search-keywords

This script searches for the keywords, found in a .txt file, in the "Materials and Methods" section of each .txt file (created from .pdf files).

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 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/LBMCF/search-keywords.git

  # Go into the repository
  $ cd search-keywords

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

Download

You can download the latest installable version of search-keywords.

How To Use

  $ python3 search_keywords.py --help
  usage: search_keywords.py [-h] -ft FOLDER_TXT -fp FOLDER_PDF -kw KEYWORDS
                            [-o OUTPUT] [--version]

  This script searches for the keywords, found in a .txt file, in the 'Materials
  and Methods' section of each .txt file (created from .pdf files).

  optional arguments:
    -h, --help            show this help message and exit
    -ft FOLDER_TXT, --folder_txt FOLDER_TXT
                          Folder containing the .txt files
    -fp FOLDER_PDF, --folder_pdf FOLDER_PDF
                          Folder containing .pdf files, used at the end of the
                          search to make copies of .pdf files that meet the
                          condition in the 'Materials and Methods' section
    -kw KEYWORDS, --keywords KEYWORDS
                          .txt file containing keywords, there must be one
                          keyword for each line
    -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.