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saintbioutils

Repository of utility and miscellaneous functions for using in bioinformatics pipelines, primarily in Python

https://github.com/hobnobmancer/saintbioutils

Science Score: 64.0%

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

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ✓
    Committers with academic emails
    1 of 3 committers (33.3%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (9.3%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

Repository of utility and miscellaneous functions for using in bioinformatics pipelines, primarily in Python

Basic Info
  • Host: GitHub
  • Owner: HobnobMancer
  • License: mit
  • Language: Python
  • Default Branch: master
  • Size: 45.9 KB
Statistics
  • Stars: 1
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 10
Created over 4 years ago · Last pushed almost 3 years ago
Metadata Files
Readme License Citation

README.md

saintBioutils

DOI
pyani PyPi version

Repository containing utility and miscellaneous scripts and functions for use in bioinformatic pipelines, primarily written in Python3.

The name is derived from the primary host organisation (University of St Andrews) when the repo was firsted established.

Table of contents

Installation

Quick and Easy

The easiest way to install saintBioutils and include the (sub)modules and functions is to install the package via pip, using the following command:
bash pip3 install saintBioutils This ensures all dependencies are installed

From Source

To install from source, clone the repository: bash git clone https://github.com/HobnobMancer/saintBioutils.git Then install the package, which ensures all dependencies are also installed:
bash python3 <path to the setup.py file>

Directories

  • genbank - Scripts for downloading and parsing genomic assemblies from NCBI GenBank
  • uniprot - Scripts and functions related to calling to, retrieving from and parsing data from UniProt and its API
  • utilities - Script and functions for utility functions for script/program utility operations

Copyright and License

MIT License

Copyright (c) 2020-2021 University of St Andrews
Copyright (c) 2020-2021 University of Strathclyde
Copyright (c) 2020-2021 UJames Hutton Institute

Owner

  • Name: Emma Hobbs
  • Login: HobnobMancer
  • Kind: user
  • Location: Cambridge, UK
  • Company: EMBL-EBI

InterPro and InterProScan Bioinformatics developer at EMBL-EBI

Citation (CITATION.cff) 

cff-version: 0.0.1
message: "If you use this software, please cite it as below."
authors:
  - family-names: E. E. M.
    given-names: Hobbs
    orcid: https://orcid.org/0000-0002-8470-4739
title: HobnobMancer/saintBioutils
version: v0.0.24
date-released: 2022-05-12

GitHub Events

Total
Last Year

Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 55
  • Total Committers: 3
  • Avg Commits per committer: 18.333
  • Development Distribution Score (DDS): 0.491
Top Committers
Name Email Commits
HobnobMancer h****r@P****n 28
Emma Hobbs 5****r@u****m 15
HobnobMancer e****1@s****k 12
Committer Domains (Top 20 + Academic)
st-andrews.ac.uk: 1 paddington.localdomain: 1

Issues and Pull Requests

Last synced: 8 months ago

All Time
  • Total issues: 1
  • Total pull requests: 6
  • Average time to close issues: 9 minutes
  • Average time to close pull requests: 1 minute
  • Total issue authors: 1
  • Total pull request authors: 1
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 6
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 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
  • HobnobMancer (1)
Pull Request Authors
  • HobnobMancer (6)
Top Labels
Issue Labels
bug (1)
Pull Request Labels
bug (2)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 111 last-month
  • Total dependent packages: 2
  • Total dependent repositories: 1
  • Total versions: 25
  • Total maintainers: 2
pypi.org: saintbioutils

A package of utility and miscellaneous functions for using in bioinformaticspipelines, primarily in Python.

  • Versions: 25
  • Dependent Packages: 2
  • Dependent Repositories: 1
  • Downloads: 111 Last month
Rankings
Dependent packages count: 3.1%
Dependent repos count: 21.8%
Average: 22.4%
Downloads: 25.4%
Forks count: 29.8%
Stargazers count: 31.9%
Maintainers (2)
HobnobMancer widdowquinn
Last synced: 7 months ago

Dependencies

setup.py pypi
  • biopython >=1.76
  • tqdm *