bed2idt 1.0.1

Converts primer.bed files to IDT ordering templates

bed2idt

This command-line interface (CLI) generates IDT input files from a 7-column primer bed file.

Description

The IDT Input File Generator CLI allows you to convert a primer bed file into IDT input files. IDT (Integrated DNA Technologies) is a company that provides custom DNA synthesis services. This tool automates the process of generating input files for ordering primers from IDT.

Installation

From pip

pip instal bed2idt

From Poetry / source

git clone https://github.com/ChrisgKent/bed2idt

poetry install && poetry build

Usage

To use the CLI, run the following command:

bed2idt [options] [command] [command-options]

Options

The CLI supports the following options:

• -b, --bedfile: Path to the primer bed file (required).
• -o, --output: The output location for the generated IDT input file(s) (default: output.xlsx).
• plate command:
  • -s, --splitby: Specifies whether the primers should be split across more than one plate. Valid options are pool, ref, none, next (default: pool).
  • -f, --fillby: Specifies how the plates should be filled. Valid options are rows or cols (default: rows).
• tube command:
  • -s, --scale: The concentration of the primers. Valid options are 25nm, 100nm, 250nm, 1um, 2um, 5um, 10um, 4nmU, 20nmU, PU, or 25nmS (default: 25nm).
  • -p, --purification: The purification method for the primers. Valid options are STD, PAGE, HPLC, IEHPLC, RNASE, DUALHPLC, or PAGEHPLC (default: STD).
• --force: Overrides the output directory if it already exists.

Examples

1. Generate 96-well plate IDT input files for a primer bed file named primer.bed and save/overide the output as output.xlsx, split by pools:

   bed2idt -b primer.bed --force plate --splitby pools

2. Generate tube IDT input files for a primer bed file named primer.bed, save the output as custom_output.xlsx, and specify a purification method:

   bed2idt -b primer.bed -o custom_output.xlsx tube --purification PAGE

3. Generate IDT input files for a primer bed file named primer.bed without splitting the primers across multiple plates:

   bed2idt -b primer.bed plate --splitby none

4. Generate IDT input files primer.xlsx for a primer.bed file named primer.bed, splitting the plate by pool, and filling plates by col:

   bed2idt -b primer.bed -o primer.xlsx plate --splitby pools --filllby cols

Note: Make sure to replace python with the appropriate command for running Python on your system.