peptfilter
Filters peptides based on length and amino acid occurrence.
The peptfilter command takes one or more (tryptic) peptides as input and returns them as output if they satisfy all filter criteria. By default, peptides with length between 5 and 50 are retained. This command runs entirely locally and doesn't connect to any server.
Input
The peptfilter command accepts (tryptic) peptides as input from standard input. A single peptide per line is expected.
Example
$ cat input.txt AAR AALTER $ cat input.txt | peptfilter AALTER
Output
The peptfilter command outputs all input peptides that satisfy all filter criteria to standard output. By default, peptides with a length lower than 5 or higher than 50 are removed. The length filter can be changed by using the --minlen and --maxlen parameters. Peptides can also be filtered based on whether or not they lack or contain certain amino acids. This can be done with the --lacks and --contains parameters.
Fasta support
The peptfilter command supports input in a fasta-like format (for example generated by the prot2pept command). This format consists of a fasta header (a line starting with a >), followed by one or more lines containing one peptide each. When this format is detected, the fasta headers will automatically be included in the output.
Example
$ cat input.txt > header 1 AALTER AAR LGAALGAGLAVIGAGIGIGK > header 2 PEPTIDE $ cat intput.txt | peptfilter > header 1 AALTER LGAALGAGLAVIGAGIGIGK > header 2 PEPTIDE
Command-line options
--minlen Specify minimum length
By default, only peptides with a minimal length of 5 are retained. By using the --minlen parameter, this value can be changed.
Example
$ cat input.txt AALTER AAR $ cat input.txt | peptfilter --minlen 3 AALTER AAR
--maxlen Specify maximum length
By default, only peptides with a maximal length of 50 are retained. By using the --maxlen parameter, this value can be changed.
Example
$ cat input.txt AALTER AAR $ cat input.txt | peptfilter --maxlen 4 AAR
--contains / -c Specify mandatory amino acids
By using the --contains parameter, you can specify the amino acids that a peptide must contain. All specified amino acids must be present in the peptide for it to be retained.
Example
$ cat input.txt AALTER AARAAR $ cat input.txt | peptfilter --contains RL AALTER
--lacks / -l Specify forbidden amino acids
By using the --lacks parameter, you can specify the amino acids that a peptide can not contain. The peptide may have none of the specified amino acids for it to be retained.
Example
$ cat input.txt AALTER AARAAR $ cat input.txt | peptfilter --lacks VL AARAAR
--help / -h Display help
This flag displays the help.