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

Install primalbedtools using pip:

pip install primalbedtools

or conda:

conda install bioconda::primalbedtools

Basic Usage

primalbedtools <command> [options]

Commands

remap

Remap BED file coordinates from one reference to another using a multiple sequence alignment.

primalbedtools remap --bed <bed_file> --msa <msa_file> --from_id <source_id> --to_id <target_id>

Arguments:

• --bed: Input BED file (required)
• --msa: Multiple sequence alignment file (required)
• --from_id: Source sequence ID to remap from (required)
• --to_id: Target sequence ID to remap to (required)

Example:

primalbedtools remap --bed primers.bed --msa alignment.fasta --from_id MN908947.3 --to_id BA.2

sort

Sort BED file by chromosome, amplicon number, and primer direction.

primalbedtools sort <bed_file>

Arguments:

• bed: Input BED file

Example:

primalbedtools sort primers.bed > primers.sorted.bed

update

Update primer names to v2 format (prefix_number_DIRECTION_index).

primalbedtools update <bed_file>

Arguments:

• bed: Input BED file

Example:

primalbedtools update primers.v1.bed > primers.v2.bed

amplicon

Generate amplicon information from primer pairs.

primalbedtools amplicon <bed_file> [--primertrim]

Arguments:

• bed: Input BED file
• -t, --primertrim: Generate primer-trimmed amplicon information

Example:

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

merge

Merge primers with the same properties (chromosome, amplicon number, direction).

primalbedtools merge <bed_file>

Arguments:

• bed: Input BED file

Example:

primalbedtools merge primers.bed > primers.merged.bed

fasta

Convert BED file to FASTA format.

primalbedtools fasta <bed_file>

Arguments:

• bed: Input BED file

Example:

primalbedtools fasta primers.bed > primers.fasta

validate_bedfile

Validate a BED file for internal consistency (correct primer pairings, etc.).

primalbedtools validate_bedfile <bed_file>

Arguments:

• bed: Input BED file

Example:

primalbedtools validate_bedfile primers.bed

validate

Validate a BED file against a reference genome.

primalbedtools validate <bed_file> <fasta_file>

Arguments:

• bed: Input BED file
• fasta: Reference FASTA file

Example:

primalbedtools validate primers.bed reference.fasta

downgrade

Downgrade a BED file from v2 to v1 primer name format.

primalbedtools downgrade <bed_file> [--merge-alts]

Arguments:

• bed: Input BED file
• --merge-alts: Merge alternative primers (removes _alt suffixes)

Example:

# Downgrade with alternative primers
primalbedtools downgrade primers.v2.bed > primers.v1.bed

# Downgrade without alternative primers
primalbedtools downgrade primers.v2.bed --merge-alts > primers.v1.merged.bed