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A converter from .bam to .png for specific genomic region.

Project description

BamSnap

BamSnap: a lightweight command-based visualization tool for sequencing reads in BAM files

For more details, see BamSnap Documentation.

Installation

Prerequisites

Install with pip

pip install bamsnap

Install with github

git clone https://github.com/parklab/bamsnap
cd bamsnap
python setup.py install

Usage

Simple usage

$ bamsnap -bam test.bam -pos 1:7364529 -out test.png

For more details, see BamSnap Documentation.

Usage with docker

$ docker pull danielmsk/bamsnap
$ docker run --rm -it -v /local_directory_path:/directory_path_in_image danielmsk/bamsnap bamsnap \
    -bam /directory_path_in_image/test.bam \
    -pos 1:7364529 \
    -out /directory_path_in_image/test.png

Example Use Case

Project details


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Source Distribution

bamsnap-0.2.19.tar.gz (20.9 MB view hashes)

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Built Distribution

bamsnap-0.2.19-py3-none-any.whl (20.9 MB view hashes)

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