https://github.com/abhijeetsingh1704/proteincleaner

a python utility to clean PROTEIN sequences and headers
https://github.com/abhijeetsingh1704/proteincleaner

convertion fasta genbank

Last synced: 3 months ago
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a python utility to clean PROTEIN sequences and headers

• Host: GitHub
• URL: https://github.com/abhijeetsingh1704/proteincleaner
• Owner: abhijeetsingh1704
• License: mit
• Created: 2022-05-28T15:56:51.000Z (about 3 years ago)
• Default Branch: main
• Last Pushed: 2022-05-28T16:04:22.000Z (about 3 years ago)
• Last Synced: 2025-01-26T12:09:47.634Z (5 months ago)
• Topics: convertion, fasta, genbank
• Language: Python
• Homepage:
• Size: 6.84 KB
• Stars: 1
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# 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_<.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