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
sqlite3. Obviously MySQL or SQLite needs to be installed as well.
For best performance, Python2 with Googles re2 module is recommended!
By default, the program searches for the
brepsdb.db SQLite database in the same
directory. The most basic example would be:
> python brepscmd.py -i sequences.fasta
sequences.fasta is a file containing sequences in FASTA format. The output
will be printed into the command line.
> python brepscmd.py -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 brepscmd.py -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: