Skip to main content

Create multi-sample text-pileups of streaming SAM/BAM files.

Project description

Streaming Pileupy

https://img.shields.io/pypi/v/streaming_pileupy.svg https://img.shields.io/travis/winni2k/streaming_pileupy.svg Documentation Status Updates

Create multi-sample text-pileups of streaming SAM/BAM files.

Features

Streaming Pileupy creates a pileup of a single SAM/BAM file using the read group SM identifier to split reads by sample:

# extract sample names from read group SM tag
samtools view -H input.bam \
  | grep '^@RG' \
  | perl -pne 's/.*SM:(\S+).*/$1/' \
  | sort | uniq > sample_names.txt

# create read-group aware pileup
spileup input.bam sample_names.txt

Base quality filtering

Bases with less than a certain quality can be filtered with -Q.

Missing features

  • Read beginning and end annotations in pileup output
  • Deletion annotations in pileup output
  • Filter output bases on BED file

Credits

This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.

History

0.5.0 (2020-05-05)

  • Add base quality filter (-Q)

0.4.0 (2020-05-05)

  • Add support for python 3.6

0.3.0 (2020-05-05)

  • Add support for basic pileup functionality

0.2.1 (2020-05-04)

  • First release on PyPI.

Project details


Download files

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

Files for streaming-pileupy, version 0.5.7
Filename, size File type Python version Upload date Hashes
Filename, size streaming_pileupy-0.5.7.tar.gz (5.9 kB) File type Source Python version None Upload date Hashes View

Supported by

AWS AWS Cloud computing Datadog Datadog Monitoring DigiCert DigiCert EV certificate Facebook / Instagram Facebook / Instagram PSF Sponsor Fastly Fastly CDN Google Google Object Storage and Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Salesforce Salesforce PSF Sponsor Sentry Sentry Error logging StatusPage StatusPage Status page