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Scrapes all the results of all the genome analysis performed by MiGA Online web tool and wirte them in a file.

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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

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Scrapes all the results of all the genome analysis performed by MiGA Online web tool and wirte them in a file.

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