MiGAscraping

Scrapes all the results of every genome analysis performed with MiGA (Microbial Genomes Atlas) Online web tool from your MiGA account and write them in a file. MiGA Online.

• You must have a MiGA account where you uploaded your genomes.
• Works using Selenium and ChromeDriver.

Requeriments:

• Python Installed (Recommended version 3.8 or above)
• MiGA account.
• Selenium library (use pip install selenium)
• Driver for launching the automation (chromedriver)
  • Be sure to match the version of Chrome you have
  • Download URL

Script options:

python3 run_MiGAscraping.py -d <driver-path> -o <out-path-dir> -p <float> -u <username 'email'> -hi <hide_Option:'yes'or'no'>

• -d --driverpath DRIVERPATH
  • The ChromeDriver path (Optional). Default path: usr/bin/chromedrive.
• -o --outdir OUTPUTDIRECTORY
  • Output directory (Optional). Default path: current directory.
• -p --pvalue PVALUE
  • p_value to asses the genome taxonomy (Optional). Default value: 0.05.
• -u --username USERNAME
  • Username of the MiGA Online account.
• -hi --hide HIDEOPTION
  • Hide the browser. Options: 'yes' or 'no'. Default option: 'no'.

Once you execute the script you will be asked to introduce the password of MiGA Online account.

Example of bash execution:

python3 run_MiGAscraping.py -p driverpath/chromedriver -o results_dir/ -p 0.05 -u example@exampleaccount.com -hi yes

Move the chromedriver to the default path

sudo mv path/to/chromedriver usr/bin