Skip to main content

Easy sequence alignment plots

Project description

shabam

A python tool to plot BAM or CRAM sequence reads.

Installation

install cairo if not already installed:

# macOS via conda, or via homebrew (choose one, then set the library path)
conda install cairo pkgconfig
brew install cairo pkg-config

Install shabam:

pip install shabam

The dream

from shabam import seqplot
seqplot('example.bam', chrom='1', start=30243, end=30321,
    fastafile='reference.fasta', out='plot.svg')

Reality

Plotting options

  • shade reads by strand with by_strand=True
  • plot multiple sequence files together with a list of paths e.g. ['child.bam', 'mom.bam', 'dad.bam']
  • export PDF, PNG, SVG or PS formatted plots with matching filename extensions

Command line version

shabam \
  --seqfiles tests/data/example.bam \
  --chrom 1 \
  --start 30243 \
  --end 30321 \
  --fastafile tests/data/reference.fasta \
  --out plot.svg

Further improvements to the dream

  • Use consensus sequence when we don't provide a reference sequence
  • Allow custom colors
  • Compute proportion of variants at any site
  • Plot read depth
  • At positions with proportion of variants > threshold, reflect proportion with base colors
  • Option to scale plotted base size, currently at 10 pixels per base
  • Optionally shade plots deepVariant style:
    • red channel: nucleotide
    • blue channel: read strand
    • green channel: base quality
    • alpha: base supports ref or alt
  • Flatten vertical plotting in high depth sequence data
  • Down-sample reads for extremely high depth sequence data (>1000X)

Credit

Initial cigar parsing code lifted with permission from pybamview.

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

shabam-1.0.0.tar.gz (10.1 kB view details)

Uploaded Source

File details

Details for the file shabam-1.0.0.tar.gz.

File metadata

  • Download URL: shabam-1.0.0.tar.gz
  • Upload date:
  • Size: 10.1 kB
  • Tags: Source
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/1.13.0 pkginfo/1.5.0.1 requests/2.22.0 setuptools/41.0.1 requests-toolbelt/0.9.1 tqdm/4.32.1 CPython/3.7.3

File hashes

Hashes for shabam-1.0.0.tar.gz
Algorithm Hash digest
SHA256 95afc4dc420c345b93fc8d3d9482d032d8329e4612def0f205999525780c15bb
MD5 91c37ddc1de3796070fe2f89db32a191
BLAKE2b-256 10249d4bc77bc708565a8907776c48e94090362702b6e71db5cd0f9fec819aa1

See more details on using hashes here.

Supported by

AWS Cloud computing and Security Sponsor Datadog Monitoring Fastly CDN Google Download Analytics Pingdom Monitoring Sentry Error logging StatusPage Status page