Data

Tools

Indexes

Applications

Experiments

Open Source Science

customsintaxdb

Given a list of species get sequences and complete taxonomic classification of a list of entries

https://github.com/diegomic/customsintaxdb

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
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (8.8%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

Given a list of species get sequences and complete taxonomic classification of a list of entries

Basic Info
  • Host: GitHub
  • Owner: diegomic
  • License: gpl-3.0
  • Language: Python
  • Default Branch: main
  • Size: 32.2 KB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created almost 4 years ago · Last pushed about 2 years ago
Metadata Files
Readme License Citation

README.md

customSintaxDB

Given a list of species get sequences and complete taxonomic classification of a list of entries

Getting started

To dowload this repository from GitHub, the following commands can be run.

git clone https://github.com/diegomic/customSintaxDB.git

customSintaxDB.py can run in any computer with python 3 (>3.6) installed. The following additional packages are required: - biopython (tested with v.1.79) - argparse

To install all the required package run:

pip install -r requirements.txt

Usage:

``` usage: customSintaxDB.py [-h] -l LIST -o OUTPUT -g GENE [--email EMAIL] [--apikey APIKEY] [--maxtries MAXTRIES] [--sleepbetweentries SLEEPBETWEENTRIES]

optional arguments: -h, --help show this help message and exit -l LIST, --list LIST File with the list of entry to search (default: None) -o OUTPUT, --output OUTPUT Output File basename (default: None) -g GENE, --gene GENE gene to search in entrez (default: None)

Entrez - NCBI's E-utilities: --email EMAIL Email to use for make queries through to NCBI's E-utilities, if email is empty a warning is raised by the Entrez module. To make use of NCBI's E-utilities, NCBI requires you to specify your email address with each request. (default: None) --apikey APIKEY API key to use for make queries through to NCBI's E-utilities, if empty a warning is raised by the Entrez module. Personal API key from NCBI. If not set, only 3 queries per second are allowed. Ten queries per seconds otherwise with a valid API key. (default: None) --maxtries MAXTRIES Configures how many times failed requests will be automatically retried on error. (default: 3) --sleepbetweentries SLEEPBETWEENTRIES The delay, in seconds, before retrying a request on error. (default: 15) ```

Citing

TODO ADD citations

Owner

  • Login: diegomic
  • Kind: user

Citation (CITATION.cff) 

# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.2.0
title: >- CustomSintaxDB --  Create a custom Sintax Database from a list of taxons
message: >-
  If you use this software, please cite it using the
  metadata from this file.
type: software
authors:
  - given-names: Diego
    family-names: Micheletti
    orcid: 'https://orcid.org/0000-0001-9175-9853'

GitHub Events

Total
Last Year