format-input

This script reads the exported (.csv|.txt) files from Scopus, Web of Science, PubMed, PubMed Central, Dimensions or Google Scholar exported from Publish or Perish 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,scholar,txt} -i
                       INPUT_FILE [-o OUTPUT] [--version]

This script reads the exported (.csv|.txt) files from Scopus, Web of Science, PubMed,
PubMed Central, Dimensions or Google Scholar (exported from Publish or Perish)
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,scholar,txt}, --type_file {scopus,wos,pubmed,pmc,dimensions,scholar,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 | scholar: Indicates that the file (.csv) was
                        exported from Publish or Perish (Google Scholar option) | 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.