Struct umgap::commands::prot2tryp::ProtToTryp

pub struct ProtToTryp {
    pub pattern: String,
}

Splits the peptides in a FASTA stream into tryptic peptides

The umgap prot2tryp command takes one or more amino acid sequences as input and applies an in silico trypsine digest.

The input is given in a FASTA format on standard input with a single peptide per FASTA header, which may be hardwrapped with newlines. The peptides resulting from the digest are written in FASTA format to standard output, with multiple peptides per FASTA header, separated by newlines.

$ cat input.fa
>header1
AYKKAGVSGHVWQSDGITNCLLRGLTRVKEAVANRDSGNGYINKVYYWTVDKRATTRDALDAGVDGIMTNYPDVITDVLN
$ umgap prot2tryp tryptic-lca.index < input.fa
>header1
AYK
K
AGVSGHVWQSDGITNCLLR
GLTR
VK
EAVANR
DSGNGYINK
VYYWTVDK
R
ATTR
DALDAGVDGIMTNYPDVITDVLN

Using the -p flag, you can change the splitting pattern. The default pattern ([KR])([^P]) splits between any Lysine (K) or Arginine (R), followed by any amino acid that is not Proline (P).

Fields

pattern: String

The cleavage-pattern (regex), i.e. the pattern after which the next peptide will be cleaved for tryptic peptides)

Trait Implementations

impl Debug for ProtToTryp

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

Formats the value using the given formatter.

impl StructOpt for ProtToTryp

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.