Given a set of protein sequences filters out those with non-standard residues. If not input file given it reads from the standard input and if not output file given it writes to standard output.
usage: noXseq [-h] [-f {fasta,clustal,embl,genbank,imgt,phd,pir,tab}] [-v] [inseqfile] [outseqfile]
It can be inserted in command pipes.
This is a Python script, so, you can just run the uniqseq.py file or put a symbolic link in any directory of your PATH. The second option is recommend.
- Python3
- Biopython
- argparse
It runs in Linux, probably in Mac OS too, but not tested.
noXseq multiple_sequences_and_some_with_non_standard_aas.fasta only_sequences_without_non_standard_aas.fasta
noXseq multiple_sequences_and_some_with_non_standard_aas.pir only_sequences_without_non_standard_aas.pir -f pir
cat multiple_sequences_and_some_with_non_standard_aas.fasta | noXseq > only_sequences_without_non_standard_aas.fasta