The umgap filter command a FASTA stream of peptides as input and outputs a filtered stream.

Usage

The input is given in FASTA format on standard input. Per FASTA header, there may be multiple peptides separated by newlines. Each of these peptides are checked against the filter criteria and written to standard output they pass them. The criteria are specified as options:

  • -m 5 sets the minimum length of the peptides to 5.
  • -M 50 sets the maximum length of the peptides to 50.
  • -c LIK requires the peptides to contain amino acids Leucine (L), Isoleucine (I) and Lysine (K).
  • -l LIK removes the peptides containing the amino acids Leucine, Isoleucine or Lysine.
$ cat input.fa
>header1
AYKKAGVSGHVWQSDGITNCLLRGLTRVKEAVANRDSGNGYINKVYYWTVDKRATTRDALDAGVDGIMTNYPDVITDVLN
AYK
K
AGVSGHVWQSDGITNCLLR
GLTR
VK
EAVANR
DSGNGYINK
$ umgap filter < input.fa
>header1
AGVSGHVWQSDGITNCLLR
EAVANR
DSGNGYINK
$ umgap filter -m 0 -c R -l K < input.fa
>header1
AGVSGHVWQSDGITNCLLR
GLTR
EAVANR
-h / --help
Prints help information
-V / --version
Prints version information
-c / --contains c
Amino acid symbols that a sequence must contain [none by default]
-l / --lacks l
Amino acid symbols that a sequence may not contain [none by default]
-M / --maxlen M
Maximum length allowed [default: 50]
-m / --minlen m
Minimum length required [default: 5]