-book.cs.brown.edu/ch01-00-getting-started.html).
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### Step 3
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Mira-oxide requires rust-nightly to run the [zoe](https://github.com/CDCgov/zoe) crate.
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Install the nightly version of rust.
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```
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rustup toolchain install nightly
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```
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Using nightly for mira-oxide
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```
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rustup override set nightly
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```
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### Step 4
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Create a new package using Cargo
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```
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A folder with a the name that you specified should have been created. Inside that folder there should be a Cargo.toml file and a src folder containing a main.rs file.
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### Step 4
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Create a new package using Cargo
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```
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cargo new new_package_name
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```
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A folder with a the name that you specified should have been created. Inside that folder there should be a Cargo.toml file and a src folder containing a main.rs file.
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### Step 5
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Start Working!
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Add your dependencies to the package's Cargo.toml and start editing your src/main.rs
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### Step 5
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### Step 6
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Run your program!
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cargo run -p new_package_name -- #any inputs needed to run your package
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```
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### Step 6
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### Step 7
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Provide usage documentation.
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Create a README.md witin your package folder. Within that README provide a descritpion of the package, it's inputs, it's outputs and how to execute the package.
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Create a README.md within your package folder. Within that README provide a description of the package, it's inputs, it's outputs and how to execute the package.
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For additional information on rust workspaces, [see here](https://rust-book.cs.brown.edu/ch14-03-cargo-workspaces.html).
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## Current Packages
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- [mutations_of_interest_table](mutations_of_interest_table/)
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- [all_sample_hamming_dist](all_sample_hamming_dist/)
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- [all_sample_nt_diffs](all_sample_nt_diffs/)
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## Public Domain Standard Notice
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This repository constitutes a work of the United States Government and is not

‎all_sample_hamming_dist/Cargo.toml‎

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[package]
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name = "all_sample_hamming_dist"
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version = "0.1.0"
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edition = "2024"
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[dependencies]
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clap.workspace = true
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either.workspace = true
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zoe.workspace = true

‎all_sample_hamming_dist/README.md‎

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# All Sample Hamming Distance
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The all_sample_nt_diffs package takes a fasta file containing all your samples of interest after they have been aligned as an input. The outputs is a hamming distance matrix that provides the hamming distance between all of the sequences within the fasta file provided.
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### FASTA file Input:
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```
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>sample-1-rep-1
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ATGGAGAGAATAAAAGAACTGAGAGATCTAATGTCACAGTCTCGCACTCGCGAGATACTA
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ACCAAAACCACTGTTGACCACATGGCCATAATCAAGAAGTACACATCAGGAAGACAAGAA
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>sample-1-rep-2
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ATGGAGAGAATAAAAGAACTGAGAGATCTAATGTTACAGTCTCGCACTCGCGAGATACTA
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ACCAAAACCACTGTTGACCACATGGCCATAATCAAGAAGTACACATCAGGAAGACAAGAA
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>sample-1-rep-3
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ATGGAGAGAATAAAAGAACTGAGAGATCTAATGTCACAGTCTCGCACTCGCGAGATACTA
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ACCAAAACCACTGTTGACCACATGGCCATAATCAAGAAGTACACATCAGGAAGACCTGAA
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```
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After cloning the mira-oxide repo, execute this command to create a hamming distance matrix for the samples provided:
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```
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cargo run -p all_sample_hamming_dist -- -i <PATH>/input.fasta -o <PATH>/outputs.csv
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```
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If you would like the output to have another deliminator (default: ","), then the `-d` flag can be used to pass another deliminator.
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### The hamming distances output should be structured like this:
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```
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seqeunces,sample-1-rep-1,sample-1-rep-2,sample-1-rep-3
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sample-1-rep-1, 0, 1, 2
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sample-1-rep-2, 1, 0, 3
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sample-1-rep-3, 2, 3, 0
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```

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