Sequentially Blast every fasta file (.faa or .fas) on a folder against a local database
- Python 2.7
- Blast+ executables (https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download)
- Linux (tested and developed on Ubuntu 14.0.4, but will most likely work on WINDOWS and MAC too)
- Organize your files as follows on a folder:
- MultiBLAST.py
- database files (obtained via makeblast, with
makeblastdb -in [yourGenes].pfasta -dbtype prot) - folder with fasta files (.faa or .fas) to blast (must be the only existing folder in the directory)
- Run MultiBLAST.py from the command-line as follows
python MultiBLAST.py [-t [#]] - For more help, type
python MultiBLAST.py -h
I developed this script to help me with a project I was involved in. As much as I tried to make it work on many different scenarios, it is still probably biased to work with the files I was using. Nevertheless, it should work fine for protein blasts. If you want to call more blast+ parameters, edit the variable standard_blast inside the loop_blast function.