Struct umgap::commands::pept2lca::PeptToLca

pub struct PeptToLca {
    pub one_on_one: bool,
    pub fst_file: PathBuf,
    pub fst_in_memory: bool,
    pub chunk_size: usize,
}

Maps a FASTA stream of peptides to taxon IDs

The umgap pept2lca command takes one or more amino acid sequences and looks up the corresponding taxon ID in an index file (as build by the umgap buildindex command).

The input is given in FASTA format on standard input. Per FASTA header, there can be multiple sequences, each on a line. In the following example we match tryptic peptides on their lowest common ancestor in the NCBI taxonomy.

$ cat input.fa
>header1
AAALTER
ENFVYLAK
$ umgap pept2lca tryptic-peptides.index < input.fa
>header1
2
3398

By default, sequences not found in the index are ignored. Using the -o (--on-on-one) flag, they are mapped to 0, instead.

$ cat input.fa
>header1
NOTATRYPTICPEPTIDE
ENFVYLAK
$ umgap pept2lca -o tryptic-peptides.index < input.fa
>header1
0
3398

Fields

one_on_one: bool

Map unknown sequences to 0 instead of ignoring them

fst_file: PathBuf

An index that maps 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.

Trait Implementations

impl Debug for PeptToLca

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

Formats the value using the given formatter.

impl StructOpt for PeptToLca

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.