https://github.com/sablokgaurav/graphanalyzer

graphanalyzer python package for dealing with paf and gfa alignments.
https://github.com/sablokgaurav/graphanalyzer

alignments bioinformatics genomes graphalignments graphs graphs-algorithms machinelearning

Last synced: 9 days ago
JSON representation

graphanalyzer python package for dealing with paf and gfa alignments.

• Host: GitHub
• URL: https://github.com/sablokgaurav/graphanalyzer
• Owner: gauravcodepro
• License: mit
• Created: 2024-02-29T10:29:35.000Z (10 months ago)
• Default Branch: main
• Last Pushed: 2024-05-02T08:52:45.000Z (8 months ago)
• Last Synced: 2024-08-08T15:11:16.747Z (4 months ago)
• Topics: alignments, bioinformatics, genomes, graphalignments, graphs, graphs-algorithms, machinelearning
• Language: Python
• Homepage:
• Size: 503 KB
• Stars: 1
• Watchers: 1
• Forks: 2
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • Changelog: CHANGELOG.md
  • Contributing: CONTRIBUTING.md
  • License: LICENSE

Awesome Lists containing this project

• awesome-pangenomes - graphanalyzer

README

        
# graphanalyzer

a graphanalyzer package that uses the information from the paf and the gfa files for the graph alignment and uses the concurrency to process the alignments and other variables and uses a dataframe approach. You can find the code in the src/graphanalyzer.py and you can use those as import in your script untill the complete package is available from pip. a heuristic binary search implementation of the node in the graph clustering. It follows the stack implementation so that that the weight to the next node can be assigned on the search pattern. Written in a combination of C++ and python. Added the support for the visualization of graphics. Update: 2024-3-1: Adding the support for the deadlock programming to enable the multi threads. Adding the complete support for analyzing all the PAF, GFA  and also the LAV files from the alignment for the index similarity. 

Update: 2024-3-12: Adding the support for the graph linearization for direct import to view the pangenome graphs in the linear format. 

Gaurav  \

Academic Staff Member \

Bioinformatics \

Institute for Biochemistry and Biology \

University of Potsdam \

Potsdam,Germany 

## Installation

```bash

$ pip install graphanalyzer

```

## License

`graphanalyzer` was created by Gaurav Sablok, Universitat Potsdam, Germany. It is licensed under the terms of the MIT license.

## Credits

`graphanalyzer` was created with [`cookiecutter`](https://cookiecutter.readthedocs.io/en/latest/) and the `py-pkgs-cookiecutter` [template](https://github.com/py-pkgs/py-pkgs-cookiecutter).