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drukbam's Introduction

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

❗ ❗ versions <1.1.4 are deprecated and should not be used anymore ❗ ❗

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 file
official matplotlib colors are allowed color list
pltstyle can be changed style list

drukbam's People

Contributors

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drukbam's Issues

Conda install not working

Hello,

I am getting an error when trying to install with conda:

$ conda install -c stephanholgerd drukbam
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.

PackagesNotFoundError: The following packages are not available from current channels:

  - drukbam

Current channels:

  - https://conda.anaconda.org/stephanholgerd/osx-64
  - https://conda.anaconda.org/stephanholgerd/noarch
  - https://repo.anaconda.com/pkgs/main/osx-64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/r/osx-64
  - https://repo.anaconda.com/pkgs/r/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page

Could you please help me?

Thanks

Index error: string index out of range when trying to plot alignments using a reference fasta

Hi! :) Great tool to visualize specific regions of alignments! I am trying to use it together with a reference fasta, but I keep getting the following error:

multiprocessing.pool.RemoteTraceback: 
"""
Traceback (most recent call last):
  File "/Users/leti/miniconda3/envs/nanoporeProcessing/lib/python3.9/multiprocessing/pool.py", line 125, in worker
    result = (True, func(*args, **kwds))
  File "/Users/leti/miniconda3/envs/nanoporeProcessing/lib/python3.9/multiprocessing/pool.py", line 51, in starmapstar
    return list(itertools.starmap(args[0], args[1]))
  File "/Users/leti/miniconda3/envs/nanoporeProcessing/lib/python3.9/site-packages/DrukBam/vcfParse.py", line 51, in PlotV
    ploter.Plot()
  File "/Users/leti/miniconda3/envs/nanoporeProcessing/lib/python3.9/site-packages/DrukBam/MapPlot.py", line 77, in Plot
    self.PlotNuc()
  File "/Users/leti/miniconda3/envs/nanoporeProcessing/lib/python3.9/site-packages/DrukBam/MapPlot.py", line 297, in PlotNuc
    self.CalcPlot.PlotNucChunk(d,self.ax,chunk[1][1],chunk[1][2],flag=self.flag)
  File "/Users/leti/miniconda3/envs/nanoporeProcessing/lib/python3.9/site-packages/DrukBam/PlotCalc.py", line 287, in PlotNucChunk
    if self.fasta != 'None' and fastaChunk[fastapos]==query_alignment_sequence[p]:
IndexError: string index out of range
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/Users/leti/miniconda3/envs/nanoporeProcessing/bin/DrukBam", line 11, in <module>
    sys.exit(main())
  File "/Users/leti/miniconda3/envs/nanoporeProcessing/lib/python3.9/site-packages/DrukBam/__main__.py", line 101, in main
    ploter.MultiPlot()
  File "/Users/leti/miniconda3/envs/nanoporeProcessing/lib/python3.9/site-packages/DrukBam/vcfParse.py", line 59, in MultiPlot
    results = pool.starmap(self.PlotV, multi)
  File "/Users/leti/miniconda3/envs/nanoporeProcessing/lib/python3.9/multiprocessing/pool.py", line 372, in starmap
    return self._map_async(func, iterable, starmapstar, chunksize).get()
  File "/Users/leti/miniconda3/envs/nanoporeProcessing/lib/python3.9/multiprocessing/pool.py", line 771, in get
    raise self._value
IndexError: string index out of range
/Users/leti/miniconda3/envs/nanoporeProcessing/lib/python3.9/multiprocessing/resource_tracker.py:216: UserWarning: resource_tracker: There appear to be 1 leaked semaphore objects to clean up at shutdown  
  warnings.warn('resource_tracker: There appear to be %d '

This is the command I am running
vcf -b ../risk_alleles/sorted_reads_risk.bam -v ../VCF/testparsing.vcf --padding 100 -i test_region_1 --maxcoverage 20 --highlight --fasta ref/chr11_500k.fasta

I do not have any issues when running it without the --fasta flag, so I am assuming there is some problem with the reference file, but I cannot figure out what it is - I made sure that all the SNPs I want to show fall within the interval of the reference genome that I dowloaded. Do you have any idea of what could be going wrong?

`ValueError: invalid literal for int() with base 10: '151=1'` in PlotCalc.py

Hi!

Your tool looks amazing and perfect for programmatically creating visualisations for a pipeline I am working on.
However I haven't been able to get it to run on my data, I'm getting this back, from my command:

DrukBam region \
    -s 1 -e 16569 -c chrM \
    -b hifi_reads.bam \
    --fasta ref.fasta \
    --outfmt png \
    -i test \
    --chunksize 16569 \
    --threads 4

Output:

9449it [01:37, 97.30it/s] 
/home/UNIXHOME/cnolan/miniconda3/envs/drukbam/lib/python3.9/site-packages/DrukBam/PlotCalc.py:149: UserWarning: FixedFormatter should only be used together with FixedLocator
  ax.set_xticklabels([str("{:,}".format(start)),str("{:,}".format(end))], rotation=40, ha='right')
Traceback (most recent call last):
  File "/home/UNIXHOME/cnolan/miniconda3/envs/drukbam/bin/DrukBam", line 11, in <module>
    sys.exit(main())
  File "/home/UNIXHOME/cnolan/miniconda3/envs/drukbam/lib/python3.9/site-packages/DrukBam/__main__.py", line 82, in main
    ploter.Plot()
  File "/home/UNIXHOME/cnolan/miniconda3/envs/drukbam/lib/python3.9/site-packages/DrukBam/MapPlot.py", line 77, in Plot
    self.PlotNuc()
  File "/home/UNIXHOME/cnolan/miniconda3/envs/drukbam/lib/python3.9/site-packages/DrukBam/MapPlot.py", line 297, in PlotNuc
    self.CalcPlot.PlotNucChunk(d,self.ax,chunk[1][1],chunk[1][2],flag=self.flag)
  File "/home/UNIXHOME/cnolan/miniconda3/envs/drukbam/lib/python3.9/site-packages/DrukBam/PlotCalc.py", line 218, in PlotNucChunk
    chunk_cigarstring=self.CigChunker(cig)
  File "/home/UNIXHOME/cnolan/miniconda3/envs/drukbam/lib/python3.9/site-packages/DrukBam/PlotCalc.py", line 180, in CigChunker
    cigL=cigL+parseCig(cig)[1]
  File "/home/UNIXHOME/cnolan/miniconda3/envs/drukbam/lib/python3.9/site-packages/DrukBam/PlotCalc.py", line 176, in parseCig
    liste=([cig[p]]*int(cig[:p]))
ValueError: invalid literal for int() with base 10: '151=1'

Looks like a problem with parsing a CIGAR string? Any help troubleshooting would be appreciated

Is --threads parameter working?

I run this program with "--threads 32" option, but the CPU utilization still shows only one process working.
Should I miss something or is it a bug?
The drukbam version was 1.1.4, and my configuration is Ubuntu 22.04.4 LTS x86_64 with AMD Ryzen 9 5950X.

Thanks in advance!