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https://github.com/shenwei356/gtaxon
gTaxon - a fast cross-platform NCBI taxonomy data querying (gi2taxid, taxid2taxon, name2taxid, LCA) tool, with cmd client and REST API server for both local and remote server.
https://github.com/shenwei356/gtaxon
bioinformatics client golang lca restful server taxonomy
Last synced: 26 days ago
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gTaxon - a fast cross-platform NCBI taxonomy data querying (gi2taxid, taxid2taxon, name2taxid, LCA) tool, with cmd client and REST API server for both local and remote server.
- Host: GitHub
- URL: https://github.com/shenwei356/gtaxon
- Owner: shenwei356
- License: mit
- Created: 2016-02-13T13:00:49.000Z (over 8 years ago)
- Default Branch: master
- Last Pushed: 2016-07-24T06:30:24.000Z (almost 8 years ago)
- Last Synced: 2024-02-09T08:39:03.784Z (4 months ago)
- Topics: bioinformatics, client, golang, lca, restful, server, taxonomy
- Language: Go
- Homepage: http://github.com/shenwei356/gtaxon
- Size: 13.1 MB
- Stars: 15
- Watchers: 4
- Forks: 2
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Lists
- awesome-bio-go - gTaxon - platform NCBI taxonomy data querying tool with (Sequence Analysis and Manipulation)
README
# gTaxon
## Introduction
gTaxon - a fast cross-platform NCBI taxonomy data querying tool,
with cmd client and REST API server for both local and remote server.
[http:///github.com/shenwei356/gtaxon](http:///github.com/shenwei356/gtaxon)
## Supporting querying types
| Query type | Function | Local/Remote |
|------------------|------------------------------------------|--------------|
| gi_taxid_nucl | query TaxId by Gi (nucl) | Both |
| gi_taxid_prot | query TaxId by Gi (prot) | Both |
| taxid2taxon | query Taxon by TaxId | Remote |
| name2taxid | query TaxId by Name | Remote |
| lca | query Lowest Common Ancestor by TaxIds | Remote |
## Features
- Easy to install. **Only ONE single executable binary file**.
No scared source compilation, installing extra packages,
configuring environment variables
- **Cross platform**. gTaxon is implemented in [golang](https://golang.org).
Executable binary files for most popular operating system (Linux, Mac OS X,
Windows, \*BSD ) are available.
See [Release](https://github.com/shenwei356/gtaxon/releases) page.
- Supporting querying from **both LOCAL and REMOTE server** by REST API,
which is also easily called by various clients of other languages.
gTaxon has command-line client `gtaxon cli local` for local query and
`gtaxon cli remote` for remote query.
- **Fast**. See Section Performance.
## Performance
### gi2taxid
[Detail](https://github.com/shenwei356/gtaxon/blob/master/testdata/PERFORMANCE.md)
Note: 1) bolt database utilizes the operating system's page cache,
so repeat queries are faster than the first query. 2) "remote query" actually is from local host
with minimum network latency
| dataset | local query | remote query | remote query (repeated) |
|----------------|-----------------|------------------|-------------------------|
| small (0.25K) | 0.013 s | 0.013 s | 0.009s |
| medium (25K) | 0.38 s | 0.57 s | 0.178s |
| large (2.5M) | 17 s | 1min 38s | 20 s |
## Download && Install
Steps:
1. Just download and uncompress the executable binary files of your operating system from [Release](https://github.com/shenwei356/gtaxon/releases) page.
2. Rename it to `gtaxon.exe` (for Windows) or `gtaxon` (for other operating systems) for convenience, and then run it in command-line interface, no compilation, no dependencies.
You can also add the directory of the executable file to environment variable `PATH`, so you can run `gtaxon` anywhere.
1. For windows, the simplest way is copy it to ` C:\WINDOWS\system32`.
2. For Linux, simply copy it to `/usr/local/bin` or add the path of gtaxon to environment variable `PATH`:
chmod a+x /PATH/OF/GTAXON/gtaxon
echo export PATH=\$PATH:/PATH/OF/GTAXON >> ~/.bashrc
## Usage
### Loading data to database
1. Initializing database.
gtaxon db init
2. Importing data
Supported file types includes:
================================================
data type files
------------------------------------------------
gi_taxid_nucl gi_taxid_nucl.dmp.gz
gi_taxid_prot gi_taxid_prot.dmp.gz
nodes nodes.dmp
names names.dmp
divisions division.dmp
gencodes gencode.dmp
================================================
For gi2taxid
# ~ 16 min for me
gtaxon db import -f -t gi_taxid_prot gi_taxid_prot.dmp.gz
For taxon query
gtaxon db import -f -t nodes nodes.dmp
gtaxon db import -f -t names names.dmp
gtaxon db import -f -t divisions division.dmp
gtaxon db import -f -t gencodes gencode.dmp
### Querying from local (Only for gi2taxid)
- few queries
gtaxon cli local -t gi_taxid_prot 139299181 139299182
- from file
gtaxon cli local -t gi_taxid_prot -f gi_list_file
### Querying from remote server
1. Starting server
gtaxon server
2. Query TaxId by Gi (gi_taxid_nucl or gi_taxid_prot)
- few queries
gtaxon cli remote -t gi_taxid_prot 139299181 139299182
- from files
gtaxon cli remote -H 192.168.1.101 -P 8080 -t gi_taxid_prot -f gi_list_file
3. Query TaxId by Name (name2taxid)
Limiting name class, using regular expression
gtaxon cli remote -t name2taxid --use-regexp --name-class "scientific name" sapiens
[INFO] Query TaxId by Name from host: 127.0.0.1:8080
sapiens 9606(Homo sapiens),1035824(Trichuris sp. ex Homo sapiens JP-2011),1573476(Homo sapiens/Rattus norvegicus xenograft),324570(Phrynium sapiense),63221(Homo sapiens neanderthalensis),1383439(Homo sapiens/Mus musculus xenograft),741158(Homo sapiens ssp. Denisova),399796(Macrobiotus sapiens),349050(Ficus casapiensis),1131344(Homo sapiens x Mus musculus hybrid cell line),270523(Tetragonula sapiens)
gtaxon cli remote -t name2taxid --use-regexp --name-class "genbank common name" human mouse
[INFO] Query TaxId by Name from host: 127.0.0.1:8080
human 121226(Pediculus humanus capitis),121225(Pediculus humanus),51028(Enterobius vermicularis),121224(Pediculus humanus corporis),433352(Diplogonoporus grandis),36087(Trichuris trichiura),115427(Dermatobia hominis),9606(Homo sapiens)
mouse 42410(Peromyscus eremicus),1595964(Apomys sacobianus),10105(Mus minutoides),221913(Pseudomys hermannsburgensis),240587(Thalpomys cerradensis),409025(Peromyscus melanocarpus) ...
4. Query Taxon by TaxId (taxid2taxon)
gtaxon cli remote -t taxid2taxon 9
# result is similar with result of example 5)
5. Query Lowest Common Ancestor by TaxIds (lca)
gtaxon cli remote -t lca 9606,63221
[INFO] Query LCA by TaxIds from host: 127.0.0.1:8080
Query TaxIDs: 9606,63221
Taxon: {
"TaxId": 9606,
"ScientificName": "Homo sapiens",
"OtherNames": [
{
"ClassCDE": "authority",
"DispName": "Homo sapiens Linnaeus, 1758"
},
{
"ClassCDE": "genbank common name",
"DispName": "human"
},
{
"ClassCDE": "common name",
"DispName": "man"
}
],
"ParentTaxId": 9605,
"Rank": "species",
"Division": "Primates",
"GeneticCode": {
"GCId": 1,
"GCName": "Standard"
},
"MitoGeneticCode": {
"MGCId": 2,
"MGCName": "Vertebrate Mitochondrial"
},
"Lineage": "cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Euarchontoglires; Primates; Haplorrhini; Simiiformes; Catarrhini; Hominoidea; Hominidae; Homininae; Homo",
"LineageEx": [
{
"TaxId": 131567,
"ScientificName": "cellular organisms",
"Rank": "no rank"
},
{
"TaxId": 2759,
"ScientificName": "Eukaryota",
"Rank": "superkingdom"
},
{
"TaxId": 33154,
"ScientificName": "Opisthokonta",
"Rank": "no rank"
},
{
"TaxId": 33208,
"ScientificName": "Metazoa",
"Rank": "kingdom"
},
{
"TaxId": 6072,
"ScientificName": "Eumetazoa",
"Rank": "no rank"
},
{
"TaxId": 33213,
"ScientificName": "Bilateria",
"Rank": "no rank"
},
{
"TaxId": 33511,
"ScientificName": "Deuterostomia",
"Rank": "no rank"
},
{
"TaxId": 7711,
"ScientificName": "Chordata",
"Rank": "phylum"
},
{
"TaxId": 89593,
"ScientificName": "Craniata",
"Rank": "subphylum"
},
{
"TaxId": 7742,
"ScientificName": "Vertebrata",
"Rank": "no rank"
},
{
"TaxId": 7776,
"ScientificName": "Gnathostomata",
"Rank": "no rank"
},
{
"TaxId": 117570,
"ScientificName": "Teleostomi",
"Rank": "no rank"
},
{
"TaxId": 117571,
"ScientificName": "Euteleostomi",
"Rank": "no rank"
},
{
"TaxId": 8287,
"ScientificName": "Sarcopterygii",
"Rank": "no rank"
},
{
"TaxId": 1338369,
"ScientificName": "Dipnotetrapodomorpha",
"Rank": "no rank"
},
{
"TaxId": 32523,
"ScientificName": "Tetrapoda",
"Rank": "no rank"
},
{
"TaxId": 32524,
"ScientificName": "Amniota",
"Rank": "no rank"
},
{
"TaxId": 40674,
"ScientificName": "Mammalia",
"Rank": "class"
},
{
"TaxId": 32525,
"ScientificName": "Theria",
"Rank": "no rank"
},
{
"TaxId": 9347,
"ScientificName": "Eutheria",
"Rank": "no rank"
},
{
"TaxId": 1437010,
"ScientificName": "Boreoeutheria",
"Rank": "no rank"
},
{
"TaxId": 314146,
"ScientificName": "Euarchontoglires",
"Rank": "superorder"
},
{
"TaxId": 9443,
"ScientificName": "Primates",
"Rank": "order"
},
{
"TaxId": 376913,
"ScientificName": "Haplorrhini",
"Rank": "suborder"
},
{
"TaxId": 314293,
"ScientificName": "Simiiformes",
"Rank": "infraorder"
},
{
"TaxId": 9526,
"ScientificName": "Catarrhini",
"Rank": "parvorder"
},
{
"TaxId": 314295,
"ScientificName": "Hominoidea",
"Rank": "superfamily"
},
{
"TaxId": 9604,
"ScientificName": "Hominidae",
"Rank": "family"
},
{
"TaxId": 207598,
"ScientificName": "Homininae",
"Rank": "subfamily"
},
{
"TaxId": 9605,
"ScientificName": "Homo",
"Rank": "genus"
}
]
}
## Configuration file for Convenience
Default config file is: `$HOME/.gtaxon.yaml`
This is useful when querying from remote server,
we could type few words by saving flags like host and port to config file.
See https://github.com/ogier/pflag
## REST APIs
1. gi2taxid
http://127.0.0.1:8080/gi2taxid?db=gi_taxid_prot&gi=139299191111&gi=139299181&gi=139299175
2. name2taxid
http://localhost:8080/name2taxid?regexp=true&class=genbank+common+name&name=human&name=mouse
3. taxid2taxon
http://localhost:8080/taxid2taxon?taxid=9906&taxid=2
4. lca
http://localhost:8080/lca?taxids=9606,63221&taxids=1,2
You can also write client in your favorite programming language.
## Implement details
API reference: [godoc](https://godoc.org/github.com/shenwei356/gtaxon/taxon)
- Programming language: [Go](https://golang.org)
- Database: [bolt](https://github.com/boltdb/bolt), an embedded key/value database for Go
- Web server: [gin](https://github.com/gin-gonic/gin), a fast HTTP web framework written in Go
## Caveats
- 64bit operating system is better.
- `bolt` database utilizes the operating system's page cache, larger virtual memory is better.
- Database file size is 16G after loading gi_taxid_prot.dmp.gz
- About 1.5G RAM usage after starting server