Glycome Network Definitions

Glycome Network Definitions¶

The glycome network smoothing method presented in “Klein, J., Carvalho, L., & Zaia, J. (2018). Application of network smoothing to glycan LC-MS profiling. Bioinformatics, 34(20), 3511-3518. https://doi.org/10.1093/bioinformatics/bty397” requires a network definition.

Building a Network¶

The first step is to build a network for a glycan list, embodied in a GlycanHypothesis in a database file. This produces a new text file defining the nodes of the network and builds edges between them.

glycresoft build-hypothesis glycan-network build-network¶

glycresoft build-hypothesis glycan-network build-network [OPTIONS]
                                                         DATABASE_CONNECTION
                                                         HYPOTHESIS_IDENTIFIER

Options

-o, --output-path <path>¶: Path to write to instead of stdout

-e, --edge-strategy <choice>¶: Strategy to use to decide when two nodes are connected by an edge [default: manhattan]

Choices: [

manhattan]

Arguments

DATABASE_CONNECTION¶: Required argument <string> A connection URI for a database, or a path on the file system

HYPOTHESIS_IDENTIFIER¶: Required argument <string> The ID number or name of the glycan hypothesis to use

Adding Pre-Defined Network Neighborhoods¶

Add pre-programmed neighborhood rules to a network, writing them out to a new text file.

glycresoft build-hypothesis glycan-network add-prebuilt-neighborhoods¶

glycresoft build-hypothesis glycan-network add-prebuilt-neighborhoods 
    [OPTIONS]

Options

-i, --input-path <path>¶

-o, --output-path <path>¶

-n, --name <choice>¶: Set the neighborhood name [required]

Choices: [

n-glycan; mammalian-n-glycan]

Adding a Custom Network Neighborhood¶

Add a custom neighborhood to a network, writing them out to a new text file. A neighborhood is composed of one or more rule expressions.

glycresoft build-hypothesis glycan-network add-neighborhood¶

glycresoft build-hypothesis glycan-network add-neighborhood 
    [OPTIONS]

Options

-i, --input-path <path>¶

-o, --output-path <path>¶

-n, --name <string>¶: Set the neighborhood name [required]

-r, --range-rule <string>¶: Format: <expression:str> <low:int> <high:int> <required:bool> (May specify more than once)

-e, --expression-rule <string>¶: Format: <bool-expression:str> <required:bool> (May specify more than once)

-a, --ratio-rule <string>¶: Format: <numerator-expr:str> <denominator-expr:str> <threshold:float> <required:bool> (May specify more than once)

glycresoft documentation