DELi Configuration

DELi uses a .deli config file to control some of its more advanced settings. To avoid arbitrary code execution, DELi does not initialize the config file when installed via pip. Instead it will create one the first time you every use DELi (and it will raise a warning to let you know it did so). You can also create one yourself using deli config init. A valid DELi config file is required for DELi to run or be imported. DELi will raise a DELiConfigError if it detects something wrong with the config file.

Note

Any settings that might impact the outcome of a DELi command (like deli decode) are not part of the config file. The config file if for settings related to how DELi outputs data, where it looks for files, and defining mappings.

File Format

The config file follows the config (.ini) format, with sections and key-value pairs. DELi looks for a handful of sections:

  • deli.data: holds settings related to the DELi Data Directory

  • deli.buildingblocks: holds settings related to how to handle building blocks

  • deli.hamming: holds settings related to hamming encoding/decoding

Warning

The config file is case sensitive.

deli.data

This section has only one key: deli_data_dir. This is the path to the DELi Data Directory. This is the default location DELi will look for your DELi data files. All other methods of setting the DELi Data Directory (like with the ENV variable or the set_deli_data_dir function) will override this setting.

deli.buildingblocks

This section has only one key: bb_mask. This is the token DELi will use when masking building blocks. This happens during things like Di/Monosynthon ID creation, where specific cycles are aggregated (and then masked). The default is “###”.

. _deli-config-hamming-section

deli.hamming

This section has one key: nuc_2_int. This is the mapping of nucleotide to integer values Hamming encoding/decoding happens using quaternary number space, thus must first covert the DNA into the numbers 0, 1, 2, and 3. How this is done must be the same for encoding and decoding. If you used a specific mapping when encoding, you must use the same mapping when decoding and this is how you tell DELi to change that. The default is A:0,T:1,C:2,G:3.

Note

The nuc_2_int mapping is only used for Hamming encoding/decoding using a hamming matrix. If you are using the “random” decoding method, this setting is not used.

The hamming section also has an infinite number of sub sections, with each being the name of a specific hamming matrix. These follow the naming convention deli.hamming.<NAME>. They each have to keys to fill out: hamming_order and custom_order. You can read more about how this works in the custom hamming docs.

Warning

The “:” character is reserved for the error correction parser, thus DELi will not allow the use of it in the names of hamming matrices. If you try to use it, DELi will raise a DELiConfigError.