bed2myra 0.1.0

Convert primer.bed files to scripts for automated MYRA pooling

Bed2Myra

Bed2Myra is a command-line tool designed to automate the generation of input files for the MYRA liquid handling robot.

It calculates the required transfer volumes based on primer weights and generates:

1. Sample Sheets: Defining the source layout.
2. Transfer Sheets: Instructions for the robot to move specific volumes from source wells to destination tubes.

Features

• Automated Mapping: Matches primers from a BED file to their physical location in source plates using an Excel specification sheet.
• Volume Calculation: Automatically calculates transfer volumes based on primer weight (pw tag in BED file) and a user-defined multiplier.
• Safety Checks: Enforces volume limits (Min: 1µL, Max: 50µL) to ensure safe pipetting.
• Replicate Support: Easily generate instructions for multiple technical replicates (e.g., triplicates) in a single run.
• Batch Processing: Process multiple source plates in one command.

Installation

This project is managed with uv.

Local Development

Clone the repository and install dependencies:

git clone <repository-url>
cd bed2myra
uv sync

Usage

Run the tool using uv run:

uv run bed2myra -b <bed_file> -s <spec_sheet> -p <plate_names> [options]

Arguments

Short	Long	Required	Description	Default
-b	--primer-bed	Yes	Path to the primer BED file containing weights (pw tag).	-
-s	--plate-spec	Yes	Path to the Excel file (.xlsx) containing plate specifications.	-
-p	--plate-names	Yes	Name(s) of the source plate(s) to process. Supports multiple names.	-
-m	--volume-multiplier	No	Multiplier factor for the volume calculation.	1.0
-r	--replicates	No	Number of replicate destination tubes to create.	1
-o	--output-dir	No	Directory to save the generated CSV files.	./output/
	--output-prefix	No	Prefix for the output filenames.	myra

Example

Generate files for two plates (plate_1 and plate_2) with 3 replicates each, using a 1.5x volume multiplier:

uv run bed2myra \
  -b data/primers.bed \
  -s data/plate_layout.xlsx \
  -p "plate_1" "plate_2" \
  -r 3 \
  -m 1.5 \
  -o ./myra_files/

Input File Formats

1. Primer BED File

A standard BED-like file describing the primers. It must contain a weight tag (format pw=<float>) in the description/tags column to calculate volumes or will default to 1μL.

Example:

NC_000962.3  528752  528772  primer_1_LEFT_1   1  +  ACCAACG...  pw=3.267
NC_000962.3  529173  529193  primer_1_RIGHT_1  1  -  CTTGTCG...  pw=3.267

2. Plate Specification (Excel)

An Excel file (.xlsx) defining where each primer is located in the source plates. Modelled off the IDT Plate Specs.xlsx but only required columns:

• Plate Name: The identifier for the plate (matches -p argument).
• Sequence Name: The ID of the primer (must match the name column in the BED file).
• Well Position: The specific well (e.g., A1, B2).

Plate Name	Well Position	Sequence Name
plate_1	A1	primer_1_LEFT_1
plate_1	A2	primer_1_RIGHT_1

Outputs

The tool generates two types of CSV files in the output directory:

1. Sample File (<prefix>_sample_<plate_name>.csv):
   • Contains the source layout: Well (Position) and Source Name (Primer ID).
2. Transfer File (<prefix>_transfer_<plates>.csv):
   • Instructions for the MYRA robot.
   • Columns: Well (Destination replicate ID), Sources (Primer ID), Volume (Calculated µL).