Abstractions: layers over GFA types

Abstractions over GFA formats

class gfagraphs.abstractions.GFAFormat(value, names=<not given>, *values, module=None, qualname=None, type=None, start=1, boundary=None)

Describes the different possible gfa-like formats. Please refer to http://gfa-spec.github.io/GFA-spec/GFA1.html for examples and full description of the format.

Parameters

Enum (str) – One of rGFA | GFA1 | GFA1.1 | GFA1.2 | GFA2 | unknown

class gfagraphs.abstractions.GFALine(value, names=<not given>, *values, module=None, qualname=None, type=None, start=1, boundary=None)

Describes the different GFA line formats. Please refer to http://gfa-spec.github.io/GFA-spec/GFA1.html for examples and full description of the format.

Parameters

Enum (str) – One of S | L | W | P | H | # | ?. See GFA-spec.

class gfagraphs.abstractions.Orientation(value, names=<not given>, *values, module=None, qualname=None, type=None, start=1, boundary=None)

Describes the way a node is read. Minus is reversecomp and plus is forward. Please refer to http://gfa-spec.github.io/GFA-spec/GFA1.html for examples and full description of the format.

Parameters

Enum (str) – Could be a GFA-compatible tag (+ or -) or ? to specify ‘Any’ or = to specify ‘both’.

gfagraphs.abstractions.reverse(orientation: Orientation) → Orientation

Returns the orientation of the reverse edge

Parameters

orientation (Orientation) – The orientation the edge is pointing on

Returns

The complementary operation

Return type

Orientation