https://github.com/ibchgenomic/bacdive
bacdive microbial genotypes genomeinformatics
https://github.com/ibchgenomic/bacdive
bacdive bioinformatics dsmz metagenomes microbial-genomes microbial-genomics webpack
Last synced: 2 months ago
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bacdive microbial genotypes genomeinformatics
- Host: GitHub
- URL: https://github.com/ibchgenomic/bacdive
- Owner: IBCHgenomic
- License: mit
- Created: 2025-01-17T19:13:59.000Z (4 months ago)
- Default Branch: main
- Last Pushed: 2025-03-07T17:00:10.000Z (2 months ago)
- Last Synced: 2025-03-11T23:15:32.935Z (2 months ago)
- Topics: bacdive, bioinformatics, dsmz, metagenomes, microbial-genomes, microbial-genomics, webpack
- Language: Rust
- Homepage:
- Size: 6.83 MB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# bacdive
- This analyses the isolates table from the [BacDive](https://bacdive.dsmz.de/) and return json for the rest api.
- All bacdive tools merged today into a single restapi.
- please see the last commit message and if it says compiled binary then it is completed or else still in development version.
```
cargo build
```
```
gauravsablok@genome bacdive main ? ./target/debug/bacdive -h
analyses bacdive data for local analysis
Usage: bacdive
Commands:
id
species please provide the species that need to be searched
strain please provide the category2 that you want to look,
id-list this will list all the available unique ids present in the bacdive
species-list this will list all the unique species present in the bacdive
strainlist this will list all the available countries in the bacdive
id-list-analyze present the list of the unique ids present
species-list-analyze provide the species present in the bacdive
designation-list provide the designation header present in the bacdive
strain-number-list provide the strain number present in the bacdive
strainheader-list provide the strain header present in the bacdive
id-search search for the specific id and json output
species-search search for the specific species and json output
designation-search search for the specific designation and json output
strain-search search for the specific strain and json output
help Print this message or the help of the given subcommand(s)
Options:
-h, --help Print help
-V, --version Print version
```
- to get the subcommand
```
➜ bacdive git:(main) ✗ ./target/debug/bacdive id ./sample-file/bacdive-2025-01-17.csv 159652
The ids are: [BacdiveSpeciesJson { id: "159652", species: "Abditibacterium utsteinense", strain: "DSM 105287", information: " LMG 29911,Top surface sample consisting of weathered granite parent material, elevation 1382 m,Antarctica,Australia and Oceania,Environmental,Terrestrial,Geologic" }, BacdiveSpeciesJson { id: "159652", species: "same species", strain: "same strain", information: ",,,,,Climate,Cold,Alpine" }]
➜ bacdive git:(main) ✗ ./target/debug/bacdive species ./sample-file/bacdive-2025-01-17.csv Actinocatenispora-thailandica
The species and the associated information are: [BacdiveSpeciesJson { id: "7795", species: "Actinocatenispora thailandica", strain: "DSM 44816", information: " JCM 12343, PCU 235, BCRC 16831, CGMCC 4.5560, CIP 109347, NBRC 105041, NCIMB 14320,Environment, Soil, peat swamp forrestPeat swamp forest soilsoil,Thailand,Asia,Environmental,Terrestrial,Soil" }, BacdiveSpeciesJson { id: "161217", species: "Actinocatenispora thailandica", strain: "JCM 12344", information: " PCU 236,Peat swamp forest soil,Thailand,Asia,,," }]
➜ bacdive git:(main) ✗ ./target/debug/bacdive strain ./sample-file/bacdive-2025-01-17.csv DSM17304
The strain specific information are as follows:[BacdiveSpeciesJson { id: "268", species: "Aeromonas tecta", strain: "DSM 17304", information: "tap water,Switzerland,Europe,Engineered,Built environment," }]
```
Gaurav Sablok