primalbedtools 1.0.0
A collection of tools for working with primer.bed files
Requires Python: <4,>=3.9

# 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:

```bash
pip install primalbedtools
```

or conda:

```bash
conda install bioconda::primalbedtools
```

## Basic Usage

```bash
primalbedtools <command> [options]
```

## Commands

### remap

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

```bash
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:**
```bash
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.

```bash
primalbedtools sort <bed_file>
```

**Arguments:**

- `bed`: Input BED file

**Example:**
```bash
primalbedtools sort primers.bed > primers.sorted.bed
```

### update

Update primer names to v2 format (`prefix_number_DIRECTION_index`).

```bash
primalbedtools update <bed_file>
```

**Arguments:**

- `bed`: Input BED file

**Example:**
```bash
primalbedtools update primers.v1.bed > primers.v2.bed
```

### amplicon

Generate amplicon information from primer pairs.

```bash
primalbedtools amplicon <bed_file> [--primertrim]
```

**Arguments:**

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

**Example:**
```bash
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).

```bash
primalbedtools merge <bed_file>
```

**Arguments:**

- `bed`: Input BED file

**Example:**
```bash
primalbedtools merge primers.bed > primers.merged.bed
```

### fasta

Convert BED file to FASTA format.

```bash
primalbedtools fasta <bed_file>
```

**Arguments:**

- `bed`: Input BED file

**Example:**
```bash
primalbedtools fasta primers.bed > primers.fasta
```

### validate_bedfile

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

```bash
primalbedtools validate_bedfile <bed_file>
```

**Arguments:**

- `bed`: Input BED file

**Example:**
```bash
primalbedtools validate_bedfile primers.bed
```

### validate

Validate a BED file against a reference genome.

```bash
primalbedtools validate <bed_file> <fasta_file>
```

**Arguments:**

- `bed`: Input BED file
- `fasta`: Reference FASTA file

**Example:**
```bash
primalbedtools validate primers.bed reference.fasta
```

### downgrade

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

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

**Arguments:**

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

**Example:**
```bash
# 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
```