Struct umgap::commands::joinkmers::JoinKmers

pub struct JoinKmers {
    pub taxon_file: PathBuf,
}

Aggregates a TSV stream of peptides and taxon IDs

The umgap joinkmers command takes tab-separated peptides and taxon IDs, aggregates the taxon IDs where consecutive peptides are equal and outputs a tab-separated triple of peptide, consensus taxon ID and taxon rank.

The input is given on standard input. If it is sorted on the first column, a complete mapping from strings to aggregated taxa and its rank will be written to standard output. It is meant to be used after an umgap splitkmers and sort, and it’s output is ideal for umgap buildindex, but there may be further uses.

The aggregation strategy used in this command to find a consensus taxon is the hybrid approach of the umgap taxa2agg command, with a 95% factor. This keeps the result close to the lowest common ancestor, but filters out some outlying taxa.

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

$ cat input.tsv
AAAAA	34924
AAAAA	30423
AAAAA	5678
BBBBBB	48890
BBBBBB	156563
$ umgap joinkmers taxons.tsv < input.tsv
AAAAA	2759	superkingdom
BBBBBB	9153	family

Fields

taxon_file: PathBuf

An NCBI taxonomy TSV-file as processed by Unipept

Trait Implementations

impl Debug for JoinKmers

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

Formats the value using the given formatter.

impl StructOpt for JoinKmers

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.