bed2idt 0.1.0

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.

Usage

To use the CLI, run the following command:

python bed2idt/main.py [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, or none (default: pool).
• 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 primers.bed and save/overide the output as output.xlsx, split by pools:

   python bed2idt/main.py -b primers.bed --force plate --splitby pools

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

   python bed2idt/main.py -b primers.bed -o custom_output.xlsx tube --purification PAGE

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

   python bed2idt/main.py -b primers.bed plate --splitby none

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