nwr

nwr is a command line tool for NCBI taxonomy, NCBI assembly reports and Newick files, written in Rust.

Install

Current release: 0.5.10

```shell cargo install nwr

or

brew install wang-q/tap/nwr

local repo

cargo install --path . --force --offline

```

SYNOPSIS

``text $ nwr help nwr` is a command line tool for NCBI taxonomy and newick files

Usage: nwr [COMMAND]

Commands: append Append fields of higher ranks to a TSV file ardb Init the assembly database assembly Prepare ASSEMBLY materials download Download the latest releases of taxdump and assembly reports 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 help Print this message or the help of the given subcommand(s)

Options: -h, --help Print help -V, --version Print version

```

EXAMPLES

Usage of each command

For practical uses of nwr and other awesome companions, follow this page.

```shell 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

```

Development

```shell

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 restrict -d tests/nwr/ "Viruses" -c 2 -f tests/nwr/taxon.tsv -e

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/

cargo run --bin nwr assembly tests/assembly/Trichoderma.assembly.tsv

```

Database schema

```shell brew install k1LoW/tap/tbls

tbls doc sqlite://./tests/nwr/taxonomy.sqlite doc/txdb

tbls doc sqlite://./tests/nwr/ar_refseq.sqlite doc/ardb

```

txdb

ardb