nwr

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

Install

Current release: 0.6.3

```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

```

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 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

```

Newick files and LaTeX

For more detailed usages, check this.

```shell echo "(A,B);" | cargo run --bin nwr indent stdin cargo run --bin nwr indent tests/newick/hg38.7way.nwk --text ". "

nw_indent -t ". " tests/newick/hg38.7way.nwk

nworder tests/newick/hg38.7way.nwk | nwindent -

newick -ladderize tests/newick/hg38.7way.nwk

cargo run --bin nwr order --nd tests/newick/hg38.7way.nwk

echo "((A,B),C);" | cargo run --bin nwr order --ndr stdin

cargo run --bin nwr label tests/newick/hg38.7way.nwk nw_labels tests/newick/hg38.7way.nwk

echo "((A,B),C);" | cargo run --bin nwr rename stdin -n C -r F -l A,B -r D

cargo run --bin nwr stat tests/newick/hg38.7way.nwk nw_stats tests/newick/hg38.7way.nwk

nw_topology tests/newick/hg38.7way.nwk

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);" | cargo run --bin nwr comment stdin -n A -n C --color green -s '&&nwr' | cargo run --bin nwr comment stdin -l A,B --dot

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

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

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

cargo run --bin nwr tex --forest --bare tests/newick/test.forest

```

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