Models (dasi.models)

This module provides representations of Molecules and Molecular Assemblies.

Assembly(nodes, container, …[, do_raise])	Should take in a path, graph, container, seqdb to produce relevant information.
AssemblyNode(index, expandable, type, overhang)	tuple representing a location on a goal sequence
Molecule(molecule_type, alignment_group, …)	An instance of a molecule type, with a sequence and which alignments are assigned to it.
MoleculeType(name, design, use_direct, cost)	Molecule metatype.
Reaction(name, inputs, outputs[, metadata])	An activity that takes in several Molecules and produces other Molecules.
Alignment(query_region, subject_region, …)	A pair of Regions that ‘aligns’ two regions of DNA sequences.
AlignmentGroup(alignments, group_type[, …])	A representative Alignment representing a group of alignments sharing the same starting and ending position for a query sequence.
AlignmentGroupBase(alignments, group_type[, …])	A representative Alignment representing a group of alignments.
MultiPCRProductAlignmentGroup(groupings, …)	A PCR Product Alignment with redundant forward primer, reverse primer, and template alignments.
PCRProductAlignmentGroup(fwd, template, rev, …)	Represents a PCR product alignment from a template alignment and forward and reverse alignments.
AlignmentContainer(seqdb[, alignments])	Container for a set of query-to-subject alignments for a single query.
AlignmentContainerFactory(seqdb)	Class that maintains a shared list of alignments and shared sequence database.

modules

assembly	Assembly.
molecule	classes representing molecules and types of molecules
alignment	Alignments.
alignment_container	Alignment container.