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.