pygfa.graph_element package¶
Subpackages¶
- pygfa.graph_element.parser package
- Submodules
- 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
- Module contents
Submodules¶
pygfa.graph_element.edge module¶
-
class
pygfa.graph_element.edge.
Edge
(edge_id, from_node, from_orn, to_node, to_orn, from_positions, to_positions, alignment, distance=None, variance=None, opt_fields={}, is_dovetail=False)[source]¶ Bases:
object
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alignment
¶
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distance
¶
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eid
¶
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from_node
¶
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from_orn
¶
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from_positions
¶
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from_segment_end
¶
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is_dovetail
¶
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opt_fields
¶
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to_node
¶
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to_orn
¶
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to_positions
¶
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to_segment_end
¶
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variance
¶
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pygfa.graph_element.node module¶
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class
pygfa.graph_element.node.
Node
(node_id, sequence, length, opt_fields={})[source]¶ Bases:
object
A Node object that abstract the GFA1 and GFA2 Sequence concepts.
GFA graphs will operate on Nodes, by adding them directly to their structures.
Node accepts elements (ids, sequences, lengths and so on) from the more tolerant of the two specification. So, a sequence will be accepted if and only if is a valid GFA2 sequence, since GFA2 sequence is more tolerant than GFA1 sequence.
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classmethod
from_line
(segment_line)[source]¶ Given a Segment Line construct a Node from it.
If segment_line is a GFA1 Segment segment_line then the sequence length taken into account will be the value of the optional field LN if specified in the line fields.
Parameters: segment_line – A valid Segment Segment_line. Raises: InvalidSegment_lineError – If the given segment_line is not valid.
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nid
¶
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opt_fields
¶
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sequence
¶
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slen
¶
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classmethod