OnlineMultiBLASTqueries

Does multiple nucleotidic | aminoacidic sequence BLAST queries in the NCBI BLAST web from a given multiFASTA and writes the output with the results.

• The queries are parallelized using Threads.
• Works using Selenium and ChromeDriver.

Requeriments:

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

Query file:

• The query file should be a (multi)FASTA with one or more either nucleotidic or aminoacidic sequence.
• Each sequence must have unique name (header)

Script options:

python3 run_OnlineMultiBLASTqueries.py -p <driver-path> -d <in-path> -t <int> -o <out-path> -f <nucleotide|protein> -hi <yes|no>

• -p --driverpath DRIVERPATH
  • The ChromeDriver path (Optional). Default path: usr/bin/chromedrive
• -d --dir IN_FILE
  • MultiFASTA file.
• -t --threads THREADS
  • Number of threads (Optional). Default value: 1.
• -O --outfile OUT_FILE
  • Output file.
• -f --format {nucleotide, protein}
  • Sequence type: "nucleotide" | "protein".
• -hi --hide {yes, no}
  • Hide the browser. Default yes.

Example of bash execution:

python3 run_OnlineMultiBLASTqueries.py -d test/test_nucleotide.fa -o output_example.txt -f nucleotide -hi yes -t 4

Move the chromedriver to the default path

sudo mv path/to/chromedriver usr/bin