/retrieve_n50_l50_n90_l90

command line and GUI scripts that retrieve the N50, L50, N90 and L90 values by indexing input multi-fasta files

Primary LanguagePythonMIT LicenseMIT

retrieve_n50_l50_n90_l90 DOI

command line and GUI scripts that retrieve the N50, L50, N90 and L90 values by indexing input multi-fasta files

Based by: n50.py

Executables(no dependences required)

  1. linux command line executable: DOI
  2. Windows and linux GUI executable: DOI

Dependences

  1. python 3.8.3 or later
  2. argparse (for the command line script only) pip install argparse
  3. pyfaidx pip install pyfaidx
  4. numpy pip install numpy
  5. miniconda3 (for the GUI script only)
  6. Gooey (for the GUI script only) conda install -c conda-forge gooey

To run the command line version of the script you need to give at least 1 of the following arguments:

e.g. python3 retrieve_n50_l50_n90_l90.py -dir fastadir/ -txt stats.txt

To run the GUI version you need to type: python3 retrieve_n50_l50_n90_l90_gui.py on the terminal and a window will pop up