nwr

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

Install

Current release: 0.6.4

```shell cargo install nwr

or

brew install wang-q/tap/nwr

local repo

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

build under WSL 2

export CARGOTARGETDIR=/tmp cargo build

```

nwr help

``text nwr` is a command line tool for working with NCBI taxonomy, Newick files and assembly reports

Usage: nwr [COMMAND]

Commands: append Append fields of higher ranks to a TSV file ardb Init the assembly database comment Add comments to node(s) in a Newick file download Download the latest releases of taxdump and assembly reports indent Indent the Newick file info Information of Taxonomy ID(s) or scientific name(s) kb Prints docs (knowledge bases) label Labels in the Newick file lineage Output the lineage of the term member List members (of certain ranks) under ancestral term(s) order Order nodes in a Newick file rename Rename node(s) in a Newick file restrict Restrict taxonomy terms to ancestral descendants stat Statistics about the Newick file template Create dirs, data and scripts for a phylogenomic research tex Visualize the Newick tree via LaTeX 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

Subcommand groups:

• Database

  • download
  • txdb
  • ardb

• Taxonomy

  • info
  • lineage
  • member
  • append
  • restrict

• Newick

  • indent
  • order
  • label
  • rename
  • comment
  • stat
  • tex

• Assembly

  • template
  • kb

```

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

nwr common "Escherichia coli" 4932 Drosophila_melanogaster 9606 "Mus musculus"

```

Development

```shell

Concurrent tests may trigger sqlite locking

cargo test -- --test-threads=1

cargo test --color=always --package nwr --test clinwr commandtemplate -- --show-output

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 common -d tests/nwr/ "Actinophage JHJ-1" "Bacillus phage bg1"

```

Newick files and LaTeX

For more detailed usages, check this.

```shell nwr indent tests/newick/hg38.7way.nwk --text ". "

echo "((A,B),C);" | nwr order --ndr stdin nwr order --nd tests/newick/hg38.7way.nwk

nwr label tests/newick/hg38.7way.nwk

nwr rename tests/newick/abc.nwk -n C -r F -l A,B -r D

nwr stat tests/newick/hg38.7way.nwk

nwr subtree tests/newick/hg38.7way.nwk -n Human -n Rhesus -r "^ch" -m

nwr topo tests/newick/catarrhini.nwk

nw_prune tests/newick/catarrhini.nwk Homo Gorilla Pan

nwreroot tests/newick/catarrhiniwrong.nwk Cebus | nworder -c n - perl doc/reroot.pl tests/newick/catarrhiniwrong.nwk Cebus | nw_order -c n -

echo "((A,B),C);" | nwr comment stdin -n A -n C --color green | nwr comment stdin -l A,B --dot

latexmk -xelatex doc/template.tex latexmk -c doc/template.tex

nwr tex --bare tests/newick/hg38.7way.nwk

nwr tex --bl tests/newick/hg38.7way.nwk -o output.tex latexmk -xelatex output.tex latexmk -c output.tex

nwr tex --forest --bare tests/newick/test.forest

nwr common "Escherichia coli" 4932 Drosophila_melanogaster 9606 "Mus musculus" | nwr tex --bare stdin

```

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