bamdash 0.2

create a interactive coverage plot dashboard from bam files and add gb, vcf and bed tracks

Overview

BAMdash lets you create interactive coverage plots from your bam file with plotly

• requires only a .bam, .bai and the reference id to which the reads where mapped
• create a interactive html for data exploration
• create a static image (jpg, png, pdf, svg) ready for publication
• add additional tracks (supported: .vcf, .gb, .bed)
• annotate tracks with additional information
• export annoated track data as tabular files (.bed, .vcf) or json (.gb)
• developed for viral genomics
• customize all plotting parameters

Feel free to report any bugs or request new features as issues!

Automatic annotation

BAMdash automatically computes serveral statistics:

• if -bs is > 1 it computes the mean over the bin size in the coverage plot
• for each track it computes recovery and mean coverage (set -c for the min coverage) for each element in the track
• if a *.vcf is provided it annotates TRANSITION/TRANSVERSION and type of exchange (SNP, DEL, `INS)

If a *.gband *.vcf is provided BAMdash computes the aminoacid exchange and the effect in the CDS (inspired by but not as powerful as snpeff). SNP and INDEL vcf annotation supports:

• START_LOST: INDEL or SNP start at the CDS and result in a start loss
• STOP_LOST: INDEL or SNP result in the loss of the stop codon
• STOP_GAINED: INDEL or SNP result in an additional stop codon
• SYN: SNP does not lead to an amino acid change
• NON-SYN: SNP leads to an amino acid change
• AC_INSERTION: INS that does not change already present amino acids
• AC_CHANGE+AC_INSERTION: INS where the affected codon is also non-syn
• AC_DELETION: DEL that does not change already present amino acids
• AC_CHANGE+AC_DELETION: DEL where the affected codon is also non-syn

The nomenclature for the aminoacid effect is pretty simplified:

• A58Y - Exchange at pos 58 from A to Y
• A58YY- Exchange at pos 58 from A to Y and insertion of an additional Y
• FA58Y- Exchange at pos 58 from A to Y and deletion of the prior F
• A58fsX - Frameshift at pos 58

Example

Installation

via pip (recommened):

pip install bamdash

from this repo:

git clone https://github.com/jonas-fuchs/BAMdash
cd BAMcov

and then install BAMdash with:

pip install -r requirements.txt

or:

pip install .

That was already it. To check if it worked:

bamdash -v

You should see the current BAMdash version.

Usage

usage: 	

bamdash -b bam_file_path -r reference_id [additional arguments]

full usage:

  -h, --help            show this help message and exit
  -b  , --bam           bam file location
  -r  , --reference     seq reference id
  -bs  , --binsize      bins for the coverage plot
  -t [track_1 ...], --tracks [track_1 ...]
                        file location of tracks
  -c 5, --coverage 5    minimum coverage
  --slider, --no-slider
                        show slider (default: False)
  -e None, --export_static None
                        export as png, jpg, pdf, svg
  -d px px, --dimensions px px
                        width and height of the static image in px
  --dump, --no-dump     dump annotated track data (default: False)
  -v, --version         show program's version number and exit

Cutomization

BAMcov plotting settings can be adjusted in in the config.py. Therefore, you have to clone this repo.

Go to the configs location:

cd BAMdash/bamdash/scripts/

And open the config.py with a text editor, e.g.:

gedit config.py

and adjust the settings:

# pdf settings
show_log = True

# overall layout
vcf_track_proportion = 0.3
gb_track_proportion = 0.5
bed_track_proportion = 0.2
plot_spacing = 0.05

# coverage customize
coverage_fill_color = "rgba(255, 212, 135, 0.2)"
coverage_line_color = "rgba(224, 168, 68, 1)"
average_line_color = "grey"
average_line_width = 1

# track customize
track_color_scheme = "agsunset"  # for mutiple annotations tracks (genebank)
track_color_single = "rgb(145, 145, 145)"  # for single tracks (any rgb value, but no named colors)
strand_types = ["triangle-right", "triangle-left", "diamond-wide"]  # +, -, undefined strand
strand_marker_size = 8
strand_marker_line_width = 1
strand_marker_line_color = "rgba(0, 0, 0, 0.2)"
box_bed_alpha = [0.6, 0.6]  # alpha values for boxes (bed)
box_bed_size = [0.4, 0.4]  # size values for boxes (bed)
box_gb_alpha = [0.6, 0.8]  # alpha values for boxes (gb)
box_gb_size = [0.4, 0.3]  # size values for boxes (gb)

# variant customize
variant_marker_size = 13
variant_marker_line_width = 1
variant_line_color = "black"
stem_color = "grey"
stem_width = 1
snp_color = "grey"
ins_color = "blue"
del_color = "red"

To apply these new settings just repeat the installation procedure in the BAMdash dir:

pip install .

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Important disclaimer: The code is under the GPLv3 licence. The code is WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.