# bam-toolbox

## Installation

```
pip install https://github.com/AndersenLab/bam-toolbox/archive/1.0.0.tar.gz
```

## Usage

    bam-toolbox 1.0

    usage:
      bam <command> [<args>...]
      bam -h | --help
      bam --version

    commands:
      coverage

## Commands

### Coverage

Calculate depth of coverage! There are several ways to do so:

1. Calculate coverage for the whole genome, nuclear genome, and individual chromosomes. Also calculated the mtDNA:nuclear ratio which acts as a proxy for mitochondrial content.

2.

```
usage:
  bam coverage <bam> [options] [--mtchr=<mtchr>]
  bam coverage <bam> [options] <chrom:start-end>...
  bam coverage <bam> [options] --window=<size>
  bam coverage <bam> [options] --regions=<gff/bed>
```

###### Parameters

* `--header` - Output the header line.
* `--mtchr` - Specifying a mitochondrial chromosome will output the mtDNA:nuclear DNA ratio, offering an estimate of mitochondrial content. 
* `--window` - Calculate depth of coverage for given windows across the genome.
* `--regions` - Specify a bed or gff file and calculate coverage in those regions.

###### Example

```
bam coverage test.bam --tsv --header
```

__Result:__

Output is in `--tsv` format.

```
ENTITY  chrom   start   end ATTR    VALUE   DATE
CB4853  I   1   15072434    bases_mapped    1688210 2015-11-08 23:22:39.498133
CB4853  I   1   15072434    depth_of_coverage   0.112006461597  2015-11-08 23:22:39.498242
CB4853  I   1   15072434    breadth_of_coverage 0.0918075342045 2015-11-08 23:22:39.498328
CB4853  I   1   15072434    length  15072434    2015-11-08 23:22:39.498372
CB4853  I   1   15072434    pos_mapped  1383763 2015-11-08 23:22:39.498413
CB4853  II  1   15279421    bases_mapped    1605336 2015-11-08 23:22:39.923802
CB4853  II  1   15279421    depth_of_coverage   0.105065237747  2015-11-08 23:22:39.923880
...
CB4853  mt_nuclear_ratio    51.7503772943   2015-11-08 23:22:41.949819
```

__Formatted Result:__

| ENTITY   | chrom   |   start |      end | ATTR                |       VALUE | DATE                       |
|:---------|:--------|--------:|---------:|:--------------------|------------:|:---------------------------|
| CB4853   | I       |       1 | 15072434 | bases_mapped        | 1.68821e+06 | 2015-11-08 23:26:41.891988 |
| CB4853   | I       |       1 | 15072434 | depth_of_coverage   | 0.112006    | 2015-11-08 23:26:41.892087 |
| CB4853   | I       |       1 | 15072434 | breadth_of_coverage | 0.0918075   | 2015-11-08 23:26:41.892155 |
| CB4853   | I       |       1 | 15072434 | length              | 1.50724e+07 | 2015-11-08 23:26:41.892198 |
| CB4853   | I       |       1 | 15072434 | pos_mapped          | 1.38376e+06 | 2015-11-08 23:26:41.892239 |
| CB4853   | II      |       1 | 15279421 | bases_mapped        | 1.60534e+06 | 2015-11-08 23:26:42.319937 |