# BAM2PLOT
Plot your bam files!
## UPDATE
`bam2plot` no longer depends on `perbase`. Now, `bam2plot` depends on [mosdepth](https://github.com/brentp/mosdepth)
## Subcommands
```bash
You must call bam2plot with the following subcommands:
[1]: 'from_bam'
[2]: 'from_reads'
[3]: 'guci'
```
### bam2plot from_bam
```bash
usage: bam2plot [-h] -b BAM -o OUTPATH [-w WHITELIST] [-t THRESHOLD] [-r ROLLING_WINDOW]
[-i | --index | --no-index] [-s | --sort_and_index | --no-sort_and_index]
[-z ZOOM] [-c | --cum_plot | --no-cum_plot] [-p {png,svg,both}]
[-n NUMBER_OF_REFS]
sub_command
Plot your bam files!
positional arguments:
sub_command
options:
-h, --help show this help message and exit
-b BAM, --bam BAM bam file
-o OUTPATH, --outpath OUTPATH
Where to save the plots.
-w WHITELIST, --whitelist WHITELIST
Only include these references/chromosomes.
-t THRESHOLD, --threshold THRESHOLD
Threshold of mean coverage depth
-r ROLLING_WINDOW, --rolling_window ROLLING_WINDOW
Rolling window size
-i, --index, --no-index
Index bam file
-s, --sort_and_index, --no-sort_and_index
Index and sort bam file
-z ZOOM, --zoom ZOOM Zoom into this region. Example: -z='100 2000'
-c, --cum_plot, --no-cum_plot
Generate cumulative plots of all chromosomes
-p {png,svg,both}, --plot_type {png,svg,both}
How to save the plots
-n NUMBER_OF_REFS, --number_of_refs NUMBER_OF_REFS
How many references (chromosomes) to plot
```
bam2plot from_bam generates coverage plots:
... and if `-c` is added, cumulative coverage plots for each reference (*e.g.* chromosomes) for each sample:
If the flag `--highlight` is given, the regions with a coverage below the `--treshold` are highlighted:
Below is an example of how bam2plot looks when runned in the terminal:
#### Examples
Here's an example of how to use the bam2plot from_bam:
```bash
bam2plot from_bam --bam input.bam --outpath output_folder --rolling_window 50 --threshold 5 -s -c
```
### bam2plot from_reads
```bash
usage: bam2plot [-h] -r1 READ_1 [-r2 READ_2] -ref REFERENCE [-gc | --guci | --no-guci] -o OUT_FOLDER
[-r ROLLING_WINDOW] [-p {png,svg,both}]
sub_command
Align your reads and plot the coverage!
positional arguments:
sub_command
options:
-h, --help show this help message and exit
-r1 READ_1, --read_1 READ_1
Fastq file 1
-r2 READ_2, --read_2 READ_2
Fastq file 2
-ref REFERENCE, --reference REFERENCE
Reference fasta
-gc, --guci, --no-guci
Plot GC content? (default: False)
-o OUT_FOLDER, --out_folder OUT_FOLDER
Where to save the plots.
-r ROLLING_WINDOW, --rolling_window ROLLING_WINDOW
Rolling window size
-p {png,svg,both}, --plot_type {png,svg,both}
How to save the plots
```
### bam2plot guci
```bash
usage: bam2plot [-h] -ref REFERENCE -w WINDOW -o OUT_FOLDER [-p {png,svg,both}] sub_command
Plot GC content of your reference fasta!
positional arguments:
sub_command
options:
-h, --help show this help message and exit
-ref REFERENCE, --reference REFERENCE
Reference fasta
-w WINDOW, --window WINDOW
Rolling window size
-o OUT_FOLDER, --out_folder OUT_FOLDER
Where to save the plots.
-p {png,svg,both}, --plot_type {png,svg,both}
How to save the plots
```
## Dependencies
`bam2plot` depends on [mosdepth](https://github.com/brentp/mosdepth), which you can install via:
```bash
conda install -c bioconda mosdepth
```
## Installation
You can install `bam2plot` using the following pip command:
```bash
pip install bam2plot
```
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"description": "# BAM2PLOT\n\nPlot your bam files!\n\n## UPDATE\n`bam2plot` no longer depends on `perbase`. Now, `bam2plot` depends on [mosdepth](https://github.com/brentp/mosdepth)\n\n## Subcommands\n```bash\nYou must call bam2plot with the following subcommands:\n [1]: 'from_bam'\n [2]: 'from_reads'\n [3]: 'guci'\n```\n\n### bam2plot from_bam\n```bash\nusage: bam2plot [-h] -b BAM -o OUTPATH [-w WHITELIST] [-t THRESHOLD] [-r ROLLING_WINDOW]\n [-i | --index | --no-index] [-s | --sort_and_index | --no-sort_and_index]\n [-z ZOOM] [-c | --cum_plot | --no-cum_plot] [-p {png,svg,both}]\n [-n NUMBER_OF_REFS]\n sub_command\n\nPlot your bam files!\n\npositional arguments:\n sub_command\n\noptions:\n -h, --help show this help message and exit\n -b BAM, --bam BAM bam file\n -o OUTPATH, --outpath OUTPATH\n Where to save the plots.\n -w WHITELIST, --whitelist WHITELIST\n Only include these references/chromosomes.\n -t THRESHOLD, --threshold THRESHOLD\n Threshold of mean coverage depth\n -r ROLLING_WINDOW, --rolling_window ROLLING_WINDOW\n Rolling window size\n -i, --index, --no-index\n Index bam file\n -s, --sort_and_index, --no-sort_and_index\n Index and sort bam file\n -z ZOOM, --zoom ZOOM Zoom into this region. Example: -z='100 2000'\n -c, --cum_plot, --no-cum_plot\n Generate cumulative plots of all chromosomes\n -p {png,svg,both}, --plot_type {png,svg,both}\n How to save the plots\n -n NUMBER_OF_REFS, --number_of_refs NUMBER_OF_REFS\n How many references (chromosomes) to plot\n```\n\nbam2plot from_bam generates coverage plots:\n\n\n... and if `-c` is added, cumulative coverage plots for each reference (*e.g.* chromosomes) for each sample:\n\n\nIf the flag `--highlight` is given, the regions with a coverage below the `--treshold` are highlighted:\n\n\nBelow is an example of how bam2plot looks when runned in the terminal:\n\n\n#### Examples\n\nHere's an example of how to use the bam2plot from_bam:\n\n```bash\nbam2plot from_bam --bam input.bam --outpath output_folder --rolling_window 50 --threshold 5 -s -c\n```\n\n### bam2plot from_reads\n\n```bash\nusage: bam2plot [-h] -r1 READ_1 [-r2 READ_2] -ref REFERENCE [-gc | --guci | --no-guci] -o OUT_FOLDER\n [-r ROLLING_WINDOW] [-p {png,svg,both}]\n sub_command\n\nAlign your reads and plot the coverage!\n\npositional arguments:\n sub_command\n\noptions:\n -h, --help show this help message and exit\n -r1 READ_1, --read_1 READ_1\n Fastq file 1\n -r2 READ_2, --read_2 READ_2\n Fastq file 2\n -ref REFERENCE, --reference REFERENCE\n Reference fasta\n -gc, --guci, --no-guci\n Plot GC content? (default: False)\n -o OUT_FOLDER, --out_folder OUT_FOLDER\n Where to save the plots.\n -r ROLLING_WINDOW, --rolling_window ROLLING_WINDOW\n Rolling window size\n -p {png,svg,both}, --plot_type {png,svg,both}\n How to save the plots\n```\n\n### bam2plot guci\n\n```bash\nusage: bam2plot [-h] -ref REFERENCE -w WINDOW -o OUT_FOLDER [-p {png,svg,both}] sub_command\n\nPlot GC content of your reference fasta!\n\npositional arguments:\n sub_command\n\noptions:\n -h, --help show this help message and exit\n -ref REFERENCE, --reference REFERENCE\n Reference fasta\n -w WINDOW, --window WINDOW\n Rolling window size\n -o OUT_FOLDER, --out_folder OUT_FOLDER\n Where to save the plots.\n -p {png,svg,both}, --plot_type {png,svg,both}\n How to save the plots\n```\n\n\n## Dependencies\n`bam2plot` depends on [mosdepth](https://github.com/brentp/mosdepth), which you can install via:\n```bash\nconda install -c bioconda mosdepth\n```\n## Installation\n\nYou can install `bam2plot` using the following pip command:\n\n```bash\npip install bam2plot\n```\n",
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