.. _gene_info_db: Gene Info Configuration ======================= .. FIXME: Extend Gene Info Configuration description. This file is responsible for configuring which gene info information, gene terms, gene weights and chromosomes are available to the GPF system. Example Configuration --------------------- .. code-block:: ini [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 ____________ .. FIXME: Fill me .. code-block:: ini geneInfoFile = <> [geneTerms.] -------------------------- id __ .. code-block:: ini id = Identifier of the gene term. Default value is from the ``[geneTerms.]`` section name. file ____ .. FIXME: Fill me .. code-block:: ini file = <> webFormatStr ____________ .. FIXME: Fill me .. code-block:: ini webFormatStr = <> webLabel ________ .. FIXME: Fill me .. code-block:: ini webLabel = <> .. _gene_weights: [geneWeights] ------------- This is an optional section containing a list of selected gene weights. weights _______ .. code-block:: ini weights = ,,<...> A comma-separated list of selected gene weights. If this property is missing, then all defined weights with section name ``[geneWeights.]`` in this file are selected. [geneWeights.] ------------------------------ id __ .. code-block:: ini id = Identifier of the gene weight. Default value is from the ``[geneWeights.]`` section name. file ____ .. code-block:: ini file = The absolute path to the gene weight's histogram file. desc ____ .. code-block:: ini desc = A brief description of the gene weight. bins ____ .. code-block:: ini bins = The amount of bins in the gene weight's histogram. The value must be an integer. yscale ______ .. code-block:: ini yscale = The scale for the Y axis of the gene weight's histogram. xscale ______ .. code-block:: ini xscale = The scale for the X axis of the gene weight's histogram. range ______ .. code-block:: ini range = <,> The range domain of the gene weight - its lowest and largest possible values separated by a comma. [chromosomes] ------------- .. FIXME: Fill me file ____ .. code-block:: ini file = <>