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LCrossmanLCrossman
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Merge branch 'main' into main
2 parents 99af687 + 483a767 commit f1c7851

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Lines changed: 219376 additions & 1623 deletions

‎.github/workflows/microbiorust-py_benchmarks.yml‎

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@@ -44,13 +44,24 @@ jobs:
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# 2. PUT HISTORY
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- name: Restore results
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run: |
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if [ -d "old_pages/results/github-runner/" ]; then
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echo "Restoring previous benchmark results..."
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mkdir -p microbiorust-py/.asv/results/github-runner/
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cp -r old_pages/results/github-runner/* microbiorust-py/.asv/results/github-runner/
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#there were difficulties with a subfolder being created sometimes
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ASV_ROOT_RESULTS_DIR="microbiorust-py/.asv/results/"
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ASV_MACHINE_RESULTS_DIR="microbiorust-py/.asv/results/github-runner/"
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if [ -d "old_pages/results" ]; then
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echo "Restoring previous benchmark results from old_pages/results..."
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mkdir -p "${ASV_ROOT_RESULTS_DIR}"
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rsync -av old_pages/results/ "${ASV_ROOT_RESULTS_DIR}"
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else
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echo "No previous results found. Starting fresh."
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fi
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if [ -d "old_pages/results/github-runner/" ]; then
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echo "restoring results from old_pages/results/github-runner"
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mkdir -p "${ASV_MACHINE_RESULTS_DIR}"
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rsync -av old_pages/results/github-runner/ "${ASV_MACHINE_RESULTS_DIR}"
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else
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echo "No machine specific results found"
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fi
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# 3. ADD NEW DATA POINT
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- name: Run Benchmarks
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- name: Save results for next time
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run: |
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# Make sure the destination exists inside the HTML folder
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mkdir -p microbiorust-py/.asv/html/results
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mkdir -p microbiorust-py/.asv/html/results/
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# Copy the accumulated JSON files (Old + New) into the publish dir
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cp -r microbiorust-py/.asv/results/* microbiorust-py/.asv/html/results/
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rsync -av microbiorust-py/.asv/results/ microbiorust-py/.asv/html/results/
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# 6. UPLOAD EVERYTHING
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- name: Deploy to GitHub Pages
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github_token: ${{ secrets.GITHUB_TOKEN }}
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publish_dir: microbiorust-py/.asv/html
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publish_branch: gh-pages
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‎ROADMAP.md‎

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@@ -24,12 +24,12 @@ Integration of common types and parsers such as:
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Protein parameters such as:
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- [x] Hydrophobicity
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- [x] Molecular weight
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- [ ] Counted amino acids & as percentage
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- [x] Counted amino acids & as percentage
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- [x] Aromaticity
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- [ ] Parsing phylogenetic trees
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- [ ] Parsing multiple sequence alignments
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- [ ] Methylation data parsing
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- [ ] Consider pyo3 integration
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- [x] pyo3 integration
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**Testing - bioinformatics**
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- [ ] Testing & updating parsers with various edge case files such as gbk with the CONTIG(JOIN) structure

‎microBioRust/Cargo.toml‎

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@@ -27,10 +27,11 @@ path = "src/lib.rs"
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paste = "1.0"
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itertools = "0.14.0"
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protein-translate = "0.2.0"
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bio = "2.3.0"
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bio = "3.0.0"
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anyhow = "1.0"
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thiserror = "2.0.12"
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regex = "1.5"
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chrono = "0.4.38"
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clap = { version = "4.5.19", features = ["derive"] }
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lazy_static = "1.5"
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‎microBioRust/new_output_embl.gbk‎

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LOCUS source_1 928 bp DNA linear CON 24-NOV-2025
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DEFINITION Escherichia coli K-12 substr. MG1655.
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ACCESSION source_1
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KEYWORDS .
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SOURCE Escherichia coli K-12 substr. MG1655
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ORGANISM Escherichia coli K-12 substr. MG1655
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FEATURES Location/Qualifiers
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source 1..910
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/organism="K-12 substr. MG1655"
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/mol_type="DNA"
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/strain="K-12 substr. MG1655"
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/db_xref="PRJNA57779"
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gene complement(1..354)
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/locus_tag="b3304"
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CDS complement(1..354)
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/locus_tag="b3304"
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/codon_start="1"
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/gene="rplR"
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/translation="MDKKSARIRRATRARRKLQELGATRLVVHRTPRHIYAQVIAPNGS
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LVAASTVEKAIAEQLKYTGNKDAAAAVGKAVAERALEKGIKDVSFDRSGFQYHGRVQAL
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DAAREAGLQ"
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/product="50S ribosomal subunit protein L18"
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gene complement(364..897)
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/locus_tag="b3305"
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CDS complement(364..897)
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/locus_tag="b3305"
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/codon_start="1"
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/gene="rplF"
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/translation="MSRVAKAPVVVPAGVDVKINGQVITIKGKNGELTRTLNDAVEVKH
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NTLTFGPRDGYADGWAQAGTARALLNSMVIGVTEGFTKKLQLVGVGYRAAVKGNVINLS
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GFSHPVDHQLPAGITAECPTQTEIVLKGADKQVIGQVAADLRAYRRPEPYKGKGVRYAD
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VVRTKEAKK"
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/product="50S ribosomal subunit protein L6"
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ORIGIN
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1 acctctacct tagaactgaa ggccagcttc acgggcagca tctgccagtg cctggacacg
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61 accatgatat tggaacccgg aacggtcaaa ggatacatct ttgatgcctt tttccagagc
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121 gcgttcagcg acagctttac ccacagctgc agccgcgtct ttgttaccgg tgtacttcag
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181 ttgttcagcg atagcttttt ctacagtaga agcagctacc agaacttcag aaccgttcgg
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241 tgcaattacc tgtgcgtaaa tgtgacgcgg ggtacgatgt accaccaggc gagttgcgcc
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301 cagctcctgg agcttgcggc gtgcgcgggt cgcacgacgg atacgagcag atttcttatc
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361 catagtgtta ccttacttct tcttagcctc tttggtacgc acgacttcgt cggcgtaacg
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421 aacacccttg cctttataag gctcaggacg acggtaggcg cgcagatccg ctgcaacctg
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481 gccgatcacc tgcttatcag cgcctttcag cacgatttca gtctgagtcg gacattcagc
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541 agtgataccc gcaggcagct gatggtcaac aggatgagag aaacccagag acaggttaat
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601 cacattgcct ttaaccgctg cacggtaacc tacaccaacc agctgcagct tcttagtgaa
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661 gccttcggta acaccgataa ccattgagtt cagcagggca cgcgcggtac cagcctgtgc
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721 ccaaccgtct gcgtaaccat cacgcggacc gaaggtcagg gtattatctg catgtttaac
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781 ttcaacagca tcgttgagag tacgagtcag ctcgccgttt ttacctttga tcgtaataac
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841 ctgaccgttg atttttacgt caacgccggc aggaacaacg accggtgctt tagcaacacg
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901 agacattttt tcc
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//

‎microBioRust/new_output_embl.gff‎

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##gff-version 3
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##sequence-region source_1 1 910
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source_1 . CDS 1 354 0 - 0 id=b3304;name=source_1;gene=rplR;locus_tag=b3304;product=50S ribosomal subunit protein L18
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source_1 . CDS 364 897 0 - 0 id=b3305;name=source_1;gene=rplF;locus_tag=b3305;product=50S ribosomal subunit protein L6
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##FASTA
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acctctaccttagaactgaaggccagcttcacgggcagcatctgccagtgcctggacacg
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accatgatattggaacccggaacggtcaaaggatacatctttgatgcctttttccagagc
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gcgttcagcgacagctttacccacagctgcagccgcgtctttgttaccggtgtacttcag
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ttgttcagcgatagctttttctacagtagaagcagctaccagaacttcagaaccgttcgg
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tgcaattacctgtgcgtaaatgtgacgcggggtacgatgtaccaccaggcgagttgcgcc
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cagctcctggagcttgcggcgtgcgcgggtcgcacgacggatacgagcagatttcttatc
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catagtgttaccttacttcttcttagcctctttggtacgcacgacttcgtcggcgtaacg
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aacacccttgcctttataaggctcaggacgacggtaggcgcgcagatccgctgcaacctg
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gccgatcacctgcttatcagcgcctttcagcacgatttcagtctgagtcggacattcagc
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agtgatacccgcaggcagctgatggtcaacaggatgagagaaacccagagacaggttaat
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cacattgcctttaaccgctgcacggtaacctacaccaaccagctgcagcttcttagtgaa
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gccttcggtaacaccgataaccattgagttcagcagggcacgcgcggtaccagcctgtgc
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ccaaccgtctgcgtaaccatcacgcggaccgaaggtcagggtattatctgcatgtttaac
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ttcaacagcatcgttgagagtacgagtcagctcgccgtttttacctttgatcgtaataac
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ctgaccgttgatttttacgtcaacgccggcaggaacaacgaccggtgctttagcaacacg
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agacattttttcc

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