bam-lorenz-coverage

This is a free software package that very easily allows you to generate Lorenz plots and Coverage plots, directly from a BAM file. It can also output the tables as text documents so you can generate custom plots. There is also support to only analyse specific regions.

Implemented in:

• Python3 + Matplotlib + Pysam

Citing bam-lorenz-coverage

When using bam-lorenz-coverage for scientific applications, please cite the following manuscript:

10.1093/gigascience/giab080

Hoogstrate Y; Komor MA; Böttcher R; van Riet J; van de Werken HJG;
van Lieshout S; Hoffmann R; van den Broek E; Bolijn AS; Dits N; Sie D;
van der Meer D; Pepers F; Bangma CH; van Leenders GJLH; Smid M;
French PJ; Martens JWM; van Workum W; van der Spek PJ; Janssen B;
Caldenhoven E; Rausch C; de Jong M; Stubbs AP; Meijer GA; Fijneman RJA;
Jenster GW:

Fusion transcripts and their genomic breakpoints in poly(A)+ and
rRNA-minus RNA sequencing data. GigaScience (2021).

http://dx.doi.org/10.1093/gigascience/giab080

This will indirectly help me further maintaining this software package. Thank you in advance, Youri

Note (how this works)

By the time of writing, pysam.tools.depth could not write sequentially to a python variable. As work around, the tools spawns one thread writing the output of pysam.tools.depth to a FIFO (named pipe) in the /tmp folder whereas the other thread parses this FIFO. This is why the tool runs two parallel threads.

Installation:

$ git clone https://github.com/yhoogstrate/bam-lorenz-coverage.git
$ cd bam-lorenz-coverage
$ virtualenv -p python3 .venv
$ source .venv/bin/activate
$ python setup.py install

$ bam-lorenz-coverage --help

Possible issues:

• pysam is currently incompatible with python 3.7 - manual installation of pysam is still possible (git clone + python setup.py install)
  • This issue has been resolved
• matplotlib depends on Tk but does not throw an error if it is missing during installation, only at runtime
  • debian/ubuntu: sudo apt-get install python3-tk
  • arch: pacman -Sy tk

Usage:

Usage: bam-lorenz-coverage [OPTIONS] INPUT_ALIGNMENT_FILE

Options:
  --version                  Show the version and exit.
  -l, --lorenz-table TEXT    Output table Lorenz-curve (for stdout use: -)
  -c, --coverage-table TEXT  Output table Coverage-graph (for stdout use: -)
  -L, --lorenz-svg TEXT      Output figure Lorenz-curve (SVG).
  -C, --coverage-svg TEXT    Output figure Coverage-graph (SVG).
  -s, --stats TEXT           Output additional stats to text-file
  -r, --region TEXT          Scan depth only in selected region <chr:from-to>
                             (all positions: 1-based)
  -b, --bed-regions TEXT     Scan depth only in selected positions or regions
                             (BED file: start: 0-based & end: 1-based)
  --help                     Show this message and exit.

The lowercase arguments (-l, -c) allow extraction of the raw data tables for custom plotting. The uppercase arguments (-L, -C) directly generate a plot. The implemented plot only contains one sample per plot. For multi-sample plots, use the column tables and your imagination.

Examples:

Default:

The default SVG output figures (-C, -L) show one sample per figure, and look as follows:

Custom, using the tables:

Using the output tables (-l, -c) you can also create custom plots, for instance: