OVEN — Open Vector Editor with New Features

A plasmid editor for VS Code, built on Open Vector Editor.

Open .gb, .gbk, .fasta, .fa and .dna files in a tab, then design primers, collect them into an order, search your existing primer collection, edit codons, and align Sanger reads against the plasmid on screen.

Install

Search for OVEN in the Extensions view (Cmd/Ctrl+Shift+X), or:

code --install-extension gordonrix.oven

If you have sanekun.openvectoreditor installed, uninstall it first — otherwise both offer to open .gb files.

npm install
npm run package
code --install-extension oven-*.vsix --force

What this fork adds

Upstream is a viewer: it embeds Open Vector Editor in a VS Code tab and saves the file back. Added here:

• Primer cart — collect primers across plasmid files into one order, with sessions, CSV export and cross-referencing against primers you already own
• Primer search over your own primer collection, 3′-anchored, with attach-to-sequence
• New Primer as a side panel, with an editable 5′ tail and mismatches marked in red
• Sanger alignment against the open plasmid, with chromatograms, translated mutated codons, and origin-spanning reads handled
• Change Amino Acid — any codon, not just synonyms, with codon usage tables
• Keyboard shortcuts for primer search, new primer and the copy variants — see Keyboard shortcuts
• Melting temperature and GC for the current selection, in the status bar
• File → Save and Cmd/Ctrl+S, greying out when nothing has changed
• DNA base editing enabled, and the Create menu populated — upstream left OVE's readOnly default in place, which hid every item in it
• Sequences open split, sequence on the left and the circular map in a tab on the right
• Persistent UI state — cut-site filter, search columns and widths, codon-table organism

Plus fixes to Open Vector Editor itself: origin-spanning features corrupting on save, three .ab1 parser bugs, chromatogram scaling, and short annotation labels never being drawn.

The vendored OVE bundle is patched rather than forked, and every patch is tracked and checksummed — see patches/README.md. Patches and issue drafts for upstream are in upstream/.

Primer cart

Collect primers across plasmid files into one list you can paste into an oligo order.

1. Highlight a region and use Create → New Primer — the menu bar, the right-click menu, or Cmd/Ctrl+Shift+K. It opens as a panel beside the sequence; Set From Selection fills in the binding site on the strand the Strand radio names.

   Type on the front of the Bases box to add a 5′ tail; bases that do not match the template turn red. The annotation covers the annealing footprint only, but the full sequence goes to the cart and the file.

2. Add to Cart picks up any primer; ones you create are added automatically.

3. The cart is global across files and survives restarts.

4. Copy puts names and sequences on the clipboard; Export CSV writes the full table.

Sessions keep separate orders apart — see OVEN: New Cart Session and OVEN: Switch or Manage Cart Sessions.

Your primer inventory

Point oven.inventoryPath at a spreadsheet of primers you have already ordered and the cart marks each one: green if you already have it (with its ID), orange if it is new.

The file needs a name column and a sequence column; everything else is up to you. .xlsx, .xlsm, .csv, .tsv and .txt all work.

Columns you do not name are still read, and offered in the search results under Columns. Header matching is exact first, then case-insensitive.

Primer search

Click Primer Search, or right-click the sequence, to find every primer in your inventory that binds the open plasmid. Clicking a row scrolls to that site.

Matching is exact and 3′-anchored, so tailed primers are found; the unmatched tail shows in Tail bp, and 100% match hides them. The search can be scoped to a selection.

Attach adds a primer_bind annotation over the annealing footprint, keeping the full sequence in a /Sequence qualifier; press Save to write it to the file. Cmd+Z will not undo it — remove it from Properties → Primers.

Choosing columns

Columns in the toolbar picks what the table shows: the computed Tm, Anneal bp and Tail bp, plus any column of your inventory file. Pos, Str, Name and Attach are always shown.

Your choice is remembered across files; Reset to defaults puts it back. Drag a divider to resize a column, double-click one to reset all widths. Click a header to sort.

The Filter box searches names, sequences and the columns you are showing.

Other settings: oven.searchMinAnneal (default 15), oven.searchFullLengthOnly, oven.searchMaxHits.

Alignment

Click Align in an open plasmid to check clones against it. .ab1, .gb, .gbk and .fasta reads are all accepted; a multi-record FASTA becomes one track per record.

Four ways to add reads:

• Right-click the files in the Explorer → Add to Alignment (handles a multi-selection)
• Browse… in the panel
• Paste — copy in Finder, click the panel, Cmd+V
• Drag and drop onto the panel, holding ⇧ Shift

Shift matters: without it VS Code opens what you drop as a new tab instead.

The reference sits pinned along the top, each read gets a row with its chromatogram, and mutated codons show the amino acid they now encode.

Each read gets a verdict:

Hover a read for its counts, identity, strand and rotation.

Reads that cross the origin are handled, and the reference is never rotated, so its coordinates hold.

Trace ends below oven.alignTrimQuality (default 20) are trimmed before aligning; set it to 0 to align the full read. oven.alignMaxReads (default 50) caps one alignment.

MAFFT

Alignment needs MAFFT, installed separately:

brew install mafft                      # macOS
conda install -c bioconda mafft         # any platform

If it is missing, the panel says so when it opens and offers a Locate MAFFT… button and Re-check.

OVEN looks on your PATH, then where Homebrew and conda install — including named conda environments, the usual reason a mafft that works in the terminal is invisible here. VS Code reads your PATH at startup, so installing MAFFT with the editor open needs a window reload.

Run OVEN: Check MAFFT Installation to see which binary was found. oven.mafftPath sets one explicitly; oven.mafftArgs (default --auto) passes your own strategy. --adjustdirection is always added.

Editing

Change Amino Acid — right-click a residue in a translation and pick any codon in the genetic code, not just that residue's synonyms.

It is laid out the way a codon table is printed, and every codon carries its fraction (share of that amino acid's codons) and frequency (per thousand), for S. cerevisiae, E. coli, H. sapiens and M. musculus — from the Codon Usage Database (Nakamura et al. 2000).

Set oven.allowSequenceEditing to false to lock the bases, or oven.readOnly to lock the file entirely.

Selection readout

Selecting a region gives you, in one line:

DNA | Editable | Selecting 22 bps from 101 to 122 (45.5% GC) | Melting Temp: 64.5 | Length: 6537 bps

Melting temperature uses SantaLucia (1998) by default, as NEB's calculator does; click the readout to switch to Breslauer. Outside 8–100 bp it shows —.

oven.showSelectionStatsByDefault (on) switches both status-bar items on the first time you open a sequence; toggling them yourself in the View menu always wins.

Other

• Select a DNA file → Open With → OVEN, and set it as the default if you like
• Sequences open with the Circular Map in a tab on the right, beside the sequence. oven.viewType changes that: sequence or circular for a single pane with the other as a tab you switch to. Reopen the file for a change to take effect
• Save with File → Save or cmd/ctrl+S, in every format including .dna
• Filter Cut Sites is remembered between files, rather than resetting each time
• Search hits are marked with a dark grey bar showing which strand they matched
• OVEN: Open Demo Editor opens an empty editor to try things in, backed by no file

Keyboard shortcuts

The ones this fork adds. View → View Editor Hotkeys lists these alongside Open Vector Editor's own.

Plain ⌘C copies the selection.

Rebinding. oven.searchPrimersHotkey and oven.newPrimerHotkey take Open Vector Editor's notation — mod is Cmd or Ctrl, joined with +, as in mod+alt+n. Empty means no shortcut, and the file must be reopened.

Avoid anything VS Code binds at the workbench level, such as mod+j or mod+shift+f (Search: Find in Files) — those never reach the editor, so the shortcut appears to do nothing.

Settings

Anything that reads like oven.something is a VS Code setting. Press Cmd/Ctrl+, and type OVEN; they are grouped under Extensions → OVEN. To edit them as text, run Preferences: Open User Settings (JSON) and add entries like:

{
  "oven.inventoryPath": "/Users/you/Documents/Primers Inventory.xlsx",
  "oven.newPrimerHotkey": "alt+p"
}

Most take effect immediately; the ones that change how the editor is built — oven.newPrimerHotkey, oven.searchPrimersHotkey, oven.readOnly, oven.viewType — need the file reopened.

Known issues

Inherited from upstream:

• .dna files: primers already in the file are displayed and preserved on save, but new primers created in the UI are not written back. Use .gb if you need that. The primer cart is unaffected.

Fork notice

This is a fork of sanekun/ove-vscode, which is licensed under GPL-3.0. This fork is also GPL-3.0; see LICENSE.

It is based on upstream v1.2.0, which was published to the Marketplace but never pushed to git, so those sources were imported from the published VSIX — see the vendor-1.2.0 tag, which records a sha256 for every imported file.

Release notes

See CHANGELOG.md.