BamSnap
BamSnap: a lightweight command-based visualization tool for sequencing reads in BAM files
For more details, see BamSnap Documentation.
Installation
Prerequisites
- python 3.4+
- Pillow (Python Imaging Library)
- pysam
- pyfaidx
- pytabix
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
- 1000 Genome Data: 1000 genomic loci in 2504 individuals
- BamSnap Plot Gallery
Release files for bamsnap-cgap 0.3.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| bamsnap-cgap-0.3.0.tar.gz | 20.9 MB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| bamsnap_cgap-0.3.0-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 41.8 MB
Release files / bamsnap-cgap-0.3.0.tar.gz
| Download URL | bamsnap-cgap-0.3.0.tar.gz |
|---|---|
| Size | 20.9 MB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
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|
|
BLAKE2b-256 checksum How to use checksums |
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|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/3.4.2 importlib_metadata/4.8.1 pkginfo/1.7.1 requests/2.26.0 requests-toolbelt/0.9.1 tqdm/4.62.2 CPython/3.7.11
|
Release files / bamsnap_cgap-0.3.0-py3-none-any.whl
| Download URL | bamsnap_cgap-0.3.0-py3-none-any.whl |
|---|---|
| Size | 20.9 MB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
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|
|
BLAKE2b-256 checksum How to use checksums |
043bf03803b68a1b1f85334716c2668654bdbd698d6405635c8514101ff990bb
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/3.4.2 importlib_metadata/4.8.1 pkginfo/1.7.1 requests/2.26.0 requests-toolbelt/0.9.1 tqdm/4.62.2 CPython/3.7.11
|
