PrimalBedTools

PrimalBedTools is a library for manipulating and processing BED files, particularly focused on primer-related operations. It provides several functions for common BED file operations including coordinate remapping, sorting, updating, and amplicon generation.

Functions are wrapped in a CLI for ease of use.

Installation

pip install primalbedtools

Usage

primalbedtools <command> [options]

Commands

Remap

Remaps coordinates in a BED file using a multiple sequence alignment (MSA).

primalbedtools remap --bed input.bed --msa alignment.fasta --from_id source_id --to_id target_id

Required arguments:

• --bed: Input BED file
• --msa: Multiple sequence alignment file in FASTA format
• --from_id: Source sequence ID to remap from
• --to_id: Target sequence ID to remap to

Sort

Sorts entries in a BED file.

primalbedtools sort input.bed

Required arguments:

• bed: Input BED file to sort

Update

Updates information in a BED file, particularly primer names.

primalbedtools update input.bed

Required arguments:

• bed: Input BED file to update

Amplicon

Creates an amplicon BED file from primer pairs.

primalbedtools amplicon input.bed [--primertrim]

Required arguments:

• bed: Input BED file containing primer information

Optional arguments:

• -t, --primertrim: Generate primer-trimmed amplicons

Examples

1. Remap coordinates from one reference to another:

primalbedtools remap --bed primers.bed --msa refs.fasta --from_id ref1 --to_id ref2

2. Sort a BED file:

primalbedtools sort input.bed > sorted.bed

3. Generate amplicons with primer trimming:

primalbedtools amplicon primers.bed --primertrim > trimmed_amplicons.bed

Output

All commands output modified BED files to stdout while preserving the original header information. The amplicon command outputs either standard or primer-trimmed amplicon coordinates based on the provided options.