Set up Autism Genes ToolΒΆ

  1. Create autismGeneTool.conf file in $DAE_DB_DIR (example config below)

default_dataset = "IossifovWE2014"

[[gene_sets]]
category = "autism_gene_sets"
display_name = "Autism Gene Sets"
sets = [
    { set_id="autism candidates from Iossifov PNAS 2015", collection_id = "main" },
    { set_id="autism candidates from Sanders Neuron 2015", collection_id = "main" },
]

[[gene_sets]]
category = "relevant_gene_sets"
display_name = "Relevant Gene Sets"

sets = [
    { set_id="CHD8 target genes", collection_id="main" },
    { set_id="chromatin modifiers", collection_id="main" },
    { set_id="essential genes", collection_id="main" },
    { set_id="FMRP Darnell", collection_id="main" },
]

[[genomic_scores]]
category = "autism_scores"
display_name = "Autism Scores"
scores = [
    {score_name="SFARI gene score", format="%%s"},
]

[[genomic_scores]]
category = "protection_scores"
display_name = "Protection Scores"
scores = [
    {score_name="RVIS_rank", format="%%s"},
    {score_name="LGD_rank", format="%%s"},
    {score_name="pLI_rank", format="%%s"},
    {score_name="pRec_rank", format="%%s"},
]

[datasets.IossifovWE2014]
[[datasets.IossifovWE2014.person_sets]]
set_name="affected"
collection_name="status"
[[datasets.IossifovWE2014.person_sets]]
set_name="unaffected"
collection_name="status"

[[datasets.IossifovWE2014.statistics]]
id = "denovo_lgds"
display_name = "LGDs"
effects = ["LGDS"]
category = "denovo"

[[datasets.IossifovWE2014.statistics]]
id = "denovo_missense"
display_name = "missense"
effects = ["missense"]
category = "denovo"

[[datasets.IossifovWE2014.statistics]]
id = "denovo_intron"
display_name = "intron"
effects = ["intron"]
category = "denovo"

  1. Link the newly added autismGeneTool.conf file path in the gpf_instance.yaml file:

autism_gene_tool_config:
  conf_file: "%($DAE_DB_DIR)s/autismGeneTool.conf"

  1. Delete the agpdb file in $DAE_DB_DIR, if it exists

  2. Run ./generate_autism_gene_profile.py tool, which is located in gpf/dae/dae/tools (make sure $DAE_DB_DIR is set correctly)