Install

See the README

Getting help

Github

reporting issues

Script docs

• Help for CLdb command:
  • CLdb -h
• Help for CLdb subcommands:
  • CLdb -- subcommand -h OR CLdb --perldoc -- subcommand
  • Example:
    • CLdb --perldoc -- array2fasta
• Help for CLdb sub-subcommands:
  • CLdb -- subcommand -- subsubcommand -h
  • OR CLdb -- subcommand --perldoc -- subsubcommand
    • NOTE: --perldoc flag used after the subcommand
  • Example:
    • CLdb -- arrayBlast --perldoc -- run

Examples

• Some E. coli genomes

Running CLdb in Jupyter notebooks

• The example notebooks use a combination of python and bash.
• bash commands start with "!".
  • CLdb commands are run through bash.
    • Example: !CLdb -h
• The working directory is always set to the notebook directory for each cell in the notebook.
  • Therefore, I have to change to the directory of interest before running the CLdb command.

• Example CLdb command:

  workDir = '/home/nick/path/to/CLdb/'
  !cd $workDir; CLdb -- makeDB

  • This code sets the working directory and runs the CLdb command in that directory
• Another example:

  myDir = '/home/sue/path/to/blast/dir/'
  !cd $myDir; CLdb -- array2fasta -- -da CLdb.sqlite -clust -cut 1 > spacers_cut1.fna