Data

Tools

Indexes

Applications

Experiments

Open Source Science

integrons

Integron analysis tools. Scripts necessary to reproduce the validation of IntFinder (version 1.0).

https://github.com/kalilamali/integrons

Science Score: 44.0%

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
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (6.6%) to scientific vocabulary

Keywords

fasta integrons intfinder kma python
Last synced: 6 months ago · JSON representation ·

Repository

Integron analysis tools. Scripts necessary to reproduce the validation of IntFinder (version 1.0).

Basic Info
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Topics
fasta integrons intfinder kma python
Created almost 6 years ago · Last pushed almost 3 years ago
Metadata Files
Readme Citation

README.md

IntFinder development and validation

This repository contains the scripts necessary to reproduce the validation of IntFinder (version 1.0).

  1. Download this repository. git clone https://github.com/kalilamali/integrons
  2. Download IntFinder. git clone https://bitbucket.org/genomicepidemiology/intfinder.git
  3. Download IntFinder database. git clone https://bitbucket.org/genomicepidemiology/intfinder_db.git cd intfinder_db python3 INSTALL.py 1 cd ..
  4. Download KMA. git clone https://bitbucket.org/genomicepidemiology/kma.git cd kma && make mv kma /usr/bin/ cd ..
  5. Your folders and scripts should look like this: /Integrons /intfinder /intfinder_db /kma /validation_seqs CITATION.cff get_mr0_test_cases.py get_mr1_test_cases.py get_mr2_test_cases.py group_intfinder.py mrs.py README.md
  6. Create the test cases according to the metamorphic relations (MRs). python3 get_mr0_test_cases.py python3 get_mr1_test_cases.py python3 get_mr2_test_cases.py
  7. Run IntFinder for each test case. python3 mrs.py python3 mrs.py > report.tsv # FAQ:

group_intfinder.py uses kma's location:\ /usr/bin/kma\ if kma is not in that location please update the script.

If you get:\ ModuleNotFoundError: No module named 'tabulate'\ ModuleNotFoundError: No module named 'cgecore'\ It can be fixed with the following comands: pip3 install tabulate pip3 install cgecore

Notes:

Online website: https://cge.food.dtu.dk/services/IntFinder-1.0

IntFinder database expanded to detect integron classes 1, 2, and 3: https://figshare.com/articles/dataset/intfinder_db/14096915

Owner

  • Name: Karen Loaiza (KLOC)
  • Login: kalilamali
  • Kind: user
  • Location: Denmark
  • Company: Statens Serum Institut

🧬👩🏻‍💻📊 Bioinformatician working on bacterial genomics at @SSI_dk

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
  - family-names: Loaiza
    given-names: Karen
    orcid: https://orcid.org/0000-0002-4282-1152
title: "IntFinder validation."
version: 1.0
date-released: 2021-08-27
repository-code: https://github.com/kalilamali/integrons

GitHub Events

Total
Last Year

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 8
  • Total Committers: 3
  • Avg Commits per committer: 2.667
  • Development Distribution Score (DDS): 0.25
Past Year
  • Commits: 1
  • Committers: 1
  • Avg Commits per committer: 1.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
kalilamali k****i@o****m 6
kalilamali k****i@h****m 1
Karen 4****i 1