Struct umgap::commands::taxa2tree::TaxaToTree

pub struct TaxaToTree {
    pub url: bool,
}

Visualizes a stream of taxon IDs using the Unipept API

The umgap taxa2tree command, similar to the unipept taxa2tree command, takes one or more taxon IDs and returns a visualized taxonomic tree of these taxa using the Unipept API server.

The input is given in a FASTA format on standard input. Each FASTA record contains one taxon ID. A HTML file is written to standard output containing a visualization of the taxonomic tree containing all these taxa. With -u, a URL to the visualization hosted online is printed instead.

$ cat input.txt
>header1
817
329854
1099853
$ umgap taxa2tree < input.txt > output.html
$ umgap taxa2tree --url < input.txt
https://bl.ocks.org/a686a37e1dcd43dd4ec7d467487bd6a1

Fields

url: bool

Host the result online and return the URL

Trait Implementations

impl Debug for TaxaToTree

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

Formats the value using the given formatter.

impl StructOpt for TaxaToTree

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.