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 objectsave_folder_name
(str): folder name where the result will be savedref_fasta_file
(list): list of string of the file’s path or file-like object, default = NoneAuto
(bool): default = False, ifref_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:
- Go to the NCBI’s database.
- In the search bar write
Escherichia coli str. K-12 substr. MG1655, complete genome
. - Choose one of the results (depending on what you want in your analysis).
- 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.