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 = <>