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# gapmm2: gapped alignment using minimap2

This tool is a wrapper for minimap2 to run spliced/gapped alignment, ie aligning transcripts to a genome.   You are probably saying, yes minimap2 runs this with `-x splice --cs` option (you are correct).  However, there are instances where the terminal exons from stock minimap2 alignments are missing. This tool detects those alignments that have unaligned terminal eons and uses `edlib` to find the terminal exon positions. The tool then updates the PAF output file with the updated information.

#### Rationale

We can pull out a gene model in GFF3 format that has a short 5' terminal exon:

```
scaffold_9	funannotate	gene	408904	409621	.	-	.	ID=OPO1_006919;
scaffold_9	funannotate	mRNA	408904	409621	.	-	.	ID=OPO1_006919-T1;Parent=OPO1_006919;product=hypothetical protein;
scaffold_9	funannotate	exon	409609	409621	.	-	.	ID=OPO1_006919-T1.exon1;Parent=OPO1_006919-T1;
scaffold_9	funannotate	exon	409320	409554	.	-	.	ID=OPO1_006919-T1.exon2;Parent=OPO1_006919-T1;
scaffold_9	funannotate	exon	409090	409255	.	-	.	ID=OPO1_006919-T1.exon3;Parent=OPO1_006919-T1;
scaffold_9	funannotate	exon	408904	409032	.	-	.	ID=OPO1_006919-T1.exon4;Parent=OPO1_006919-T1;
scaffold_9	funannotate	CDS	409609	409621	.	-	0	ID=OPO1_006919-T1.cds;Parent=OPO1_006919-T1;
scaffold_9	funannotate	CDS	409320	409554	.	-	2	ID=OPO1_006919-T1.cds;Parent=OPO1_006919-T1;
scaffold_9	funannotate	CDS	409090	409255	.	-	1	ID=OPO1_006919-T1.cds;Parent=OPO1_006919-T1;
scaffold_9	funannotate	CDS	408904	409032	.	-	0	ID=OPO1_006919-T1.cds;Parent=OPO1_006919-T1;
```

If we then map this transcript against the genome, we get the following PAF alignment.

```
$ minimap2 -x splice --cs genome.fasta cds-transcripts.fa | grep 'OPO1_006919'
OPO1_006919-T1	543	13	543	-	scaffold_9	658044	408903	409554	530	530	60	NM:i:0	ms:i:530	AS:i:466	nn:i:0	ts:A:+	tp:A:P	cm:i:167	s1:i:510	s2:i:0	de:f:0	rl:i:0	cs:Z::129~ct57ac:166~ct64ac:235
```

The `--cs` flag in minimap2 can be used to parse the coordinates (below) and you can see we are missing the 5' exon.

```
>>> cs2coords(408903, 13, 543, '-', ':129~ct57ac:166~ct64ac:235')
([(409320, 409554), (409090, 409255), (408904, 409032)],
```

So if we run this same alignment with `gapmm2` we are able to properly align the 5' terminal exon.

```
$ gapmm2 genome.fa cds-transcripts.fa | grep 'OPO1_006919'
OPO1_006919-T1	543	0	543	-	scaffold_9	658044	408903	409621	543	543	60	tp:A:P	ts:A:+	NM:i:0	cs:Z::129~ct57ac:166~ct64ac:235~ct54ac:13
```

```
>>> cs2coords(408903, 0, 543, '-', ':129~ct57ac:166~ct64ac:235~ct54ac:13')
([(409609, 409621), (409320, 409554), (409090, 409255), (408904, 409032)]
```



#### Usage:

`gapmm2` can be run as a command line script:

```
$ gapmm2
usage: gapmm2 [-o] [-f] [-t] [-m] [-i] [-d] [-h] [--version] reference query

gapmm2: gapped alignment with minimap2. Performs minimap2/mappy alignment with splice options and refines terminal alignments with edlib.

Positional arguments:
  reference           reference genome (FASTA)
  query               transcipts in FASTA or FASTQ

Optional arguments:
  -o , --out          output in PAF format (default: stdout)
  -f , --out-format   output format [paf,gff3] (default: paf)
  -t , --threads      number of threads to use with minimap2 (default: 3)
  -m , --min-mapq     minimum map quality value (default: 1)
  -i , --max-intron   max intron length, controls terminal search space (default: 500)
  -d, --debug         write some debug info to stderr (default: False)

Help:
  -h, --help          Show this help message and exit
  --version           Show program's version number and exit
```



### Python API

It can also be run as a python module. The module provides several functions for working with spliced alignments:

#### `aligner` function

The main function for aligning transcripts to a genome. It can write an output file in either PAF or GFF3. It returns a dictionary with alignment statistics.

```python
>>> from gapmm2.align import aligner
>>> stats = aligner('genome.fa', 'transcripts.fa', out_fmt="gff3", output="output.gff3")
>>> stats
{'n': 6926, 'low-mapq': 0, 'refine-left': 409, 'refine-right': 63}
```

#### `cs2coords` function

This function parses the CIGAR string (cs) from minimap2 and converts it to genomic coordinates, identifying exons, introns, and other alignment features.

```python
>>> from gapmm2.align import cs2coords
>>> cs2coords(408903, 0, 543, '-', ':129~ct57ac:166~ct64ac:235~ct54ac:13')
([(409609, 409621), (409320, 409554), (409090, 409255), (408904, 409032)], [(0, 13), (13, 248), (248, 414), (414, 543)], 0, 0, True)
```


### Installation

You can install gapmm2 using pip:

```bash
pip install gapmm2
```

Or you can install the latest development version directly from GitHub:

```bash
pip install git+https://github.com/nextgenusfs/gapmm2.git
```

You can also install from conda:

```bash
conda install -c bioconda gapmm2
```

### Dependencies

Gapmm2 requires the following Python packages:

- mappy (Python bindings for minimap2)
- edlib (for sequence alignment)
- natsort (for natural sorting)

These dependencies will be automatically installed when you install gapmm2 using pip or conda. Note that I've recently seen some seqmentation faults from mappy, so as of v25.4.13 it will run `minimap2` directly instead of mappy if `minimap2 ` is installed.

### Development

#### Testing

Gapmm2 includes a test suite that can be run using pytest. To run the tests, first install pytest:

```bash
pip install pytest pytest-cov
```

Then run the tests from the root directory of the repository:

```bash
python -m pytest tests/ --cov=gapmm2
```

#### Code Formatting

This project uses [pre-commit](https://pre-commit.com/) to ensure code quality and consistency. The pre-commit hooks run Black (code formatter), isort (import sorter), and flake8 (linter).

To set up pre-commit:

1. Install pre-commit:

```bash
pip install pre-commit
```

2. Install the git hooks:

```bash
pre-commit install
```

3. (Optional) Run against all files:

```bash
pre-commit run --all-files
```

After installation, the pre-commit hooks will run automatically on each commit to ensure your code follows the project's style guidelines.
