PyGFA
latest
Contents:
pygfa
PyGFA
Docs
»
Index
Edit on GitHub
Index
A
|
C
|
D
|
E
|
F
|
G
|
H
|
I
|
L
|
N
|
O
|
P
|
R
|
S
|
T
|
U
|
V
A
add_edge() (pygfa.gfa.GFA method)
add_field() (pygfa.graph_element.parser.line.Line method)
add_graph_element() (pygfa.gfa.GFA method)
add_node() (pygfa.gfa.GFA method)
add_subgraph() (pygfa.gfa.GFA method)
alignment (pygfa.graph_element.edge.Edge attribute)
all_simple_paths() (in module pygfa.algorithms.simple_paths)
are_elements_oriented() (in module pygfa.serializer.gfa2_serializer)
as_dict() (pygfa.graph_element.subgraph.Subgraph method)
as_graph_element() (pygfa.gfa.GFA method)
C
clear() (pygfa.gfa.GFA method)
Containment (class in pygfa.graph_element.parser.containment)
D
dfs_edges() (in module pygfa.algorithms.traversal)
distance (pygfa.graph_element.edge.Edge attribute)
DovetailIterator (class in pygfa.dovetail_operations.iterator)
dovetails_all_simple_paths() (in module pygfa.dovetail_operations.simple_paths)
dovetails_iter() (pygfa.dovetail_operations.iterator.DovetailIterator method)
dovetails_linear_path() (in module pygfa.dovetail_operations.linear_paths)
dovetails_linear_path_iter() (pygfa.dovetail_operations.iterator.DovetailIterator method)
dovetails_linear_path_traverse_edges_iter() (pygfa.dovetail_operations.iterator.DovetailIterator method)
dovetails_linear_path_traverse_nodes_iter() (pygfa.dovetail_operations.iterator.DovetailIterator method)
dovetails_linear_paths() (in module pygfa.dovetail_operations.linear_paths)
dovetails_nbunch_iter() (pygfa.dovetail_operations.iterator.DovetailIterator method)
dovetails_neighbors() (pygfa.dovetail_operations.iterator.DovetailIterator method)
dovetails_neighbors_iter() (pygfa.dovetail_operations.iterator.DovetailIterator method)
dovetails_remove_dead_ends() (in module pygfa.dovetail_operations.operations)
dovetails_remove_small_components() (in module pygfa.dovetail_operations.operations)
dovetails_subgraph() (pygfa.gfa.GFA method)
dump() (pygfa.gfa.GFA method)
E
Edge (class in pygfa.graph_element.edge)
(class in pygfa.graph_element.parser.edge)
EDGE (pygfa.gfa.Element attribute)
edge() (pygfa.gfa.GFA method)
edges() (pygfa.gfa.GFA method)
edges_iter() (pygfa.gfa.GFA method)
eid (pygfa.graph_element.edge.Edge attribute)
Element (class in pygfa.gfa)
elements (pygfa.graph_element.subgraph.Subgraph attribute)
F
Field (class in pygfa.graph_element.parser.line)
fields (pygfa.graph_element.parser.line.Line attribute)
FormatError
Fragment (class in pygfa.graph_element.parser.fragment)
from_file() (pygfa.gfa.GFA class method)
from_line() (pygfa.graph_element.edge.Edge class method)
(pygfa.graph_element.node.Node class method)
(pygfa.graph_element.subgraph.Subgraph class method)
from_node (pygfa.graph_element.edge.Edge attribute)
from_orn (pygfa.graph_element.edge.Edge attribute)
from_positions (pygfa.graph_element.edge.Edge attribute)
from_segment_end (pygfa.graph_element.edge.Edge attribute)
from_string() (pygfa.gfa.GFA method)
(pygfa.graph_element.parser.containment.Containment class method)
(pygfa.graph_element.parser.edge.Edge class method)
(pygfa.graph_element.parser.fragment.Fragment class method)
(pygfa.graph_element.parser.gap.Gap class method)
(pygfa.graph_element.parser.group.OGroup class method)
(pygfa.graph_element.parser.group.UGroup class method)
(pygfa.graph_element.parser.header.Header class method)
(pygfa.graph_element.parser.line.Line class method)
(pygfa.graph_element.parser.line.OptField class method)
(pygfa.graph_element.parser.link.Link class method)
(pygfa.graph_element.parser.path.Path class method)
(pygfa.graph_element.parser.segment.SegmentV1 class method)
(pygfa.graph_element.parser.segment.SegmentV2 class method)
G
Gap (class in pygfa.graph_element.parser.gap)
get() (pygfa.gfa.GFA method)
get_static_fields() (pygfa.graph_element.parser.line.Line class method)
get_subgraph() (pygfa.gfa.GFA method)
GFA (class in pygfa.gfa)
GFA1SerializationError
GFA2SerializationError
GFAError
H
Header (class in pygfa.graph_element.parser.header)
I
InvalidEdgeError
InvalidElementError
InvalidFieldError
InvalidLineError
InvalidNodeError
InvalidSearchParameters
InvalidSubgraphError
is_dazzler_trace() (in module pygfa.graph_element.parser.field_validator)
is_dovetail (pygfa.graph_element.edge.Edge attribute)
is_edge() (in module pygfa.graph_element.edge)
is_field() (in module pygfa.graph_element.parser.line)
is_gfa1_cigar() (in module pygfa.graph_element.parser.field_validator)
is_gfa2_cigar() (in module pygfa.graph_element.parser.field_validator)
is_node() (in module pygfa.graph_element.node)
is_optfield() (in module pygfa.graph_element.parser.line)
is_path() (pygfa.graph_element.subgraph.Subgraph method)
is_segmentv1() (in module pygfa.graph_element.parser.segment)
is_segmentv2() (in module pygfa.graph_element.parser.segment)
is_subgraph() (in module pygfa.graph_element.subgraph)
is_valid() (in module pygfa.graph_element.parser.field_validator)
(pygfa.graph_element.parser.line.Line class method)
L
left() (pygfa.dovetail_operations.iterator.DovetailIterator method)
left_degree() (pygfa.dovetail_operations.iterator.DovetailIterator method)
left_degree_iter() (pygfa.dovetail_operations.iterator.DovetailIterator method)
left_end_iter() (pygfa.dovetail_operations.iterator.DovetailIterator method)
Line (class in pygfa.graph_element.parser.line)
Link (class in pygfa.graph_element.parser.link)
N
name (pygfa.graph_element.parser.line.Field attribute)
nbunch_iter() (pygfa.gfa.GFA method)
neighbors() (pygfa.gfa.GFA method)
nid (pygfa.graph_element.node.Node attribute)
Node (class in pygfa.graph_element.node)
NODE (pygfa.gfa.Element attribute)
node() (pygfa.gfa.GFA method)
nodes() (pygfa.gfa.GFA method)
nodes_connected_component() (in module pygfa.operations)
nodes_connected_components() (in module pygfa.operations)
nodes_iter() (pygfa.gfa.GFA method)
O
OGroup (class in pygfa.graph_element.parser.group)
opt_fields (pygfa.graph_element.edge.Edge attribute)
(pygfa.graph_element.node.Node attribute)
(pygfa.graph_element.subgraph.Subgraph attribute)
OptField (class in pygfa.graph_element.parser.line)
P
Path (class in pygfa.graph_element.parser.path)
point_to_node() (in module pygfa.serializer.gfa1_serializer)
pprint() (pygfa.gfa.GFA method)
PREDEFINED_OPTFIELDS (pygfa.graph_element.parser.containment.Containment attribute)
(pygfa.graph_element.parser.header.Header attribute)
(pygfa.graph_element.parser.line.Line attribute)
(pygfa.graph_element.parser.link.Link attribute)
(pygfa.graph_element.parser.path.Path attribute)
(pygfa.graph_element.parser.segment.SegmentV1 attribute)
pygfa (module)
pygfa.algorithms (module)
pygfa.algorithms.simple_paths (module)
pygfa.algorithms.traversal (module)
pygfa.dovetail_operations (module)
pygfa.dovetail_operations.iterator (module)
pygfa.dovetail_operations.linear_paths (module)
pygfa.dovetail_operations.operations (module)
pygfa.dovetail_operations.simple_paths (module)
pygfa.gfa (module)
pygfa.graph_element (module)
pygfa.graph_element.edge (module)
pygfa.graph_element.node (module)
pygfa.graph_element.parser (module)
pygfa.graph_element.parser.containment (module)
pygfa.graph_element.parser.edge (module)
pygfa.graph_element.parser.field_validator (module)
pygfa.graph_element.parser.fragment (module)
pygfa.graph_element.parser.gap (module)
pygfa.graph_element.parser.group (module)
pygfa.graph_element.parser.header (module)
pygfa.graph_element.parser.line (module)
pygfa.graph_element.parser.link (module)
pygfa.graph_element.parser.path (module)
pygfa.graph_element.parser.segment (module)
pygfa.graph_element.subgraph (module)
pygfa.operations (module)
pygfa.serializer (module)
pygfa.serializer.gfa1_serializer (module)
pygfa.serializer.gfa2_serializer (module)
pygfa.serializer.utils (module)
R
remove_edge() (pygfa.gfa.GFA method)
remove_edges() (pygfa.gfa.GFA method)
remove_field() (pygfa.graph_element.parser.line.Line method)
remove_node() (pygfa.gfa.GFA method)
remove_subgraph() (pygfa.gfa.GFA method)
REQUIRED_FIELDS (pygfa.graph_element.parser.containment.Containment attribute)
(pygfa.graph_element.parser.edge.Edge attribute)
(pygfa.graph_element.parser.fragment.Fragment attribute)
(pygfa.graph_element.parser.gap.Gap attribute)
(pygfa.graph_element.parser.group.OGroup attribute)
(pygfa.graph_element.parser.group.UGroup attribute)
(pygfa.graph_element.parser.line.Line attribute)
(pygfa.graph_element.parser.link.Link attribute)
(pygfa.graph_element.parser.path.Path attribute)
(pygfa.graph_element.parser.segment.SegmentV1 attribute)
(pygfa.graph_element.parser.segment.SegmentV2 attribute)
right() (pygfa.dovetail_operations.iterator.DovetailIterator method)
right_degree() (pygfa.dovetail_operations.iterator.DovetailIterator method)
right_degree_iter() (pygfa.dovetail_operations.iterator.DovetailIterator method)
right_end_iter() (pygfa.dovetail_operations.iterator.DovetailIterator method)
S
search() (pygfa.gfa.GFA method)
search_on_edges() (pygfa.gfa.GFA method)
search_on_nodes() (pygfa.gfa.GFA method)
search_on_subgraph() (pygfa.gfa.GFA method)
SegmentV1 (class in pygfa.graph_element.parser.segment)
SegmentV2 (class in pygfa.graph_element.parser.segment)
sequence (pygfa.graph_element.node.Node attribute)
serialize_edge() (in module pygfa.serializer.gfa1_serializer)
(in module pygfa.serializer.gfa2_serializer)
serialize_gfa() (in module pygfa.serializer.gfa1_serializer)
(in module pygfa.serializer.gfa2_serializer)
serialize_graph() (in module pygfa.serializer.gfa1_serializer)
(in module pygfa.serializer.gfa2_serializer)
serialize_node() (in module pygfa.serializer.gfa1_serializer)
(in module pygfa.serializer.gfa2_serializer)
serialize_subgraph() (in module pygfa.serializer.gfa1_serializer)
(in module pygfa.serializer.gfa2_serializer)
slen (pygfa.graph_element.node.Node attribute)
sub_id (pygfa.graph_element.subgraph.Subgraph attribute)
Subgraph (class in pygfa.graph_element.subgraph)
SUBGRAPH (pygfa.gfa.Element attribute)
subgraph() (pygfa.gfa.GFA method)
subgraphs() (pygfa.gfa.GFA method)
subgraphs_iter() (pygfa.gfa.GFA method)
T
to_node (pygfa.graph_element.edge.Edge attribute)
to_orn (pygfa.graph_element.edge.Edge attribute)
to_positions (pygfa.graph_element.edge.Edge attribute)
to_segment_end (pygfa.graph_element.edge.Edge attribute)
type (pygfa.graph_element.parser.line.Line attribute)
(pygfa.graph_element.parser.line.OptField attribute)
U
UGroup (class in pygfa.graph_element.parser.group)
UnknownDataTypeError
V
validate() (in module pygfa.graph_element.parser.field_validator)
value (pygfa.graph_element.parser.line.Field attribute)
variance (pygfa.graph_element.edge.Edge attribute)
Read the Docs
v: latest
Versions
latest
Downloads
pdf
htmlzip
On Read the Docs
Project Home
Builds
Free document hosting provided by
Read the Docs
.