Usage

Automated testing

First download the `example FASTA file <https://raw.githubusercontent.com/AliYoussef96/BCAW-Tool/master/tests/Ecoli.fasta >`_ containing a coding sequence then run:

from BCAWT import BCAWT_auto_test

BCAWT_auto_test.auto_test(["Ecoli.fasta"])

BCAWT_auto_test.auto_check_files()

>> test is completed 'successfully'

to automatically run a test on the resulting files.

Main Usage

from BCAWT import BCAWT

BCAWT.BCAW([‘Ecoli.fasta’],’result_folder’,genetic_code_=11,Auto=True)

Important Note: BCAW Tool expects coding sequences

Input

  • main_fasta_file (list): list of string of the file’s path or file-like object
  • save_folder_name (str): folder name where the result will be saved
  • ref_fasta_file (list): list of string of the file’s path or file-like object, default = None
  • Auto (bool): default = False, if ref_fasta_file is not None.
  • genetic_code (int): default = 1, the genetic code ID from the NCBI table

To obtain FASTA file for a species of interest

Say that the species of interest is Escherichia coli str. K-12 substr. MG1655:

  1. Go to the NCBI’s database.
  2. In the search bar write Escherichia coli str. K-12 substr. MG1655, complete genome.
  3. Choose one of the results (depending on what you want in your analysis).
  1. On the write of the page, you will find send to option. From sent to select Coding Sequences then FASTA nucleotides Finally, press on Create File

For NCBI Genomes Download questions, see their FAQ.