PROTEINcleaner
a python utility to clean PROTEIN sequences and headers
usage: PROTEINcleaner [-h] -i INPUT [-f INPUT_FORMAT] [-o OUTPUT]
[-F OUTPUT_FORMAT] [-c Y/y or N/n] [-v Y/y or N/n] [-V]
Cleans invalid bases/residues in PROTEIN sequence file i.e., replaces invalid bases with Xs
Citation: Singh, Abhijeet. PROTEINcleaner: a python utility to clean PROTEIN sequences and headers.
ResearchGate 2022, http://dx.doi.org/10.13140/RG.2.2.11468.49283,
Available at GitHub: https://github.com/abhijeetsingh1704/PROTEINcleaner
required arguments:
-i INPUT, --input INPUT
input file
options:
-h, --help show this help message and exit
-f INPUT_FORMAT, --input_format INPUT_FORMAT
format of input file
1 = fasta (default)
2 = genbank
-o OUTPUT, --output OUTPUT
output file (default: Clean<time>_<input_file><.ext>)
-F OUTPUT_FORMAT, --output_format OUTPUT_FORMAT
format of output fasta file
1 = interleaved fasta (default)
2 = fasta-2line
3 = tab-delimited
-c Y/y or N/n, --clean_header Y/y or N/n
clean and replace special characters in header
with underscore "_" (default: N)
-v Y/y or N/n, --verbose Y/y or N/n
print progress to the terminal (default: verbose)
-V, --version show program's version number and exit
Citation
Citation: Singh, Abhijeet. PROTEINcleaner: a python utility to clean PROTEIN sequences and headers. ResearchGate 2022, http://dx.doi.org/10.13140/RG.2.2.11468.49283, Available at GitHub: https://github.com/abhijeetsingh1704/PROTEINcleaner