Struct umgap::commands::prot2tryp2lca::ProtToTrypToLca

pub struct ProtToTrypToLca {
    pub one_on_one: bool,
    pub fst_file: PathBuf,
    pub fst_in_memory: bool,
    pub chunk_size: usize,
    pub pattern: String,
    pub min_length: usize,
    pub max_length: usize,
    pub contains: String,
    pub lacks: String,
}

Digests a FASTA stream of peptides and maps all tryptic peptides to taxon IDs

The umgap prot2tryp2lca command takes one or more peptides and splits these into tryptic peptides, possibly filters them, and outputs their lowest common ancestors. It is a combination of the umgap prot2tryp, umgap filter and umgap pept2lca commands to allow more efficient parallel computing (c.f. their documentation for details).

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 command prints the lowest common ancestors for each tryptic peptide found in each given peptide to standard output.

$ cat input.fa
>header1
AYKKAGVSGHVWQSDGITNCLLRGLTRVKEAVANRDSGNGYINKVYYWTVDKRATTRDALDAGVDGIMTNYPDVITDVLN
$ umgap prot2tryp2lca tryptic-lca.index < input.fa
>header1
571525
1
571525
6920

Fields

one_on_one: bool

Map unknown sequences to 0 instead of ignoring them

fst_file: PathBuf

An index that maps tryptic peptides to taxon IDs

fst_in_memory: bool

Load index in memory instead of memory mapping the file contents. This makes querying significantly faster, but requires some initialization time.

chunk_size: usize

Number of reads grouped into one chunk. Bigger chunks decrease the overhead caused by multithreading. Because the output order is not necessarily the same as the input order, having a chunk size which is a multiple of 12 (all 6 translations multiplied by the two paired-end reads) will keep FASTA records that originate from the same reads together.

pattern: String

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

min_length: usize

Minimum length of tryptic peptides to be mapped

max_length: usize

Maximum length of tryptic peptides to be mapped

contains: String

Amino acid symbols that a peptide must contain to be processed

lacks: String

Amino acid symbols that a peptide may not contain to be processed

Trait Implementations

impl Debug for ProtToTrypToLca

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

Formats the value using the given formatter.

impl StructOpt for ProtToTrypToLca

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.