Struct umgap::commands::filter::Filter

pub struct Filter {
    pub min_length: usize,
    pub max_length: usize,
    pub contains: String,
    pub lacks: String,
}

Filters a FASTA stream of peptides

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

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 (which is the default).
• -M 50 sets the maximum length of the peptides to 50 (which is the default).
• -c LIK requires the peptides to contain amino acids Leucine (L), Isoleucine (I) and Lysine (K) (none by default).
• -l LIK removes the peptides containing the amino acids Leucine, Isoleucine or Lysine (none by default).

$ 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

Fields

min_length: usize

Minimum length required

max_length: usize

Maximum length allowed

contains: String

Amino acid symbols that a sequence must contain

lacks: String

Amino acid symbols that a sequence may not contain

Trait Implementations

impl Debug for Filter

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.

impl StructOpt for Filter

fn clap<'a, 'b>() -> App<'a, 'b>

Returns clap::App corresponding to the struct.

fn from_clap(matches: &ArgMatches<'_>) -> Self

Builds the struct from clap::ArgMatches. It’s guaranteed to succeed if matches originates from an App generated by StructOpt::clap called on the same type, otherwise it must panic.

fn from_args() -> Self

where Self: Sized,

Builds the struct from the command line arguments (std::env::args_os). Calls clap::Error::exit on failure, printing the error message and aborting the program.

fn from_args_safe() -> Result<Self, Error>

where Self: Sized,

Builds the struct from the command line arguments (std::env::args_os). Unlike StructOpt::from_args, returns clap::Error on failure instead of aborting the program, so calling .exit is up to you.

fn from_iter<I>(iter: I) -> Self

where Self: Sized, I: IntoIterator, <I as IntoIterator>::Item: Into<OsString> + Clone,

Gets the struct from any iterator such as a Vec of your making. Print the error message and quit the program in case of failure.

fn from_iter_safe<I>(iter: I) -> Result<Self, Error>

where Self: Sized, I: IntoIterator, <I as IntoIterator>::Item: Into<OsString> + Clone,

Gets the struct from any iterator such as a Vec of your making.