BrEPS command line tool

The BrEPS command line tool (BrEPScmd) can be used to search a local copy of the database. The tool needs either Python2 or Python 3 to run.

For MySQL usage, mysqlclient for Python is recommended, as it can be used with Python2 and Python3. For Python2 MySQLdb is suitable. For SQLite, Python comes with sqlite3. Obviously MySQL or SQLite needs to be installed as well.

For best performance, Python2 with Googles re2 module is recommended!

Basic usage

By default, the program searches for the brepsdb.db SQLite database in the same directory. The most basic example would be:

> python -i sequences.fasta

where sequences.fasta is a file containing sequences in FASTA format. The output will be printed into the command line.

> python -i sequences.fasta -o results.csv

would create the file results.csv in the current directory with the search results.

For a full overview of all supported arguments, use python -h.

Tool development with BrEPScmd

BrEPScmd can be used for tool development. A full documentation of all functions provided by BrEPScmd can be found in the download section: