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bacant

This program is designed for annotation of antimicrobal resistance(AMR), transposon(Tn) and integron(In) in bacteria.

https://github.com/xthua/bacant

Science Score: 10.0%

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

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    CITATION.cff file
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    codemeta.json file
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    .zenodo.json file
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    DOI references
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    Academic publication links
    Links to: ncbi.nlm.nih.gov
  • ○
    Committers with academic emails
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    Institutional organization owner
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    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (10.9%) to scientific vocabulary

Keywords

amr bacteria fasta integron transposon
Last synced: 6 months ago · JSON representation

Repository

This program is designed for annotation of antimicrobal resistance(AMR), transposon(Tn) and integron(In) in bacteria.

Basic Info
  • Host: GitHub
  • Owner: xthua
  • License: gpl-3.0
  • Language: F*
  • Default Branch: master
  • Homepage:
  • Size: 49.8 MB
Statistics
  • Stars: 21
  • Watchers: 1
  • Forks: 7
  • Open Issues: 4
  • Releases: 5
Topics
amr bacteria fasta integron transposon
Created over 5 years ago · Last pushed almost 3 years ago
Metadata Files
Readme License

README.md

Author: Xiaoting Hua

Email: xiaotinghua@zju.edu.cn

institute: Key laboratory of Microbiol technology and Bioinformatics of Zhejiang Province

This program is designed for annotation of antimicrobal resistance(AMR), transposon(Tn) and integron(In) in bacteria.

Install:

Bacant is a python3.X script, running on linux. You should install BLAST and add it in environment variable, you can download from https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/. BLAST version is 2.7.1 in bacant.

  • First: You can download from github by git clone https://github.com/xthua/bacant.git. Then execute python setup.py install.
  • Second: You can install BacAnt from PyPI by pip install BacAnt.
  • Third: You can install BacAnt from anaconda. First,conda create -n bacant create a virtual environment.Then conda install -c bacant -c conda-forge -c bioconda bacant install bacant.

Run:

BacAnt can accept FASTA and GENBANK format file(single or multi sequences in one file). Attention on GENBANK format file, it should follow standard format. There are three input parameter, "-n" means FASTA, "-g" means GENBANK, "-D" means input dir contains FASTA or GENBANK. * Simply, you can just run: bacant -n FASTA -o outdir bacant -g GENBANK -o outdir bacant -D input_dir -o outdir * For more parameter, you can run: bacant -h * Here are some import parameter:

parameter | description ---- | ----- --nucleotide(-n) | FASTA file --genbank(-g) | GENBANK file --indir(-D) | input dirname --resultdir(-o) | output dirname --databases(-d) | reference databases,default is ResDB,IntegronDB,TransposonDB --coverages(-c) | filtering coverage, default is "60,60,60", three numbers represents AMR,In,Tn in turn --identities(-i) | filtering identity, default is "90,90,90", three numbers represents AMR,In,Tn in turn

Databases:

We have updated database to v2.0(2021.05.11) since BacAnt-v3.3.1. You can download from here. User can define their custom databases, and when run bacant ,just add parameter -p(--path) for databases dirname. Here are databases structure:

  .
  ├── IntegronDB
  │   ├── Integron.fasta    Integron reference sequences in FASTA format
  │   │                     sequence id must be description|accession,eg: In0|PAU49101
  │   ├── Integron.nhr
  │   ├── Integron.nin
  │   └── Integron.nsq
  ├── ResDB
  │   ├── Res.fasta         Resistance gene reference sequences in FASTA format
  │   │                     sequence id must be database name~~~gene~~~accession~~~description,
  │   │                     eg:  ncbi~~~1567214_ble~~~NG_047553.1~~~BLEOMYCIN BLMA family bleomycin binding protein
  │   ├── Res.nhr
  │   ├── Res.nin
  │   └── Res.nsq
  └── TransposonDB
      ├── Transposon.fasta  Transposon reference sequences in FASTA format
      │                     sequence id must be description|accession,eg: Tn2009|CP001937
      ├── Transposon.nhr
      ├── Transposon.nin
      └── Transposon.nsq

Output:

filename | description ---- | ----- *.gb | GENBANK format annotation AMR.tsv | filtered resistance annotation AMR.possible.tsv | all possible resistance annotation replicon.tsv | replicon annotation integron.filter.tsv | most like integron integron.detail.tsv | integron_finder result,detail descripton of integron structure transposon.filter.tsv | transposon element after overlap screen transposon.possible.tsv | all possible transposon element annotation.html | output visualization

Owner

  • Name: Xiaoting Hua
  • Login: xthua
  • Kind: user

Sir Run Run Shaw Hospital, Zhejiang University School of medicine

GitHub Events

Total
  • Watch event: 3
Last Year
  • Watch event: 3

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 120
  • Total Committers: 2
  • Avg Commits per committer: 60.0
  • Development Distribution Score (DDS): 0.017
Past Year
  • Commits: 5
  • Committers: 2
  • Avg Commits per committer: 2.5
  • Development Distribution Score (DDS): 0.4
Top Committers
Name Email Commits
Xiaoting Hua x****1@g****m 118
ChaseFor 4****r 2

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 8
  • Total pull requests: 2
  • Average time to close issues: 5 months
  • Average time to close pull requests: about 9 hours
  • Total issue authors: 7
  • Total pull request authors: 1
  • Average comments per issue: 2.5
  • Average comments per pull request: 0.0
  • Merged pull requests: 2
  • 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
  • ramadatta (2)
  • HeloiseMuller (1)
  • qianxin-kxy (1)
  • neptuneyt (1)
  • Dx-wmc (1)
  • mengqiyue (1)
  • aslangabriel (1)
Pull Request Authors
  • ChaseFor (2)
Top Labels
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Packages

  • Total packages: 1
  • Total downloads:
    • pypi 15 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 7
  • Total maintainers: 1
pypi.org: bacant

This program is designed for annotation of antimicrobal resistance(AMR), transposon(Tn) and integron(In) in bacteria

  • Versions: 7
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 15 Last month
Rankings
Dependent packages count: 10.0%
Forks count: 13.3%
Stargazers count: 14.8%
Average: 18.5%
Dependent repos count: 21.7%
Downloads: 32.4%
Maintainers (1)
ChaseFor
Last synced: 6 months ago

Dependencies

requirements.txt pypi
  • bcbio-gff ==0.6.6
  • biopython ==1.76
  • colorlog ==4.2.1
  • matplotlib ==3.1.3
  • numpy ==1.19.0
  • pandas ==0.25.1
  • reportlab ==3.5.32
setup.py pypi
  • bcbio-gff ==0.6.6
  • biopython ==1.76
  • colorlog ==4.2.1
  • matplotlib ==3.1.3
  • numpy ==1.19.0
  • pandas ==0.25.1
  • reportlab ==3.5.32