Alhambra File Format

Introduction

Alhambra uses a unified, YAML-based file format for both its input and output, and for describing tile systems from an abstract level to an experiment-ready sequence level.

This format can be written and modified by hand, and can also be generated and modified through Alhambra or other programmatic methods. Alhambra uses ruamel.yaml for loading and saving YAML files, which should result in comments being preserved.

Alhambra’s file format is currently designed to store the following information:

• Tile descriptions (name, structure, labels, sticky ends, sequences, etc)
• End descriptions (name, type, orientation, sequence)
• Origami seed descriptions (type, adapters)
• Xgrow parameters
• Generation information (sequence design parameters for ends, tiles, etc - a log of what Alhambra has done)

Other information can easily be added by adding extra key/value pairs.

The top level of the YAML file should be a mapping. Alhambra recognizes the following key/value pairs:

• tiles: a list of tiles
• ends: a list of sticky ends
• seed: a mapping describing the seed
• info: a mapping of system information
• guards: a list of guard strands and sequences
• xgrow_params: (or xgrow_options) a mapping of xgrow options

tiles

The value attached to the tile key should be a YAML sequence. Each sequence item should be a mapping, with the following keys recognized by Alhambra:

• name: (required, or one will be generated by Alhambra) the name of the tile. This should be a name that is compatible with peppercompiler’s component naming restrictions.
• structure: (required) a name of a TileStructure class describing the tile’s structure. Eg ‘tile_daoe_3up’.
• ends: a YAML sequence of end names. Complements should be indicated with / at the end of the name.
• label: a label option for the TileStructure, describing what label should be used, if any. At the moment, the only option most structures recognize is ‘both’, which puts two biotinylated Ts in the middle of the tile.
• color: a color for Xgrow and diagrams FIXME.
• strands (or fullseqs): a YAML sequence of strand sequence strings. Usually generated by Alhambra.

ends

The value attached to the ends jey should be a YAML sequence. Each sequence item should be mapping, with the following keys recognized by Alhambra:

• name: (required) the name of the end.
• type: the end type, as in Stickydesign, usually TD (5’ is terminal, 3’ attaches to tile), DT (5’ continues to tile, 3’ is terminal).
• fseq: The full (end plus adjacent base and complement of the complement’s adjacent base) sequence of the end, usually generated by Alhambra.

seed

• type
• adapters
• use_adapters

guards

info

• reorder
• core
• end_design