blastadmin is a command wrapper which enables users to run multiple similarity search software in a same interface.
- For those who are overwhelmed with thousands of similarity search commands which are slightly different each other.
-> blastadmin provides you a simple wrapped interface! - For those who are tired of remembering and specifying long filepath to the database every time you run a search.
-> blastadmin enables you to specify database by a unique identifier you assign, such as "nr"! - For those who want to cache search results and save computer resources.
-> blastadmin keeps track of the search history and runs a search only when needed!
- Python3.*
- sqlite3
git clone https://github.com/MitsukiUsui/blastadmin.git
cd blastadmin
sqlite3 blastadmin.sq3 < ./src/schema.sql
echo "export PATH=$PWD":'$PATH' >> ~/.bash_profile
echo "export BLASTADMIN_DATA=/path/to/data/directory/you/want" >> ~/.bash_profile
blastadmin.py has 3 types of subcommands, that is wget/cp, createdb, and search. You can run similarity search with search command whatever software you are using in the backend.
Here is a simple example with blastn search against genome of E.coli.
blastadmin.py wget ecoli-genome ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/005/845/GCF_000005845.2_ASM584v2/GCF_000005845.2_ASM584v2_genomic.fna.gz
blastadmin.py createdb blastn ecoli-genome
blastadmin.py search blastn ecoli-genome ./demo/query.fna ./result.tsv
First, you need to register a FASTA file to blastadmin by wget/cp with a unique identifier you provide. wget will automatically uncompress .gz file.
blastadmin.py wget <id> <ftp address>
blastadmin.py cp <id> <local filepath>
Second, you create a database with the FASTA you registered. This command will execute ./bin/<software>/createdb.sh inside. Actually, you don't need to explicitly call this command because search will call createdb first if the database is yet to be created or outdated.
blastadmin.py createdb <software> <id>
Last, you run similarity search with the database you created. This command will execute ./bin/<software>/search.sh inside.
blastadmin.py search <software> <id> <query> <result>