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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-COVID/maptide.git
$ cd maptide/
$ python -m venv env
$ source env/bin/activate
$ pip install --upgrade pip
$ 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: </path/to/bam>.bai)
  -m MAPPING_QUALITY, --mapping-quality MAPPING_QUALITY
                        Minimum mapping quality (default: 0)
  -b BASE_QUALITY, --base-quality BASE_QUALITY
                        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:

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]