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Open Source Science

https://github.com/acenglish/tdb

Tandem repeat database and analysis queries

https://github.com/acenglish/tdb

Science Score: 26.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (6.5%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Tandem repeat database and analysis queries

Basic Info
  • Host: GitHub
  • Owner: ACEnglish
  • License: bsd-3-clause
  • Language: Jupyter Notebook
  • Default Branch: develop
  • Size: 348 MB
Statistics
  • Stars: 6
  • Watchers: 1
  • Forks: 1
  • Open Issues: 0
  • Releases: 1
Created over 2 years ago · Last pushed about 1 year ago
Metadata Files
Readme License

README.md

tdb: Tandem repeat database and analysis queries

coverage pylint

Installation

Releases available in Releases

Alternatively, install from the repository via: bash git clone https://github.com/ACEnglish/tdb.git cd tdb/ python3 -m pip install .

Quick Start

Convert a tdb compatible VCF and run a query with: tdb create -o output.tdb input.vcf.gz tdb query allele_cnts output.tdb

Merge samples with: tdb merge --output merged.tdb --mem 20 --threads 4 output1.tdb output2.tdb Recommended 5-10GB of memory per-thread

Merge more samples into a tdb with: tdb merge --into merged.tdb output3.tdb output4.tdb ...

For merging ≥10 tdbs, use: tdb bigmerge -o merged.tdb results/samples*.tdb

Tutorials

See the wiki for details on what tdb is or jump straight into making your own custom tdb queries with notebooks/Introduction.ipynb.

Owner

  • Name: Adam English
  • Login: ACEnglish
  • Kind: user

GitHub Events

Total
  • Issues event: 2
  • Watch event: 2
  • Issue comment event: 1
  • Push event: 10
Last Year
  • Issues event: 2
  • Watch event: 2
  • Issue comment event: 1
  • Push event: 10

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 2
  • Total pull requests: 0
  • Average time to close issues: about 2 months
  • Average time to close pull requests: N/A
  • Total issue authors: 2
  • Total pull request authors: 0
  • Average comments per issue: 5.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 0
  • Average time to close issues: about 6 hours
  • Average time to close pull requests: N/A
  • Issue authors: 1
  • Pull request authors: 0
  • Average comments per issue: 1.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • gevro (1)
  • SaFE-APIOpt (1)
Pull Request Authors
Top Labels
Issue Labels
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Dependencies

setup.py pypi
  • pyarrow >=14.0
  • pysam >=0.22
  • truvari >=4.0
.github/workflows/tests.yml actions
  • actions/cache v3 composite
  • actions/checkout v3 composite
  • actions/setup-python v4 composite