This script reads the exported (.csv|.txt) files from Scopus, Web of Science, PubMed, PubMed Central, Dimensions, Cochrane, Embase, IEEE, BVS, CAB, SciELO, 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.
$ 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 coloramaTo 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 --helpYou can download the latest installable version of format-input.
$ python3 format_input.py --help
usage: format_input.py [-h] -t
{scopus,wos,pubmed,pmc,dimensions,scholar,cochrane,embase,sciencedirect,ieee,bvs,cab,scielo,txt}
-i INPUT_FILE [-o OUTPUT] [--version]
This script reads the exported (.csv|.txt) files from Scopus, Web of Science,
PubMed, PubMed Central, Dimensions, Cochrane, Embase, ScienceDirect, IEEE,
BVS, CAB, SciELO, 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,cochrane,embase,sciencedirect,ieee,bvs,cab,scielo,txt}, --type_file {scopus,wos,pubmed,pmc,dimensions,scholar,cochrane,embase,sciencedirect,ieee,bvs,cab,scielo,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) | cochrane: Indicates that the
file (.csv) was exported from Cochrane | embase:
Indicates that the file (.csv) was exported from
Embase | sciencedirect: Indicates that the file (.ris)
was exported from ScienceDirect | ieee: Indicates that
the file (.csv) was exported from IEEE | bvs:
Indicates that the file (.csv) was exported from BVS |
cab: Indicates that the file (.csv) was exported from
CAB | scielo: Indicates that the file (.csv) was
exported from SciELO | 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!- Molecular and Computational Biology of Fungi Laboratory (LBMCF, ICB - UFMG, Belo Horizonte, Brazil).
This project is licensed under the MIT License - see the LICENSE file for details.
Any use, distribution, or modification of this software must include one of the following attributions:
This software was developed by Glen Jasper (https://github.com/glenjasper), originally available at https://github.com/glenjasper/format-input
or (example citation):
Jasper G. (2024). format_input.py script. Available at: https://github.com/glenjasper/format-input (Accessed 21 July 2024)