- Bacdive:Added a complete new webminer and submitting for publication. A complete RUST async analyzer for bacdive database.
- This analyses the isolates table from the BacDive.
- Now this is a complete API RUST based for the BacDive and analyzes all of them asynchronously.
cargo build
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analyses bacdive data for local analysis.
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Gaurav Sablok
Email: [email protected]
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Usage: bacdive <COMMAND>
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
web-mine get webmine results from the bacdive
help Print this message or the help of the given subcommand(s)
Options:
-h, --help Print help
-V, --version Print version
- Example usage of the bacdive:
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 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 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," }]
bacdive id-list ./sample-file/bacdive-2025-01-17.csv
bacdive species-list ./sample-file/bacdive-2025-01-17.csv
bacdive id-list-analyze ./sample-file/bacdive-2025-01-17.csv
bacdive species-list-analyze ./sample-file/advsearch_bacdive_2025-01-20.csv
bacdive designation-list ./sample-file/advsearch_bacdive_2025-01-20.csv
bacdive strain-number-list ./sample-file/advsearch_bacdive_2025-01-20.csv
bacdive strainheader-list ./sample-file/advsearch_bacdive_2025-01-20.csv
- Web miner
bacdive web-mine 159652
Strain identifier
BacDive ID: -159652
Type strain:
Species: -Abditibacterium utsteinense
Strain Designation: -R-68213
Culture col. no.: -DSM 105287-, -LMG 29911
Strain history: -<- A. Willems, Lab. Microbiology, Ghent Univ., Belgium <- G. Tahon, Laboratory of Microbiology, Ghent University, Gent, Belgium
NCBI tax ID(s): -1960156 (species)
The command has finished:The webmine results are as follows
Gaurav Sablok [email protected]