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DrukBam\n### `DrukBam` is a  program for plotting alignment files (.bam) for all comandline aficionados.\n\nDrukBam  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.\n\n## reference free\n\u003ccenter\u003e\u003cimg src=\"exampleOutput/example_out_small_19_281367_281466classic.png\" width=\"100%\"/\u003e\u003c/center\u003e\n\n## including a reference\n\u003ccenter\u003e\u003cimg src=\"exampleOutput/example_out_small_19_281367_281466Rclassic.png\" width=\"100%\"/\u003e\u003c/center\u003e\n\n## split reads by strand\n\u003ccenter\u003e\u003cimg src=\"exampleOutput/example_out_small_19_281367_281466DRclassic.png\" width=\"100%\"/\u003e\u003c/center\u003e\n\n\n## bigger span\n\u003ccenter\u003e\u003cimg src=\"exampleOutput/example_out_small_19_281060_281666DRclassic.png\" width=\"100%\"/\u003e\u003c/center\u003e\n\n\n## changing plt style to dark or bmh\n\u003ccenter\u003e\u003cimg src=\"exampleOutput/example_out_small_19_281060_281666Ddark_bg.png\" width=\"100%\"/\u003e\u003c/center\u003e\n\n\u003ccenter\u003e\u003cimg src=\"exampleOutput/example_out_small_19_281060_281666Dbmh.png\" width=\"100%\"/\u003e\u003c/center\u003e\n\n\n## highlight soft/hard clipped reads by threshold --\u003e visualize insertion points\n\u003ccenter\u003e\u003cimg src=\"exampleOutput/BigInsertion_13_32911200_32912100DR.png-1.png\" width=\"100%\"/\u003e\u003c/center\u003e\n\n\n# Installing\n\n## requirements\n\n* pysam\n* pandas\n* matplotlib\n* tqdm\n\n\n\n## installation\n\n`DrukBam` is available  via pypi:\n\n```\npip install drukbam==1.1.4\n\n```\n\ndocker image\n\n```\ndocker pull stephanholgerdrukewitz/drukbam:1.1.4\n\n```\n\n\ndocker usage\n\n\n```\n\ndocker  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\n\n```\n\n****\n:heavy_exclamation_mark: :heavy_exclamation_mark: **versions \u003c1.1.4 are deprecated and should not be used anymore** :heavy_exclamation_mark: :heavy_exclamation_mark:\n****\n# Usage\n\u003cdetails\u003e\n  \u003csummary\u003eDrukBam vcf\u003c/summary\u003e\n\n  ```\n  usage: DrukBam vcf [-h] -b BAM -v VCF [-p PADDING] [--highlight]\n                     [--threads THREADS] [--maxcoverage MAXCOVERAGE]\n                     [--direction] [--schematic] [--style STYLE] [--fasta FASTA]\n                     [--outputdir OUTPUTDIR] [-i ID] [--chunksize CHUNKSIZE]\n                     [--outfmt OUTFMT] [--outlineoff]\n\n  optional arguments:\n    -h, --help            show this help message and exit\n\n  required arguments:\n    -b BAM, --bam BAM     Pos. sorted and indexed bam file\n    -v VCF, --vcf VCF     vcf file with variants of interest\n    -p PADDING, --padding PADDING\n                          number of nt around the variant\n    --highlight           highlight the position of interest\n\n  optional arguments:\n    --threads THREADS     number of cpu's to run in paralell, ROI \u003c1000 will\n                          always use 1 core\n    --maxcoverage MAXCOVERAGE\n                          max cov to plot\n    --direction           split reads by forward and reverse\n    --schematic           plot no nucleotide, recommended for ROI\u003e1000\n    --style STYLE         different style options for the plot, provide .ini\n                          file\n    --fasta FASTA         fasta file for reference related plotting\n    --outputdir OUTPUTDIR\n                          directory for output\n    -i ID, --id ID        output filename\n    --chunksize CHUNKSIZE\n                          max size of visualized area, can be increases but will\n                          sow down calculation\n    --outfmt OUTFMT       format of plot, choose between pdf,svg,png\n    --outlineoff          plotting of read outline\n\n```\n\u003c/details\u003e\n\n\n\u003cdetails\u003e\n  \u003csummary\u003eDrukBam region\u003c/summary\u003e\n\n  ```\n  usage: DrukBam region [-h] -b BAM -c CHROMOSOME -s START -e END\n                      [--threads THREADS] [--maxcoverage MAXCOVERAGE]\n                      [--direction] [--schematic] [--style STYLE]\n                      [--fasta FASTA] [--outputdir OUTPUTDIR] [-i ID]\n                      [--chunksize CHUNKSIZE] [--outfmt OUTFMT] [--outlineoff]\n\noptional arguments:\n  -h, --help            show this help message and exit\n\nrequired arguments:\n  -b BAM, --bam BAM     Pos. sorted and indexed bam file\n  -c CHROMOSOME, --chromosome CHROMOSOME\n                        name of chromosome/contig\n  -s START, --start START\n                        start of region of interest\n  -e END, --end END     end of the region of interest\n\noptional arguments:\n  --threads THREADS     number of cpu's to run in paralell, ROI \u003c1000 will\n                        always use 1 core\n  --maxcoverage MAXCOVERAGE\n                        max cov to plot\n  --direction           split reads by forward and reverse\n  --schematic           plot no nucleotide, recommended for ROI\u003e1000\n  --style STYLE         different style options for the plot, provide .ini\n                        file\n  --fasta FASTA         fasta file for reference related plotting\n  --outputdir OUTPUTDIR\n                        directory for output\n  -i ID, --id ID        output filename\n  --chunksize CHUNKSIZE\n                        max size of visualized area, can be increases but will\n                        sow down calculation\n  --outfmt OUTFMT       format of plot, choose between pdf,svg,png\n  --outlineoff          plotting of read outline\n\n\n```\n\u003c/details\u003e\n\n\n\n\n\n## Usage Examples:\n\nThe following command will create an image of that region:\n```\nDrukBam 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\n```\n\nThe arguments used above are:\n\n`-s` start of ROI\n\n`-e` end of ROI\n\n`-c` chromosome of ROI\n\n\n`-b` alignment file, sorted and indexed\n\n`--outfmt` format of plot\n\n`-i` ID which is used for naming the plot\n\n`--maxcoverage` yaxis max of plot\n\n`--outlineoff` dont draw outlines around every read\n\n`--fasta` location of ref. fasta\n\n\nThe following command will plot all positions in a vcf file:\n```\nDrukBam 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\n```\n\nThe arguments used above are:\n\n\n`-b` alignment file, sorted and indexed\n\n`-v` vcf file\n\n`-i` ID which is used for naming the plot\n\n`--maxcoverage` yaxis max of plot\n\n`--fasta` location of ref. fasta\n\n`--threads` number of cpu's to use,\n\n## Style changes:\n\n* 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\n* official matplotlib colors are allowed  [color list](https://matplotlib.org/2.0.2/examples/color/named_colors.html)\n* pltstyle can be changed  [style list](https://matplotlib.org/stable/gallery/style_sheets/style_sheets_reference.html)\n\n---\n\n\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FStephanHolgerD%2FDrukBam","html_url":"https://awesome.ecosyste.ms/projects/github.com%2FStephanHolgerD%2FDrukBam","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FStephanHolgerD%2FDrukBam/lists"}