maptide

Setup

Install via pip

$ pip install maptide

Build from source

Building from source requires the Rust compiler.

Installation instructions for the Rust compiler can be found here: https://www.rust-lang.org/tools/install

Once the Rust compiler is installed:

$ git clone https://github.com/CLIMB-TRE/maptide.git $ cd maptide/ $ python -m venv .venv $ source .venv/bin/activate $ pip install .

Usage

``` $ maptide -h usage: maptide [-h] [-v] [-r REGION] [-i INDEX] [-m MAPPING_QUALITY] [-b BASE_QUALITY] [-s] [-d DECIMALS] bam

positional arguments: bam Path to BAM file

options: -h, --help show this help message and exit -v, --version show program's version number and exit -r REGION, --region REGION Region to view, specified in the form CHROM:START-END (default: everything) -i INDEX, --index INDEX Path to index (BAI) file (default: .bai) -m MAPPINGQUALITY, --mapping-quality MAPPINGQUALITY Minimum mapping quality (default: 0) -b BASEQUALITY, --base-quality BASEQUALITY Minimum base quality (default: 0) -s, --stats Output additional per-position statistics (default: False) -d DECIMALS, --decimals DECIMALS Number of decimal places to display (default: 3) ```

Frequencies over all positions

$ maptide /path/to/file.bam

Frequencies over a region

$ maptide /path/to/file.bam --region chrom:start-end

If a region is specified, maptide will check for an index file with the same path as the BAM file, but with .bai appended on the end (i.e. /path/to/file.bam.bai).

If an index file does not exist in this location, maptide will still run anyway, just without an index file.

Index files that do not follow the naming convention /path/to/file.bam.bai can still be used, but a path to the file needs to be provided:

$ maptide /path/to/file.bam --region chrom:start-end --index /path/to/index.bai

Example in Python

maptide can be used within Python scripts:

```python import maptide

data = maptide.query( "path/to/file.bam", region="MN908947.3:100-200", # Obtain frequencies only in this region annotated=True, # Annotate frequencies with their bases A,C,G,T,DS,N )

chrom = "MN908947.3" # Chosen reference/chromosome in the BAM to access position = (100, 0) # Position 100, insert 0 (i.e. not an insertion)

With annotated = True, frequencies are annotated with their bases:

frequencies = data[chrom][position] print(frequencies) # {'A': 1, 'C': 122, 'G': 0, 'T': 1, 'DS': 13, 'N': 0}

If annotated = False, frequencies would be a list i.e. [1, 122, 0, 1, 13, 0]

```