Gene Info Configuration

This file is responsible for configuring which gene info information, gene terms, gene weights and chromosomes are available to the GPF system.

Example Configuration

[geneInfo]
geneInfoFile = %(wd)s/geneInfo/humanGeneInfo.txt

[geneTerms.main]
file = %(wd)s/geneInfo/GeneSets
webFormatStr = key| (|count|): |desc
webLabel = Main

[geneTerms.GO]
file = %(wd)s/geneInfo/GO-map.txt
webFormatStr = key| (|count|): |desc
webLabel = GO Terms

[geneWeights]
weights = LGD_rank,pLI

[geneWeights.LGD_rank]
file = %(wd)s/geneInfo/GeneWeights/LGD.csv
desc = LGD rank
bins = 150
yscale = linear
xscale = linear
range = 1,10000

[geneWeights.LGD_score]
file = %(wd)s/geneInfo/GeneWeights/LGD.csv
desc = LGD score
bins = 150
yscale = log
xscale = linear

[geneWeights.pLI]
file = %(wd)s/geneInfo/GeneWeights/ExAC.csv
desc = ExAC pLI
bins = 150
yscale = log
xscale = log

[chromosomes]
file = %(wd)s/geneInfo/hgTables.txt

[geneInfo]

geneInfoFile

geneInfoFile = <>

[geneTerms.<gene term id>]

id

id = <gene term identifier>

Identifier of the gene term. Default value is <gene term id> from the [geneTerms.<gene term id>] section name.

file

file = <>

webFormatStr

webFormatStr = <>

webLabel

webLabel = <>

[geneWeights]

This is an optional section containing a list of selected gene weights.

weights

weights = <gene weight id 1>,<gene weight id 2>,<...>

A comma-separated list of selected gene weights. If this property is missing, then all defined weights with section name [geneWeights.<gene weight id>] in this file are selected.

[geneWeights.<gene weight id>]

id

id = <gene weight identifier>

Identifier of the gene weight. Default value is <gene weight id> from the [geneWeights.<gene weight id>] section name.

file

file = <path to gene weight histogram file>

The absolute path to the gene weight’s histogram file.

desc

desc = <description>

A brief description of the gene weight.

bins

bins = <amount of bins>

The amount of bins in the gene weight’s histogram. The value must be an integer.

yscale

yscale = <linear / log>

The scale for the Y axis of the gene weight’s histogram.

xscale

xscale = <linear / log>

The scale for the X axis of the gene weight’s histogram.

range

range = <<min value>,<max value>>

The range domain of the gene weight - its lowest and largest possible values separated by a comma.

[chromosomes]

file

file = <>