nwr

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

Install

Current release: 0.7.0

```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 common Output the common tree of terms distance Output a TSV/phylip file with distances between all named nodes 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 pl-condense Pipeline - condense subtrees based on taxonomy prune Remove nodes from the Newick file rename Rename named/unnamed nodes in a Newick file replace Replace node names/comments in a Newick file reroot Place the root in the middle of the desired node and its parent restrict Restrict taxonomy terms to ancestral descendants subtree Extract a subtree stat Statistics about the Newick file template Create dirs, data and scripts for a phylogenomic research tex Visualize the Newick tree via LaTeX topo Topological information of the Newick file 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
  • common

• Newick

  • Information
    • label
    • stat
    • distance
  • Manipulation
    • order
    • rename
    • replace
    • topo
    • subtree
    • prune
    • reroot
    • pl-condense
  • Visualization
    • indent
    • comment
    • 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.

Get information from the tree

```shell

List all names

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

The intersection between the nodes in the tree and the provided

nwr label tests/newick/hg38.7way.nwk -r "^ch" -n Mouse -n foo nwr label tests/newick/catarrhini.nwk -n Homo -n Pan -n Gorilla -M

Is Pongo the sibling of Homininae?

nwr label tests/newick/catarrhini.nwk -n Homininae -n Pongo -DM

All leaves belong to Hominidae

nwr label tests/newick/catarrhini.nwk -t Hominidae -I

nwr label tests/newick/catarrhini.nwk -c dup nwr label tests/newick/catarrhini.comment.nwk -c full

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

Various distances

nwr distance -m root -I tests/newick/catarrhini.nwk nwr distance -m parent -I tests/newick/catarrhini.nwk nwr distance -m pairwise -I tests/newick/catarrhini.nwk nwr distance -m lca -I tests/newick/catarrhini.nwk

nwr distance -m root -L tests/newick/catarrhini_topo.nwk

Phylip distance matrix

nwr distance -m phylip tests/newick/catarrhini.nwk

```

Manipulation of the tree

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

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

nwr replace tests/newick/abc.nwk tests/newick/abc.replace.tsv nwr replace tests/newick/abc.nwk tests/newick/abc3.replace.tsv

nwr topo tests/newick/catarrhini.nwk

The behavior is very similar to nwr label, but outputs a subtree instead of labels

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

Condense the subtree to a node

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

nwr subtree tests/newick/catarrhini.nwk -t Hominidae

nwr prune tests/newick/catarrhini.nwk -n Homo -n Pan

echo "((A:1,B:1)D:1,C:1)E;" | nwr reroot stdin -n B nwr reroot tests/newick/catarrhini_wrong.nwk -n Cebus

cargo run --bin nwr pl-condense tests/newick/catarrhini.nwk -r family

```

Visualization of the tree

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

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

tectonic doc/template.tex

nwr tex tests/newick/catarrhini.nwk -o output.tex tectonic output.tex

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

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