Struct umgap::commands::snaptaxon::SnapTaxon

pub struct SnapTaxon {
    pub rank: Option<Rank>,
    pub taxons: Vec<TaxonId>,
    pub invalid: bool,
    pub taxon_file: PathBuf,
}

Snaps taxon IDs to a specific rank or listed taxa

The umgap snaptaxon command takes one or more taxon IDs. For each taxon, it searches amongst its ancestors if any are of the specified rank (e.g., -r species), or are one of the listed taxa (e.g., -t 1598 -t 1883). If so, the taxon is replaced by the most specific of these matching taxa. Otherwise, it is mapped to the root of the taxonomy.

The input is given on standard input and may be any sequence of FASTA headers and/or lines containing a single taxon ID. The FASTA headers (if any) are just copied over to standard output.

The taxonomy to be used is passed as an argument to this command. This is a preprocessed version of the NCBI taxonomy.

$ cat input.fa
>header1
888268
186802
1598
1883
$ umgap snaptaxon 2020-04-taxons.tsv -r order < ~/input.fa
>header1
38820
186802
186826
85011
$ umgap snaptaxon 2020-04-taxons.tsv -t 1239 2 < ~/input.fa
>header1
1
1239
1239
2

Fields

rank: Option<Rank>

The rank to snap towards.

taxons: Vec<TaxonId>

A taxon to snap towards (allow multiple times).

invalid: bool

Include the invalidated taxa from the taxonomy

taxon_file: PathBuf

An NCBI taxonomy TSV-file as processed by Unipept

Trait Implementations

impl Debug for SnapTaxon

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

Formats the value using the given formatter.

impl StructOpt for SnapTaxon

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.