MultiBLAST

Sequentially Blast every fasta file (.faa or .fas) on a folder against a local database

Dependencies

• 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)

How to run

• 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

Note

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.