format-input

This script reads the exported (.csv|.txt) files from Scopus, Web of Science, PubMed, PubMed Central or Dimensions databases and turns each of them into a new file with an unique format. This script will ignore duplicated records.

Table of content

Pre-requisites
- Python libraries
Installation
- Clone
- Download
How To Use
Author
Organization
License
Acknowledgments

Pre-requisites

Python libraries

  $ sudo apt install -y python3-pip
  $ sudo pip3 install --upgrade pip

  $ sudo pip3 install argparse
  $ sudo pip3 install xlsxwriter
  $ sudo pip3 install numpy
  $ sudo pip3 install pandas
  $ sudo pip3 install colorama

Installation

Clone

To clone and run this application, you'll need Git installed on your computer. From your command line:

  # Clone this repository
  $ git clone https://github.com/glenjasper/format-input.git

  # Go into the repository
  $ cd format-input

  # Run the app
  $ python3 format_input.py --help

Download

You can download the latest installable version of format-input.

How To Use

  $ python3 format_input.py --help
  usage: format_input.py [-h] -t {scopus,wos,pubmed,pmc,dimensions,txt} -i
                         INPUT_FILE [-o OUTPUT] [--version]

  This script reads the exported (.csv|.txt) files from Scopus, Web of Science,
  PubMed, PubMed Central or Dimensions databases and turns each of them into a
  new file with an unique format. This script will ignore duplicated records.

  optional arguments:
    -h, --help            show this help message and exit
    -t {scopus,wos,pubmed,pmc,dimensions,txt}, --type_file {scopus,wos,pubmed,pmc,dimensions,txt}
                          scopus: Indicates that the file (.csv) was exported
                          from Scopus | wos: Indicates that the file (.csv) was
                          exported from Web of Science | pubmed: Indicates that
                          the file (.csv) was exported from PubMed | pmc:
                          Indicates that the file (.txt) was exported from
                          PubMed Central, necessarily in MEDLINE format |
                          dimensions: Indicates that the file (.csv) was
                          exported from Dimensions | txt: Indicates that it is a
                          text file (.txt)
    -i INPUT_FILE, --input_file INPUT_FILE
                          Input file .csv or .txt
    -o OUTPUT, --output OUTPUT
                          Output folder
    --version             show program's version number and exit

  Thank you!

Author

Glen Jasper

Organization

Molecular and Computational Biology of Fungi Laboratory (LBMCF, ICB - UFMG, Belo Horizonte, Brazil).

License

This project is licensed under the MIT License - see the LICENSE file for details.