nwr is a command line tool for working with NCBI taxonomy, NeWick files and assembly
Reports, written in Rust.
Current release: 0.8.5
cargo install nwr
# or
cargo install --path . --force # --offline
# Concurrent tests may trigger sqlite locking
cargo test -- --test-threads=1
# build under WSL 2
mkdir -p /tmp/cargo
export CARGO_TARGET_DIR=/tmp/cargo
cargo build
# build for CentOS 7
# rustup target add x86_64-unknown-linux-gnu
# pip3 install cargo-zigbuild
cargo zigbuild --target x86_64-unknown-linux-gnu.2.17 --release
ll $CARGO_TARGET_DIR/x86_64-unknown-linux-gnu/release/
$ nwr help
`nwr` is a command line tool for working with NCBI taxonomy, Newick files and assembly reports
Usage: nwr [COMMAND]
Commands:
download Download the latest releases of `taxdump` and assembly reports
txdb Init the taxonomy database
ardb Init the assembly database
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)
append Append fields of higher ranks to a TSV file
restrict Restrict taxonomy terms to ancestral descendants
common Output the common tree of terms
template Create dirs, data and scripts for a phylogenomic research
kb Prints docs (knowledge bases)
seqdb Init the seq database
data Newick data commands
ops Newick operation commands
viz Newick visualization commands
mat Distance matrix commands
build Build tree from distance matrix
plot Plot commands
pl-condense Pipeline - condense subtrees based on taxonomy
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
* Assembly
* template / kb / seqdb
* Newick
* data label / data stat / data distance
* Operations
* ops order / ops rename / ops replace / ops topo / ops subtree /
ops prune / ops reroot
* Visualization
* viz indent / viz comment / viz tex
* pl-condense
* Distance matrix
* mat pair / mat phylip / mat format / mat subset / mat compare
* Build tree
* build upgma / build nj
* Plots
* plot hh / plot venn
For practical uses of nwr and other awesome companions, follow this page.
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
##sci_name tax_id
#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
# rm ~/.nwr/*.dmp
cargo test --color=always --package nwr --test cli_nwr command_template -- --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"
cargo run --bin nwr template tests/assembly/Trichoderma.assembly.tsv --ass -o stdout
export SPECIES="$HOME/data/Archaea/Protein/Sulfolobus_acidocaldarius"
cargo run --bin nwr seqdb -d ${SPECIES} --init --strain
cargo run --bin nwr seqdb -d ${SPECIES} \
--size <(
hnsm size ${SPECIES}/pro.fa.gz
) \
--clust
cargo run --bin nwr seqdb -d ${SPECIES} \
--anno <(
gzip -dcf "${SPECIES}"/anno.tsv.gz
) \
--asmseq <(
gzip -dcf "${SPECIES}"/asmseq.tsv.gz
)
cargo run --bin nwr seqdb -d ${SPECIES} --rep f1="${SPECIES}"/fam88_cluster.tsv
echo "
SELECT
*
FROM asm
WHERE 1=1
" |
sqlite3 -tabs ${SEQ_DIR}/seq.sqlite
echo "
SELECT
COUNT(distinct asm_seq.asm_id)
FROM asm_seq
WHERE 1=1
" |
sqlite3 -tabs ${SEQ_DIR}/seq.sqlite
echo "
.header ON
SELECT
'species' AS species,
COUNT(distinct asm_seq.asm_id) AS strain,
COUNT(*) AS total,
COUNT(distinct rep_seq.seq_id) AS dedup,
COUNT(distinct rep_seq.rep_id) AS rep
FROM asm_seq
JOIN rep_seq ON asm_seq.seq_id = rep_seq.seq_id
WHERE 1=1
" |
sqlite3 -tabs ${SEQ_DIR}/seq.sqlite
For more detailed usages, check this file.
# List all names
nwr data label tests/newick/hg38.7way.nwk
# The intersection between the nodes in the tree and the provided
nwr data label tests/newick/hg38.7way.nwk -r "^ch" -n Mouse -n foo
nwr data label tests/newick/catarrhini.nwk -n Homo -n Pan -n Gorilla -M
# Is Pongo the sibling of Homininae?
nwr data label tests/newick/catarrhini.nwk -n Homininae -n Pongo -DM
# All leaves belong to Hominidae
nwr data label tests/newick/catarrhini.nwk -t Hominidae -I
nwr data label tests/newick/catarrhini.nwk -c dup
nwr data label tests/newick/catarrhini.comment.nwk -c full
nwr data stat tests/newick/hg38.7way.nwk
# Various distances
nwr data distance -m root -I tests/newick/catarrhini.nwk
nwr data distance -m parent -I tests/newick/catarrhini.nwk
nwr data distance -m pairwise -I tests/newick/catarrhini.nwk
nwr data distance -m lca -I tests/newick/catarrhini.nwk
nwr data distance -m root -L tests/newick/catarrhini_topo.nwk
# Phylip distance matrix
nwr data distance -m phylip tests/newick/catarrhini.nwk
echo "((A,B),C);" | nwr ops order --ndr stdin
nwr ops order --nd tests/newick/hg38.7way.nwk
nwr ops order --list tests/newick/abcde.list tests/newick/abcde.nwk
# gene tree as the order of species tree
nwr ops order tests/newick/pmxc.nwk \
--list <(nwr data label tests/newick/species.nwk)
nwr ops rename tests/newick/abc.nwk -n C -r F -l A,B -r D
nwr ops replace tests/newick/abc.nwk tests/newick/abc.replace.tsv
nwr ops replace tests/newick/abc.nwk tests/newick/abc3.replace.tsv
nwr ops topo tests/newick/catarrhini.nwk
# The behavior is very similar to `nwr label`, but outputs a subtree instead of labels
nwr ops subtree tests/newick/hg38.7way.nwk -n Human -n Rhesus -r "^ch" -M
# Condense the subtree to a node
nwr ops subtree tests/newick/hg38.7way.nwk -n Human -n Rhesus -r "^ch" -M -c Primates
nwr ops subtree tests/newick/catarrhini.nwk -t Hominidae
nwr ops prune tests/newick/catarrhini.nwk -n Homo -n Pan
echo "((A:1,B:1)D:1,C:1)E;" |
nwr ops reroot stdin -n B
nwr ops reroot tests/newick/catarrhini_wrong.nwk -n Cebus
nwr ops reroot tests/newick/bs.nw -n C
nwr viz tex tests/newick/bs.nw | tectonic -
mv texput.pdf bs.pdf
nwr ops reroot tests/newick/bs.nw -n C | nwr viz tex stdin | tectonic -
mv texput.pdf bs.reroot.pdf
nwr pl-condense tests/newick/catarrhini.nwk -r family
nwr viz indent tests/newick/hg38.7way.nwk --text ". "
echo "((A,B),C);" |
nwr viz comment stdin -n A -n C --color green |
nwr viz comment stdin -l A,B --dot
tectonic doc/template.tex
echo "((A[color=green],B)[dot=black],C[color=green]);" |
nwr viz comment stdin -r "color="
nwr viz tex tests/newick/catarrhini.nwk -o output.tex
tectonic output.tex
nwr viz tex --bl tests/newick/hg38.7way.nwk |
tectonic - &&
mv texput.pdf hg38.7way.pdf
nwr viz tex --forest --bare tests/newick/test.forest
nwr viz common "Escherichia coli" 4932 Drosophila_melanogaster 9606 "Mus musculus" |
nwr viz tex --bare stdin
nwr mat phylip tests/mat/IBPA.fa.tsv
nwr mat pair tests/mat/IBPA.phy
nwr mat format tests/mat/IBPA.phy
nwr mat subset tests/mat/IBPA.phy tests/mat/IBPA.list
hnsm distance tests/mat/IBPA.fa -k 7 -w 1 |
nwr mat phylip stdin -o tests/mat/IBPA.71.phy
nwr mat compare tests/mat/IBPA.phy tests/mat/IBPA.71.phy --method all
# Sequences in matrices: 10 and 10
# Common sequences: 10
# Method Score
# pearson 0.935803
# spearman 0.919631
# mae 0.113433
# cosine 0.978731
# jaccard 0.759106
# euclid 1.229844
nwr build upgma tests/build/wiki.phy |
nwr viz tex stdin --bl |
tectonic - &&
mv texput.pdf wiki.upgma.pdf
nwr build nj tests/build/wiki-nj.phy |
nwr viz tex stdin --bl |
tectonic - &&
mv texput.pdf wiki.nj.pdf
neighbor
# tests/build/wiki-nj.phy
# r
# y
# r
nwr ops reroot outtree -n e
# venn
nwr plot venn \
tests/plot/rocauc.result.tsv \
tests/plot/mcox.05.result.tsv |
tectonic - &&
mv texput.pdf venn2.pdf
nwr plot venn \
tests/plot/rocauc.result.tsv \
tests/plot/mcox.05.result.tsv \
tests/plot/mcox.result.tsv |
tectonic - &&
mv texput.pdf venn3.pdf
nwr plot venn \
tests/plot/rocauc.result.tsv \
tests/plot/rocauc.result.tsv \
tests/plot/mcox.05.result.tsv \
tests/plot/mcox.result.tsv |
tectonic - &&
mv texput.pdf venn4.pdf
plotr venn tests/plot/rocauc.result.tsv tests/plot/mcox.05.result.tsv
tectonic doc/venn4.tex
# histo
nwr plot hh tests/plot/hist.tsv -g 2 --bins 20 --xl "" --unit 0.5,1.5 |
tectonic - &&
mv texput.pdf hist.pdf
nwr plot hh tests/plot/hist.tsv --bins 30 --xl "" --xmm 45,75 --unit 0.5,1.5 |
tectonic - &&
mv texput.pdf hist.pdf
cargo run --bin nwr plot hh tests/plot/adomain.tsv -g 2 --bins 40 --xl "" --yl "" --unit 0.3,0.5 |
tectonic - &&
mv texput.pdf hist.pdf
tectonic doc/heatmap.tex
# nrps
cargo run --bin nwr plot nrps tests/plot/srf.tsv --legend --color blue |
tectonic - &&
mv texput.pdf srf.pdf
tectonic doc/nrps.tex
brew install k1LoW/tap/tbls
tbls doc sqlite://./tests/nwr/taxonomy.sqlite doc/txdb
tbls doc sqlite://./tests/nwr/ar_refseq.sqlite doc/ardb
