https://github.com/StephanHolgerD/DrukBam
https://github.com/StephanHolgerD/DrukBam
Last synced: 7 months ago
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- Host: GitHub
- URL: https://github.com/StephanHolgerD/DrukBam
- Owner: StephanHolgerD
- Created: 2021-02-11T15:20:48.000Z (over 5 years ago)
- Default Branch: master
- Last Pushed: 2023-07-23T10:20:44.000Z (almost 3 years ago)
- Last Synced: 2024-08-09T21:10:32.195Z (almost 2 years ago)
- Language: Python
- Size: 8.91 MB
- Stars: 19
- Watchers: 5
- Forks: 2
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
- awesome-genome-visualization - DrukBam - genome-visualization/drukbam.png) (Alignments)
README
# DrukBam
### `DrukBam` is a program for plotting alignment files (.bam) for all comandline aficionados.
DrukBam can be used with or without a reference fasta file and allows fast plotting multiple variants or regions of interest. Please provide feedback like bugs or options you might miss, I wrote this programm because I did not found a convicning tool to provide fast plotting of alignemnts withput using a GUI like in IGV or Tablet.
## reference free
## including a reference
## split reads by strand
## bigger span
## changing plt style to dark or bmh
## highlight soft/hard clipped reads by threshold --> visualize insertion points
# Installing
## requirements
* pysam
* pandas
* matplotlib
* tqdm
## installation
`DrukBam` is available via pypi:
```
pip install drukbam==1.1.4
```
docker image
```
docker pull stephanholgerdrukewitz/drukbam:1.1.4
```
docker usage
```
docker run -it --rm -v $PWD:/data drukbam:1.1.4 DrukBam region -s 281367 -e 281468 -c 19 -b /data/test_data/test_small.bam --outfmt png -i example_out_small --maxcoverage 60 --outlineoff
```
****
:heavy_exclamation_mark: :heavy_exclamation_mark: **versions <1.1.4 are deprecated and should not be used anymore** :heavy_exclamation_mark: :heavy_exclamation_mark:
****
# Usage
DrukBam vcf
```
usage: DrukBam vcf [-h] -b BAM -v VCF [-p PADDING] [--highlight]
[--threads THREADS] [--maxcoverage MAXCOVERAGE]
[--direction] [--schematic] [--style STYLE] [--fasta FASTA]
[--outputdir OUTPUTDIR] [-i ID] [--chunksize CHUNKSIZE]
[--outfmt OUTFMT] [--outlineoff]
optional arguments:
-h, --help show this help message and exit
required arguments:
-b BAM, --bam BAM Pos. sorted and indexed bam file
-v VCF, --vcf VCF vcf file with variants of interest
-p PADDING, --padding PADDING
number of nt around the variant
--highlight highlight the position of interest
optional arguments:
--threads THREADS number of cpu's to run in paralell, ROI <1000 will
always use 1 core
--maxcoverage MAXCOVERAGE
max cov to plot
--direction split reads by forward and reverse
--schematic plot no nucleotide, recommended for ROI>1000
--style STYLE different style options for the plot, provide .ini
file
--fasta FASTA fasta file for reference related plotting
--outputdir OUTPUTDIR
directory for output
-i ID, --id ID output filename
--chunksize CHUNKSIZE
max size of visualized area, can be increases but will
sow down calculation
--outfmt OUTFMT format of plot, choose between pdf,svg,png
--outlineoff plotting of read outline
```
DrukBam region
```
usage: DrukBam region [-h] -b BAM -c CHROMOSOME -s START -e END
[--threads THREADS] [--maxcoverage MAXCOVERAGE]
[--direction] [--schematic] [--style STYLE]
[--fasta FASTA] [--outputdir OUTPUTDIR] [-i ID]
[--chunksize CHUNKSIZE] [--outfmt OUTFMT] [--outlineoff]
optional arguments:
-h, --help show this help message and exit
required arguments:
-b BAM, --bam BAM Pos. sorted and indexed bam file
-c CHROMOSOME, --chromosome CHROMOSOME
name of chromosome/contig
-s START, --start START
start of region of interest
-e END, --end END end of the region of interest
optional arguments:
--threads THREADS number of cpu's to run in paralell, ROI <1000 will
always use 1 core
--maxcoverage MAXCOVERAGE
max cov to plot
--direction split reads by forward and reverse
--schematic plot no nucleotide, recommended for ROI>1000
--style STYLE different style options for the plot, provide .ini
file
--fasta FASTA fasta file for reference related plotting
--outputdir OUTPUTDIR
directory for output
-i ID, --id ID output filename
--chunksize CHUNKSIZE
max size of visualized area, can be increases but will
sow down calculation
--outfmt OUTFMT format of plot, choose between pdf,svg,png
--outlineoff plotting of read outline
```
## Usage Examples:
The following command will create an image of that region:
```
DrukBam region -s 281367 -e 281468 -c 19 -b test_data/test_small.bam --outfmt png -i example_out --maxcoverage 60 --outlineoff --fasta test_data/chr19_first500k.fasta
```
The arguments used above are:
`-s` start of ROI
`-e` end of ROI
`-c` chromosome of ROI
`-b` alignment file, sorted and indexed
`--outfmt` format of plot
`-i` ID which is used for naming the plot
`--maxcoverage` yaxis max of plot
`--outlineoff` dont draw outlines around every read
`--fasta` location of ref. fasta
The following command will plot all positions in a vcf file:
```
DrukBam vcf -b test_data/test_small.bam -v example.vcf --padding 100 -i example_vcf --maxcoverage 60 --fasta test_data/chr19_first500k.fasta --threads 12
```
The arguments used above are:
`-b` alignment file, sorted and indexed
`-v` vcf file
`-i` ID which is used for naming the plot
`--maxcoverage` yaxis max of plot
`--fasta` location of ref. fasta
`--threads` number of cpu's to use,
## Style changes:
* color and style can be changed using the --style option and providing a [style.ini](https://github.com/StephanHolgerD/DrukBam/blob/master/style.ini) file
* official matplotlib colors are allowed [color list](https://matplotlib.org/2.0.2/examples/color/named_colors.html)
* pltstyle can be changed [style list](https://matplotlib.org/stable/gallery/style_sheets/style_sheets_reference.html)
---
```