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genbankpy

Tools to download, parse and filter GenBank files

https://github.com/robaina/genbankpy

Science Score: 67.0%

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
    Found 2 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (9.7%) to scientific vocabulary

Keywords

bioinformatics computational-biology genbank genomics ncbi python sequencing

Scientific Fields

Biology Life Sciences - 84% confidence
Last synced: 4 months ago · JSON representation ·

Repository

Tools to download, parse and filter GenBank files

Basic Info
  • Host: GitHub
  • Owner: Robaina
  • License: apache-2.0
  • Language: Python
  • Default Branch: main
  • Homepage:
  • Size: 25 MB
Statistics
  • Stars: 6
  • Watchers: 1
  • Forks: 1
  • Open Issues: 0
  • Releases: 1
Topics
bioinformatics computational-biology genbank genomics ncbi python sequencing
Created about 4 years ago · Last pushed about 3 years ago
Metadata Files
Readme License Code of conduct Citation

README.md

logo

A Python tool to download and parse GenBank files

GitHub release (latest by date) GitHub license Contributor Covenant DOI

Installation

  1. Fork git repo into local machine (click on fork) and clone, or simply clone main branch with git clone https://github.com/Robaina/GenBankpy.git

  2. CD to project directory and set conda environment if not already set: conda env create -n genbankpy -f environment.yml

  3. Activate environment: conda activate genbankpy

    Usage

You can find a jupyter notebook with usage examples here.

Citation

If you use this software, please cite it as below:

Robaina-Estévez, S. (2022). Genbankpy: a Python tool to ddownload and parse GenBank files (Version 0.0.1)[Computer software]. https://doi.org/10.5281/zenodo.7046036.

Owner

  • Name: Semidán Robaina
  • Login: Robaina
  • Kind: user
  • Location: Atlantic Ocean
  • Company: Hapdera

Computational Biology | Data Science | Python Dev. | Ph.D. Systems Biology

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
  - family-names: "Robaina-Estévez"
    given-names: "Semidán"
    orcid: "https://orcid.org/0000-0003-0781-1677"
title: "Genbankpy: A Python tool to download and parse GenBank files"
version: 0.0.1
doi: 10.5281/zenodo.7046036
date-released: 2022-09-03
url: "https://github.com/Robaina/GenBankpy"

GitHub Events

Total
Last Year

Committers

Last synced: 6 months ago

All Time
  • Total Commits: 46
  • Total Committers: 1
  • Avg Commits per committer: 46.0
  • Development Distribution Score (DDS): 0.0
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Semidán Robaina Estévez s****a@g****m 46

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 2
  • Total pull requests: 0
  • Average time to close issues: 8 months
  • Average time to close pull requests: N/A
  • Total issue authors: 1
  • Total pull request authors: 0
  • Average comments per issue: 0.5
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • 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
  • Robaina (2)
Pull Request Authors
Top Labels
Issue Labels
documentation (1) enhancement (1) bug (1)
Pull Request Labels

Dependencies

setup.py pypi
  • biopython *
  • ncbi-acc-download *
environment.yml conda
  • _libgcc_mutex 0.1
  • _openmp_mutex 4.5
  • biopython 1.79
  • bzip2 1.0.8
  • ca-certificates 2022.6.15
  • ld_impl_linux-64 2.36.1
  • libblas 3.9.0
  • libcblas 3.9.0
  • libffi 3.4.2
  • libgcc-ng 12.1.0
  • libgfortran-ng 12.1.0
  • libgfortran5 12.1.0
  • libgomp 12.1.0
  • liblapack 3.9.0
  • libnsl 2.0.0
  • libopenblas 0.3.21
  • libsqlite 3.39.2
  • libstdcxx-ng 12.1.0
  • libuuid 2.32.1
  • libzlib 1.2.12
  • ncbi-datasets-cli 13.37.2
  • ncurses 6.3
  • numpy 1.23.2
  • openssl 3.0.5
  • pip 22.2.2
  • python 3.10.6
  • python_abi 3.10
  • readline 8.1.2
  • setuptools 65.3.0
  • tk 8.6.12
  • tzdata 2022c
  • wheel 0.37.1
  • xz 5.2.6