Index

_

__init__() (dasi.design.Design method) (dasi.design.DesignResult method) (dasi.design.LibraryDesign method) (dasi.models.Alignment method), [1] (dasi.models.AlignmentContainer method) (dasi.models.AlignmentContainerFactory method) (dasi.models.AlignmentGroup method) (dasi.models.AlignmentGroupBase method) (dasi.models.AssemblyNode method) (dasi.models.MoleculeType method) (dasi.models.MultiPCRProductAlignmentGroup method) (dasi.models.PCRProductAlignmentGroup method) (dasi.models.Reaction method) _alignment_hash() (dasi.models.alignment_container.AlignmentContainer static method) (dasi.models.AlignmentContainer static method) _asdict() (dasi.models.assembly.AssemblyNode method), [1] (dasi.models.AssemblyNode method) _check_paths() (in module dasi.design.optimize) _create_pcr_product_alignment() (dasi.models.alignment_container.AlignmentContainer method) (dasi.models.AlignmentContainer method)

_design_primers() (in module dasi.models.assembly), [1] _expand_from_synthesized() (dasi.design.LibraryDesign method) _expand_synthesized_fragments() (dasi.design.LibraryDesign method) _get_primer_extensions() (in module dasi.models.assembly), [1] _get_span_cost() (dasi.command_line.DasiCLI method) _head() (dasi.models.assembly.Assembly method), [1] _make() (dasi.models.assembly.AssemblyNode class method), [1] (dasi.models.AssemblyNode class method) _make_subgroup() (dasi.models.alignment_container.AlignmentContainer method) (dasi.models.AlignmentContainer method) _multinode_to_shortest_path() (in module dasi.design.optimize) _nodes_to_fullpaths() (in module dasi.design.optimize) _optimize() (dasi.design.Design method) (dasi.design.LibraryDesign method) _replace() (dasi.models.assembly.AssemblyNode method), [1] (dasi.models.AssemblyNode method) _run() (dasi.design.Design method) (dasi.design.LibraryDesign method) _share_query_blast() (dasi.design.LibraryDesign method)

A

a() (dasi.utils.region.EmptySpan property) (dasi.utils.region.Region property) (dasi.utils.region.Span property) add_assemblies() (dasi.design.DesignResult method) add_assembly() (dasi.design.DesignResult method) add_fragments() (dasi.design.Design method) (dasi.design.LibraryDesign method) add_gap_edge() (dasi.design.graph_builder.AssemblyGraphBuilder method) add_internal_edges() (dasi.design.graph_builder.AssemblyGraphBuilder method) add_node() (dasi.design.graph_builder.AssemblyGraphBuilder method) add_primers() (dasi.design.Design method) (dasi.design.LibraryDesign method) add_queries() (dasi.design.Design method) (dasi.design.LibraryDesign method) add_templates() (dasi.design.Design method) (dasi.design.LibraryDesign method) aggregate() (dasi.utils.npdf.NumpyDataFrame method) Alignment (class in dasi.models), [1] AlignmentContainer (class in dasi.models) (class in dasi.models.alignment_container)

AlignmentContainerException AlignmentContainerFactory (class in dasi.models) (class in dasi.models.alignment_container) AlignmentException AlignmentGroup (class in dasi.models) AlignmentGroupBase (class in dasi.models) alignments() (dasi.models.alignment_container.AlignmentContainerFactory property) (dasi.models.AlignmentContainerFactory property) append() (dasi.utils.npdf.NumpyDataFrame method) apply() (dasi.utils.npdf.NumpyDataFrame method) apply_to_col_names() (dasi.utils.npdf.NumpyDataFrame method) assemble_graphs() (dasi.design.Design method) (dasi.design.LibraryDesign method) assemblies() (dasi.design.DesignResult property) Assembly (class in dasi.models.assembly), [1] AssemblyGraphBuilder (class in dasi.design.graph_builder) AssemblyGraphPostProcessor (class in dasi.design.graph_builder) AssemblyNode (class in dasi.models) (class in dasi.models.assembly), [1]

B

b() (dasi.utils.region.EmptySpan property) (dasi.utils.region.Region property) (dasi.utils.region.Span property) batch_add_edge_costs() (dasi.design.graph_builder.AssemblyGraphBuilder static method) bisect_between() (in module dasi.utils), [1]

bisect_slice_between() (in module dasi.utils), [1] blast_to_region() (in module dasi.models.alignment_container) bounds() (dasi.utils.region.EmptySpan method) (dasi.utils.region.Region method) (dasi.utils.region.Span method)

C

c() (dasi.utils.region.EmptySpan property) (dasi.utils.region.Region property) (dasi.utils.region.Span property) clean_alignments() (dasi.models.alignment_container.AlignmentContainer method) (dasi.models.AlignmentContainer method) col() (dasi.utils.npdf.NumpyDataFrame property) columns() (dasi.utils.npdf.NumpyDataFrame property) compile() (dasi.design.Design method) (dasi.design.LibraryDesign method) concat() (dasi.utils.npdf.NumpyDataFrame class method) connecting_span() (dasi.utils.region.EmptySpan method) (dasi.utils.region.Region method) (dasi.utils.region.Span method) consecutive() (dasi.utils.region.EmptySpan method) (dasi.utils.region.Region method) (dasi.utils.region.Span method) Constants (class in dasi.constants) container_list() (dasi.design.Design property) (dasi.design.LibraryDesign property) containers() (dasi.design.Design property) (dasi.design.LibraryDesign property) (dasi.models.alignment_container.AlignmentContainerFactory method) (dasi.models.AlignmentContainerFactory method)

contains_pos() (dasi.utils.region.EmptySpan method) (dasi.utils.region.Region method) (dasi.utils.region.Span method) contains_span() (dasi.utils.region.EmptySpan method) (dasi.utils.region.Region method) (dasi.utils.region.Span method) context_length() (dasi.utils.region.EmptySpan property) (dasi.utils.region.Region property) (dasi.utils.region.Span property) copy() (dasi.models.Alignment method), [1] (dasi.utils.npdf.NumpyDataFrame method) copy_groups() (dasi.models.alignment_container.AlignmentContainer method) (dasi.models.AlignmentContainer method) count() (dasi.models.assembly.AssemblyNode method), [1] (dasi.models.AssemblyNode method) create_edge() (dasi.design.graph_builder.AssemblyGraphBuilder method) cyclic() (dasi.utils.region.EmptySpan property) (dasi.utils.region.Region property) (dasi.utils.region.Span property)

D

dasi.command_line (module) dasi.constants (module) dasi.cost (module) dasi.cost.utils (module) dasi.design (module), [1] dasi.design.graph_builder (module) dasi.design.optimize (module) dasi.exceptions (module) dasi.models (module) dasi.models.alignment_container (module) dasi.models.assembly (module), [1] dasi.models.molecule (module), [1] dasi.utils (module), [1] dasi.utils.networkx (module) dasi.utils.networkx.exceptions (module) dasi.utils.networkx.shortest_path (module) dasi.utils.networkx.utils (module) dasi.utils.npdf (module) dasi.utils.region (module)

DasiCLI (class in dasi.command_line) DasiCostParameterValidationError DasiDesignException DASiException DasiInvalidMolecularAssembly DasiNoPrimerPairsException DasiOutputValidationError DasiSequenceDesignException DASiWarning data() (dasi.utils.npdf.NumpyDataFrame property) Design (class in dasi.design) DesignResult (class in dasi.design) df_to_np_ranged() (in module dasi.cost.utils) differences() (dasi.utils.region.EmptySpan method) (dasi.utils.region.Region method) (dasi.utils.region.Span method) divide() (in module dasi.utils.networkx.utils) dump() (dasi.utils.npdf.NumpyDataFrame method) dumps() (dasi.utils.npdf.NumpyDataFrame method) duplicates() (in module dasi.cost.utils)

E

EmptySpan (class in dasi.utils.region) expand() (dasi.models.alignment_container.AlignmentContainer method) (dasi.models.AlignmentContainer method) expand_overlaps() (dasi.models.alignment_container.AlignmentContainer method) (dasi.models.AlignmentContainer method)

expand_primer_pairs() (dasi.models.alignment_container.AlignmentContainer method) (dasi.models.AlignmentContainer method) expandable (dasi.models.assembly.AssemblyNode attribute), [1] (dasi.models.AssemblyNode attribute) ExternalType (class in dasi.models.molecule), [1]

F

fill_value() (dasi.utils.npdf.NumpyDataFrame method) filter_linear_records() (dasi.design.Design class method) (dasi.design.LibraryDesign class method) filter_perfect_subject() (dasi.design.Design class method) (dasi.design.LibraryDesign class method) find_groups_by_pos() (dasi.models.alignment_container.AlignmentContainer method) (dasi.models.AlignmentContainer method)

flatten_axis() (in module dasi.cost.utils) flip() (dasi.utils.region.Region method) force_context() (dasi.utils.region.EmptySpan method) (dasi.utils.region.Region method) (dasi.utils.region.Span method) FRAGMENT (dasi.constants.Constants attribute) freeze() (dasi.models.alignment_container.AlignmentContainer method) (dasi.models.AlignmentContainer method)

G

GAP (dasi.constants.Constants attribute) get() (dasi.utils.npdf.NumpyDataFrame method) (dasi.utils.npdf.NumpyDataFrameIndexer method) get_fwd() (dasi.models.MultiPCRProductAlignmentGroup method) get_groups_by_types() (dasi.models.alignment_container.AlignmentContainer method) (dasi.models.AlignmentContainer method) get_rev() (dasi.models.MultiPCRProductAlignmentGroup method) get_slice() (dasi.utils.region.EmptySpan method) (dasi.utils.region.Region method) (dasi.utils.region.Span method)

get_slice_iter() (dasi.utils.region.EmptySpan method) (dasi.utils.region.Region method) (dasi.utils.region.Span method) get_template() (dasi.models.MultiPCRProductAlignmentGroup method) group_apply() (dasi.utils.npdf.NumpyDataFrame class method) group_by() (in module dasi.utils), [1] groups_by_type() (dasi.models.alignment_container.AlignmentContainer method) (dasi.models.AlignmentContainer method)

H

hstack() (dasi.utils.npdf.NumpyDataFrame class method)

I

i() (dasi.utils.region.EmptySpan method) (dasi.utils.region.Region method) (dasi.utils.region.Span method) index (dasi.models.assembly.AssemblyNode attribute), [1] (dasi.models.AssemblyNode attribute) index() (dasi.utils.region.EmptySpan property) (dasi.utils.region.Region property) (dasi.utils.region.Span property) index_slice() (in module dasi.design.optimize) INF (dasi.constants.Constants attribute) inputs (dasi.models.molecule.Reaction attribute), [1] (dasi.models.Reaction attribute)

InternalType (class in dasi.models.molecule), [1] intersection() (dasi.utils.region.EmptySpan method) (dasi.utils.region.Region method) (dasi.utils.region.Span method) invert() (dasi.utils.region.EmptySpan method) (dasi.utils.region.Region method) (dasi.utils.region.Span method) is_compiled() (dasi.design.Design property) (dasi.design.LibraryDesign property) items() (dasi.utils.npdf.NumpyDataFrame method) (dasi.utils.npdf.NumpyDataFrameIndexer method) iter_templates() (dasi.models.MultiPCRProductAlignmentGroup method)

K

keys() (dasi.utils.npdf.NumpyDataFrame method) (dasi.utils.npdf.NumpyDataFrameIndexer method)

L

LibraryDesign (class in dasi.design) load() (dasi.utils.npdf.NumpyDataFrame class method) load_blast_json() (dasi.models.alignment_container.AlignmentContainerFactory method) (dasi.models.AlignmentContainerFactory method)

loads() (dasi.utils.npdf.NumpyDataFrame class method) log_metadata() (in module dasi.utils), [1] log_times() (in module dasi.utils), [1]

M

make_gap_iterator() (dasi.design.graph_builder.AssemblyGraphBuilder static method) make_overlap_iterator() (dasi.design.graph_builder.AssemblyGraphBuilder static method) merge() (dasi.utils.npdf.NumpyDataFrame class method) MISSING (dasi.constants.Constants attribute)

Molecule (class in dasi.models.molecule), [1] MoleculeType (class in dasi.models) (class in dasi.models.molecule), [1] MultiPCRProductAlignmentGroup (class in dasi.models) multipoint_shortest_path() (in module dasi.utils.networkx.shortest_path)

N

NetworkxUtilsException new() (dasi.utils.region.EmptySpan method) (dasi.utils.region.Region method) (dasi.utils.region.Span method)

Null (class in dasi.utils.npdf) NumpyDataFrame (class in dasi.utils.npdf) NumpyDataFrameException NumpyDataFrameIndexer (class in dasi.utils.npdf)

O

optimize_partition() (dasi.design.graph_builder.AssemblyGraphPostProcessor static method) out() (dasi.design.Design method) (dasi.design.LibraryDesign method) out_jsonschema() (dasi.design.Design method) (dasi.design.LibraryDesign method) outputs (dasi.models.molecule.Reaction attribute), [1] (dasi.models.Reaction attribute)

overhang (dasi.models.assembly.AssemblyNode attribute), [1] (dasi.models.AssemblyNode attribute) OVERLAP (dasi.constants.Constants attribute) overlaps_with() (dasi.utils.region.EmptySpan method) (dasi.utils.region.Region method) (dasi.utils.region.Span method)

P

PCR_PRODUCT (dasi.constants.Constants attribute) PCR_PRODUCT_WITH_LEFT_PRIMER (dasi.constants.Constants attribute) PCR_PRODUCT_WITH_PRIMERS (dasi.constants.Constants attribute) PCR_PRODUCT_WITH_RIGHT_PRIMER (dasi.constants.Constants attribute) PCRProductAlignmentGroup (class in dasi.models) perfect_subject() (in module dasi.utils), [1] PLASMID (dasi.constants.Constants attribute)

prefix() (dasi.utils.npdf.NumpyDataFrame method) PRIMER (dasi.constants.Constants attribute) PRIMER_EXTENSION_PRODUCT_WITH_LEFT_PRIMER (dasi.constants.Constants attribute) PRIMER_EXTENSION_PRODUCT_WITH_PRIMERS (dasi.constants.Constants attribute) PRIMER_EXTENSION_PRODUCT_WITH_RIGHT_PRIMER (dasi.constants.Constants attribute) prioritize_alignments() (dasi.models.AlignmentGroup method) prioritize_groupings() (dasi.models.MultiPCRProductAlignmentGroup method)

Q

query_key() (dasi.models.AlignmentGroup property) (dasi.models.AlignmentGroupBase property) (dasi.models.MultiPCRProductAlignmentGroup property) (dasi.models.PCRProductAlignmentGroup property)

query_keys() (dasi.design.Design property) (dasi.design.LibraryDesign property)

R

ranges() (dasi.utils.region.EmptySpan method) (dasi.utils.region.Region method) (dasi.utils.region.Span method) Reaction (class in dasi.models) (class in dasi.models.molecule), [1] redundent_alignment_groups() (dasi.models.alignment_container.AlignmentContainer class method) (dasi.models.AlignmentContainer class method)

Region (class in dasi.utils.region) reindex() (dasi.utils.region.EmptySpan method) (dasi.utils.region.Region method) (dasi.utils.region.Span method) reindex_alignments() (dasi.models.AlignmentGroup method) reindex_groupings() (dasi.models.MultiPCRProductAlignmentGroup method) reshape() (dasi.utils.npdf.NumpyDataFrame method) run() (dasi.command_line.DasiCLI method)

S

same_context() (dasi.utils.region.EmptySpan method) (dasi.utils.region.Region method) (dasi.utils.region.Span method) score_complexity_edges() (dasi.design.graph_builder.AssemblyGraphPostProcessor method) select_from_arrs() (in module dasi.utils.networkx.utils) shape() (dasi.utils.npdf.NumpyDataFrame property) SHARED_FRAGMENT (dasi.constants.Constants attribute) SHARED_SYNTHESIZED_FRAGMENT (dasi.constants.Constants attribute) size_ok() (dasi.models.Alignment method), [1] (dasi.models.AlignmentGroup method) (dasi.models.AlignmentGroupBase method) (dasi.models.MultiPCRProductAlignmentGroup method) (dasi.models.PCRProductAlignmentGroup method) slices() (dasi.utils.region.EmptySpan method) (dasi.utils.region.Region method) (dasi.utils.region.Span method) sort_cycle() (in module dasi.utils.networkx.utils) sort_with_keys() (in module dasi.utils), [1] Span (class in dasi.utils.region) SpanError square_broadcast() (in module dasi.cost.utils)

stack() (dasi.utils.npdf.NumpyDataFrame class method) status() (dasi.design.Design property) (dasi.design.LibraryDesign property) sub() (dasi.utils.region.EmptySpan method) (dasi.utils.region.Region method) (dasi.utils.region.Span method) sub_region() (dasi.models.Alignment method), [1] (dasi.models.AlignmentGroup method) (dasi.models.AlignmentGroupBase method) (dasi.models.MultiPCRProductAlignmentGroup method) (dasi.models.PCRProductAlignmentGroup method) subject_keys() (dasi.models.AlignmentGroup property) (dasi.models.AlignmentGroupBase property) (dasi.models.MultiPCRProductAlignmentGroup property) (dasi.models.PCRProductAlignmentGroup property) subject_regions() (dasi.models.AlignmentGroup property) (dasi.models.AlignmentGroupBase property) (dasi.models.MultiPCRProductAlignmentGroup property) (dasi.models.PCRProductAlignmentGroup property) suffix() (dasi.utils.npdf.NumpyDataFrame method) sympy_dijkstras() (in module dasi.utils.networkx.shortest_path)

T

t() (dasi.utils.region.EmptySpan method) (dasi.utils.region.Region method) (dasi.utils.region.Span method) TEMPLATE (dasi.constants.Constants attribute)

to_df() (dasi.utils.npdf.NumpyDataFrame method) type (dasi.models.assembly.AssemblyNode attribute), [1] (dasi.models.AssemblyNode attribute) types() (dasi.models.alignment_container.AlignmentContainer property) (dasi.models.AlignmentContainer property)

U

unfreeze() (dasi.models.alignment_container.AlignmentContainer method) (dasi.models.AlignmentContainer method)

update() (dasi.utils.npdf.NumpyDataFrame method)

V

validate() (dasi.utils.npdf.NumpyDataFrame method) values() (dasi.utils.npdf.NumpyDataFrame method) (dasi.utils.npdf.NumpyDataFrameIndexer method)

version() (dasi.command_line.DasiCLI method) vstack() (dasi.utils.npdf.NumpyDataFrame class method)

W

with_traceback() (dasi.exceptions.AlignmentContainerException method) (dasi.exceptions.AlignmentException method) (dasi.exceptions.DasiCostParameterValidationError method) (dasi.exceptions.DasiDesignException method) (dasi.exceptions.DASiException method) (dasi.exceptions.DasiInvalidMolecularAssembly method) (dasi.exceptions.DasiNoPrimerPairsException method) (dasi.exceptions.DasiOutputValidationError method) (dasi.exceptions.DasiSequenceDesignException method) (dasi.exceptions.DASiWarning method) (dasi.utils.networkx.exceptions.NetworkxUtilsException method) (dasi.utils.npdf.NumpyDataFrameException method) (dasi.utils.region.SpanError method)