nwr

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Install

Current release: 0.5.6

```bash cargo install nwr

or

brew install wang-q/tap/nwr

```

SYNOPSIS

``text $ nwr help nwr 0.5.4 wang-q <wang-q@outlook.com> nwr` is a lightweight tool for newick and taxonomy

USAGE: nwr [SUBCOMMAND]

OPTIONS: -h, --help Print help information -V, --version Print version information

SUBCOMMANDS: append Append fields of higher ranks to a TSV file ardb Init the assembly database download Download the latest release of taxdump help Print this message or the help of the given subcommand(s) info Information of Taxonomy ID(s) or scientific name(s) lineage Output the lineage of the term member List members (of certain ranks) under ancestral term(s) restrict Restrict taxonomy terms to ancestral descendants txdb Init the taxonomy database

```

EXAMPLES

nwr

```bash

Concurrent tests may trigger sqlite locking

cargo test -- --test-threads=1

debug mode has a slow connection

cargo run --release --bin nwr download

tests/nwr/

cargo run --bin nwr txdb -d tests/nwr/

cargo run --bin nwr info -d tests/nwr/ --tsv Viruses "Actinophage JHJ-1" "Bacillus phage bg1"

cargo run --bin nwr lineage -d tests/nwr/ --tsv "Actinophage JHJ-1"

echo -e '#ID\n9606\n12347' | cargo run --bin nwr restrict -d tests/nwr/ "Viruses" cargo run --bin nwr restrict -d tests/nwr/ "Viruses" -c 2 -f tests/nwr/taxon.tsv -f tests/nwr/taxon.tsv

cargo run --bin nwr member -d tests/nwr/ "Synechococcus phage S" -r "no rank" -r species cargo run --bin nwr member -d tests/nwr/ "Synechococcus phage S"

echo -e '#tax_id\n12347' | cargo run --bin nwr append -d tests/nwr/ stdin -r species -r family --id cargo run --bin nwr append -d tests/nwr/ tests/nwr/taxon-valid.tsv -c 2 -r species -r family --id

cargo run --bin nwr ardb -d tests/nwr/

The real one

nwr download

nwr txdb

nwr info "Homo sapiens" 4932

nwr lineage "Homo sapiens" nwr lineage 4932

nwr restrict "Vertebrata" -c 2 -f tests/nwr/taxon.tsv

sciname taxid

Human 9606

nwr member "Homo"

nwr append tests/nwr/taxon.tsv -c 2 -r species -r family --id

nwr ardb nwr ardb --genbank

```