GPS-mapping 1.0.1

Genetics-informed pathogenic spatial mapping

GPS

How to use:

STEP-1: Find the latent representations

root=/storage/yangjianLab/songliyang/SpatialData/Data/Brain/Human/Nature_Neuroscience_2021/processed/h5ad

ls ${root} | while read file
do
   name=($(echo ${file} | cut -d'.' -f 1)) 

   command="python3 /storage/yangjianLab/songliyang/SpatialData/spatial_ldsc_v1/Find_Latent_Representations.py \
   --spe_path ${root} \
   --spe_name ${file} \
   --annotation layer_guess \
   --type count \
   --spe_out /storage/yangjianLab/songliyang/SpatialData/Data/Brain/Human/Nature_Neuroscience_2021/annotation/${name}/h5ad"

    qsubshcom_gpu "$command" 1 50G GAT_${name} 2:00:00 "--qos gpu-huge -queue=v100,a40-tmp,a40-quad"
done

STEP-2: Find marker genes

root=/storage/yangjianLab/songliyang/SpatialData/Data/Brain/Human/Nature_Neuroscience_2021/processed/h5ad
ls ${root} | grep h5ad | while read file
do
	name=($(echo ${file} | cut -d'.' -f 1))

	command="python3 /storage/yangjianLab/songliyang/SpatialData/spatial_ldsc_v1/Latent_to_Gene_V2.py \
	--latent_representation latent_GVAE \
	--spe_path /storage/yangjianLab/songliyang/SpatialData/Data/Brain/Human/Nature_Neuroscience_2021/annotation/${name}/h5ad \
	--spe_name ${name}_add_latent.h5ad \
	--num_processes 4 \
	--type count \
	--annotation layer_guess \
	--num_neighbour 51 \
	--spe_out /storage/yangjianLab/songliyang/SpatialData/Data/Brain/Human/Nature_Neuroscience_2021/annotation/${name}/gene_markers"

	qsubshcom "$command" 4 50G mkS_${name} 24:00:00 "--qos huge -queue=intel-sc3,amd-ep2,amd-ep2-short"
done

STEP-3: markers to SNP annotations

root=/storage/yangjianLab/songliyang/SpatialData/Data/Brain/Human/Nature_Neuroscience_2021/processed/h5ad
ls ${root} | grep h5ad | while read file
do
	name=($(echo ${file} | cut -d'.' -f 1))

	command="python3 /storage/yangjianLab/songliyang/SpatialData/spatial_ldsc_v1/Make_Annotations_V2.py \
	--mk_score_file /storage/yangjianLab/songliyang/SpatialData/Data/Brain/Human/Nature_Neuroscience_2021/annotation/${name}/gene_markers/${name}_rank.feather \
	--gtf_file /storage/yangjianLab/songliyang/ReferenceGenome/GRCh37/gencode.v39lift37.annotation.gtf \
	--bfile_root /storage/yangjianLab/sharedata/LDSC_resource/1000G_EUR_Phase3_plink/1000G.EUR.QC \
	--annot_root /storage/yangjianLab/songliyang/SpatialData/Data/Brain/Human/Nature_Neuroscience_2021/annotation/${name}/snp_annotation \
	--keep_snp /storage/yangjianLab/sharedata/LDSC_resource/hapmap3_snps/hm \
	--annot_name ${name} \
	--const_max_size 500 \
	--chr {TASK_ID} \
	--ld_wind_cm 1"

	qsubshcom "$command" 5 60G annS_${name} 24:00:00 "-array=1-22 --qos huge -queue=intel-sc3,amd-ep2,amd-ep2-short"
done

STEP-4: LDSC analysis

gwas_root=/storage/yangjianLab/songliyang/GWAS_trait/LDSC
gwas_trait=/storage/yangjianLab/songliyang/GWAS_trait/GWAS_Public_Use_MaxPower.csv 
root=/storage/yangjianLab/songliyang/SpatialData/Data/Brain/Human/Nature_Neuroscience_2021/processed/h5ad

ls ${root} | grep h5ad | while read file
do

  spe_name=($(echo ${file} | awk -F "." '{print $1}')) 
  ld_pth=/storage/yangjianLab/songliyang/SpatialData/Data/Brain/Human/Nature_Neuroscience_2021/annotation/${spe_name}/snp_annotation
  out_pth=/storage/yangjianLab/songliyang/SpatialData/Data/Brain/Human/Nature_Neuroscience_2021/ldsc_enrichment/${spe_name}


  awk -F"," 'NR>1 {print $1}' ${gwas_trait} | awk -F ".txt" '{print $1}' | while read gwas_file
  do

  out_file=${out_pth}/${spe_name}_${gwas_file}.gz
  command="python3 /storage/yangjianLab/songliyang/SpatialData/spatial_ldsc_v1/Spatial_LDSC.py \
  --h2 ${gwas_root}/${gwas_file}.sumstats.gz \
  --w_file /storage/yangjianLab/sharedata/LDSC_resource/LDSC_SEG_ldscores/weights_hm3_no_hla/weights. \
  --data_name ${spe_name} \
  --num_processes 3 \
  --ld_file ${ld_pth} \
  --out_file ${out_pth}"

  qsubshcom "$command" 3 100G h2_${spe_name}_${gwas_file} 24:00:00 "--qos huge -queue=intel-sc3,amd-ep2,amd-ep2-short"
  
  done
done

STEP-5: Do Cauchy combination test for pre-defined annotation

root=/storage/yangjianLab/songliyang/SpatialData/Data/Brain/Human/Nature_Neuroscience_2021/processed/h5ad
ldsc_root=/storage/yangjianLab/songliyang/SpatialData/Data/Brain/Human/Nature_Neuroscience_2021/ldsc_enrichment/

ls ${root} | grep h5ad | while read file 
do
  spe_name=($(echo ${file} | awk -F "." '{print $1}')) 

  ls ${ldsc_root}/${spe_name} | grep '.gz' | grep -v 'Cauchy' | while read trait
  do
  
  command="python3 /storage/yangjianLab/songliyang/SpatialData/spatial_ldsc_v1/Cauchy_combination.py \
  --ldsc_path ${ldsc_root}/${spe_name} \
  --ldsc_name ${trait} \
  --spe_path  /storage/yangjianLab/songliyang/SpatialData/Data/Brain/Human/Nature_Neuroscience_2021/annotation/${spe_name}/h5ad/ \
  --spe_name ${spe_name}_add_latent.h5ad \
  --annotation layer_guess"
  
  qsubshcom "$command" 1 20G cahchy_${trait} 2:00:00 "--qos huge -queue=intel-sc3,amd-ep2,amd-ep2-short"
  # $command

  done
done