{ "cells": [ { "cell_type": "markdown", "id": "39ef732b-43b3-4e02-8396-75739315dc4d", "metadata": { "kernel": "SoS", "tags": [] }, "source": [ "# Colocalization result summary" ] }, { "cell_type": "markdown", "id": "b3bfaa7e-0648-4f65-9041-a583e3d3e137", "metadata": { "kernel": "SoS" }, "source": [ "## Goal\n", "\n", "Summarize the result based on the key four outputs to calculate FDR and power.\n", "\n", "**Fit any coloclaization method** generated by the notebooks in this repo. As long as they are summarized to have the elements: coloc_trait, coloc_set true_trait and true_variant." ] }, { "cell_type": "markdown", "id": "95492378-af15-437a-91c5-c68b6914893f", "metadata": { "kernel": "SoS" }, "source": [ "## Input\n", "\n", "File(s) of colocalization result.\n", "\n", "## Output\n", "\n", "A dataframe, each row is a summarization of one finemapping result. \n", "\n", "Example output: " ] }, { "cell_type": "code", "execution_count": 4, "id": "56d0c707-4e58-4e5e-a5fa-8e5f887a03f6", "metadata": { "kernel": "R", "tags": [] }, "outputs": [ { "data": { "text/html": [ "\n", "\n", "\n", "\t\n", "\t\n", "\n", "\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\n", "
A tibble: 6 × 12
total_causal_var_numberperfect_causal_var_numberpartial_causal_var_numbertrue_trait_numberpredict_trait_numbertotal_trait_numbertrue_set_numbertotal_set_numbersingle_set_numbermax_causalfileout_file
<int><dbl><dbl><dbl><int><dbl><dbl><int><int><int><chr><chr>
1111 5 5 51101/mnt/vast/hpc/csg/hs3393/cb_Mar/simulation_data/real_simulation_10trait/sample_0_real_simulation_1_ncausal_10_trait.rds/home/hs3393/cb_Mar/simulation_result/hyprcoloc/hyp_real_simulation_10trait/result/sample_0_real_simulation_1_ncausal_10_trait_ntr_10_hypercoloc.rds
2211 5 5 81102/mnt/vast/hpc/csg/hs3393/cb_Mar/simulation_data/real_simulation_10trait/sample_0_real_simulation_2_ncausal_10_trait.rds/home/hs3393/cb_Mar/simulation_result/hyprcoloc/hyp_real_simulation_10trait/result/sample_0_real_simulation_2_ncausal_10_trait_ntr_10_hypercoloc.rds
3302 4 4 82203/mnt/vast/hpc/csg/hs3393/cb_Mar/simulation_data/real_simulation_10trait/sample_0_real_simulation_3_ncausal_10_trait.rds/home/hs3393/cb_Mar/simulation_result/hyprcoloc/hyp_real_simulation_10trait/result/sample_0_real_simulation_3_ncausal_10_trait_ntr_10_hypercoloc.rds
44031010173303/mnt/vast/hpc/csg/hs3393/cb_Mar/simulation_data/real_simulation_10trait/sample_0_real_simulation_4_ncausal_10_trait.rds/home/hs3393/cb_Mar/simulation_result/hyprcoloc/hyp_real_simulation_10trait/result/sample_0_real_simulation_4_ncausal_10_trait_ntr_10_hypercoloc.rds
5111 4 4 41101/mnt/vast/hpc/csg/hs3393/cb_Mar/simulation_data/real_simulation_10trait/sample_1_real_simulation_1_ncausal_10_trait.rds/home/hs3393/cb_Mar/simulation_result/hyprcoloc/hyp_real_simulation_10trait/result/sample_1_real_simulation_1_ncausal_10_trait_ntr_10_hypercoloc.rds
6212 6 6 72202/mnt/vast/hpc/csg/hs3393/cb_Mar/simulation_data/real_simulation_10trait/sample_1_real_simulation_2_ncausal_10_trait.rds/home/hs3393/cb_Mar/simulation_result/hyprcoloc/hyp_real_simulation_10trait/result/sample_1_real_simulation_2_ncausal_10_trait_ntr_10_hypercoloc.rds
\n" ], "text/latex": [ "A tibble: 6 × 12\n", "\\begin{tabular}{r|llllllllllll}\n", " & total\\_causal\\_var\\_number & perfect\\_causal\\_var\\_number & partial\\_causal\\_var\\_number & true\\_trait\\_number & predict\\_trait\\_number & total\\_trait\\_number & true\\_set\\_number & total\\_set\\_number & single\\_set\\_number & max\\_causal & file & out\\_file\\\\\n", " & & & & & & & & & & & & \\\\\n", "\\hline\n", "\t1 & 1 & 1 & 1 & 5 & 5 & 5 & 1 & 1 & 0 & 1 & /mnt/vast/hpc/csg/hs3393/cb\\_Mar/simulation\\_data/real\\_simulation\\_10trait/sample\\_0\\_real\\_simulation\\_1\\_ncausal\\_10\\_trait.rds & /home/hs3393/cb\\_Mar/simulation\\_result/hyprcoloc/hyp\\_real\\_simulation\\_10trait/result/sample\\_0\\_real\\_simulation\\_1\\_ncausal\\_10\\_trait\\_ntr\\_10\\_hypercoloc.rds\\\\\n", "\t2 & 2 & 1 & 1 & 5 & 5 & 8 & 1 & 1 & 0 & 2 & /mnt/vast/hpc/csg/hs3393/cb\\_Mar/simulation\\_data/real\\_simulation\\_10trait/sample\\_0\\_real\\_simulation\\_2\\_ncausal\\_10\\_trait.rds & /home/hs3393/cb\\_Mar/simulation\\_result/hyprcoloc/hyp\\_real\\_simulation\\_10trait/result/sample\\_0\\_real\\_simulation\\_2\\_ncausal\\_10\\_trait\\_ntr\\_10\\_hypercoloc.rds\\\\\n", "\t3 & 3 & 0 & 2 & 4 & 4 & 8 & 2 & 2 & 0 & 3 & /mnt/vast/hpc/csg/hs3393/cb\\_Mar/simulation\\_data/real\\_simulation\\_10trait/sample\\_0\\_real\\_simulation\\_3\\_ncausal\\_10\\_trait.rds & /home/hs3393/cb\\_Mar/simulation\\_result/hyprcoloc/hyp\\_real\\_simulation\\_10trait/result/sample\\_0\\_real\\_simulation\\_3\\_ncausal\\_10\\_trait\\_ntr\\_10\\_hypercoloc.rds\\\\\n", "\t4 & 4 & 0 & 3 & 10 & 10 & 17 & 3 & 3 & 0 & 3 & /mnt/vast/hpc/csg/hs3393/cb\\_Mar/simulation\\_data/real\\_simulation\\_10trait/sample\\_0\\_real\\_simulation\\_4\\_ncausal\\_10\\_trait.rds & /home/hs3393/cb\\_Mar/simulation\\_result/hyprcoloc/hyp\\_real\\_simulation\\_10trait/result/sample\\_0\\_real\\_simulation\\_4\\_ncausal\\_10\\_trait\\_ntr\\_10\\_hypercoloc.rds\\\\\n", "\t5 & 1 & 1 & 1 & 4 & 4 & 4 & 1 & 1 & 0 & 1 & /mnt/vast/hpc/csg/hs3393/cb\\_Mar/simulation\\_data/real\\_simulation\\_10trait/sample\\_1\\_real\\_simulation\\_1\\_ncausal\\_10\\_trait.rds & /home/hs3393/cb\\_Mar/simulation\\_result/hyprcoloc/hyp\\_real\\_simulation\\_10trait/result/sample\\_1\\_real\\_simulation\\_1\\_ncausal\\_10\\_trait\\_ntr\\_10\\_hypercoloc.rds\\\\\n", "\t6 & 2 & 1 & 2 & 6 & 6 & 7 & 2 & 2 & 0 & 2 & /mnt/vast/hpc/csg/hs3393/cb\\_Mar/simulation\\_data/real\\_simulation\\_10trait/sample\\_1\\_real\\_simulation\\_2\\_ncausal\\_10\\_trait.rds & /home/hs3393/cb\\_Mar/simulation\\_result/hyprcoloc/hyp\\_real\\_simulation\\_10trait/result/sample\\_1\\_real\\_simulation\\_2\\_ncausal\\_10\\_trait\\_ntr\\_10\\_hypercoloc.rds\\\\\n", "\\end{tabular}\n" ], "text/markdown": [ "\n", "A tibble: 6 × 12\n", "\n", "| | total_causal_var_number <int> | perfect_causal_var_number <dbl> | partial_causal_var_number <dbl> | true_trait_number <dbl> | predict_trait_number <int> | total_trait_number <dbl> | true_set_number <dbl> | total_set_number <int> | single_set_number <int> | max_causal <int> | file <chr> | out_file <chr> |\n", "|---|---|---|---|---|---|---|---|---|---|---|---|---|\n", "| 1 | 1 | 1 | 1 | 5 | 5 | 5 | 1 | 1 | 0 | 1 | /mnt/vast/hpc/csg/hs3393/cb_Mar/simulation_data/real_simulation_10trait/sample_0_real_simulation_1_ncausal_10_trait.rds | /home/hs3393/cb_Mar/simulation_result/hyprcoloc/hyp_real_simulation_10trait/result/sample_0_real_simulation_1_ncausal_10_trait_ntr_10_hypercoloc.rds |\n", "| 2 | 2 | 1 | 1 | 5 | 5 | 8 | 1 | 1 | 0 | 2 | /mnt/vast/hpc/csg/hs3393/cb_Mar/simulation_data/real_simulation_10trait/sample_0_real_simulation_2_ncausal_10_trait.rds | /home/hs3393/cb_Mar/simulation_result/hyprcoloc/hyp_real_simulation_10trait/result/sample_0_real_simulation_2_ncausal_10_trait_ntr_10_hypercoloc.rds |\n", "| 3 | 3 | 0 | 2 | 4 | 4 | 8 | 2 | 2 | 0 | 3 | /mnt/vast/hpc/csg/hs3393/cb_Mar/simulation_data/real_simulation_10trait/sample_0_real_simulation_3_ncausal_10_trait.rds | /home/hs3393/cb_Mar/simulation_result/hyprcoloc/hyp_real_simulation_10trait/result/sample_0_real_simulation_3_ncausal_10_trait_ntr_10_hypercoloc.rds |\n", "| 4 | 4 | 0 | 3 | 10 | 10 | 17 | 3 | 3 | 0 | 3 | /mnt/vast/hpc/csg/hs3393/cb_Mar/simulation_data/real_simulation_10trait/sample_0_real_simulation_4_ncausal_10_trait.rds | /home/hs3393/cb_Mar/simulation_result/hyprcoloc/hyp_real_simulation_10trait/result/sample_0_real_simulation_4_ncausal_10_trait_ntr_10_hypercoloc.rds |\n", "| 5 | 1 | 1 | 1 | 4 | 4 | 4 | 1 | 1 | 0 | 1 | /mnt/vast/hpc/csg/hs3393/cb_Mar/simulation_data/real_simulation_10trait/sample_1_real_simulation_1_ncausal_10_trait.rds | /home/hs3393/cb_Mar/simulation_result/hyprcoloc/hyp_real_simulation_10trait/result/sample_1_real_simulation_1_ncausal_10_trait_ntr_10_hypercoloc.rds |\n", "| 6 | 2 | 1 | 2 | 6 | 6 | 7 | 2 | 2 | 0 | 2 | /mnt/vast/hpc/csg/hs3393/cb_Mar/simulation_data/real_simulation_10trait/sample_1_real_simulation_2_ncausal_10_trait.rds | /home/hs3393/cb_Mar/simulation_result/hyprcoloc/hyp_real_simulation_10trait/result/sample_1_real_simulation_2_ncausal_10_trait_ntr_10_hypercoloc.rds |\n", "\n" ], "text/plain": [ " total_causal_var_number perfect_causal_var_number partial_causal_var_number\n", "1 1 1 1 \n", "2 2 1 1 \n", "3 3 0 2 \n", "4 4 0 3 \n", "5 1 1 1 \n", "6 2 1 2 \n", " true_trait_number predict_trait_number total_trait_number true_set_number\n", "1 5 5 5 1 \n", "2 5 5 8 1 \n", "3 4 4 8 2 \n", "4 10 10 17 3 \n", "5 4 4 4 1 \n", "6 6 6 7 2 \n", " total_set_number single_set_number max_causal\n", "1 1 0 1 \n", "2 1 0 2 \n", "3 2 0 3 \n", "4 3 0 3 \n", "5 1 0 1 \n", "6 2 0 2 \n", " file \n", "1 /mnt/vast/hpc/csg/hs3393/cb_Mar/simulation_data/real_simulation_10trait/sample_0_real_simulation_1_ncausal_10_trait.rds\n", "2 /mnt/vast/hpc/csg/hs3393/cb_Mar/simulation_data/real_simulation_10trait/sample_0_real_simulation_2_ncausal_10_trait.rds\n", "3 /mnt/vast/hpc/csg/hs3393/cb_Mar/simulation_data/real_simulation_10trait/sample_0_real_simulation_3_ncausal_10_trait.rds\n", "4 /mnt/vast/hpc/csg/hs3393/cb_Mar/simulation_data/real_simulation_10trait/sample_0_real_simulation_4_ncausal_10_trait.rds\n", "5 /mnt/vast/hpc/csg/hs3393/cb_Mar/simulation_data/real_simulation_10trait/sample_1_real_simulation_1_ncausal_10_trait.rds\n", "6 /mnt/vast/hpc/csg/hs3393/cb_Mar/simulation_data/real_simulation_10trait/sample_1_real_simulation_2_ncausal_10_trait.rds\n", " out_file \n", "1 /home/hs3393/cb_Mar/simulation_result/hyprcoloc/hyp_real_simulation_10trait/result/sample_0_real_simulation_1_ncausal_10_trait_ntr_10_hypercoloc.rds\n", "2 /home/hs3393/cb_Mar/simulation_result/hyprcoloc/hyp_real_simulation_10trait/result/sample_0_real_simulation_2_ncausal_10_trait_ntr_10_hypercoloc.rds\n", "3 /home/hs3393/cb_Mar/simulation_result/hyprcoloc/hyp_real_simulation_10trait/result/sample_0_real_simulation_3_ncausal_10_trait_ntr_10_hypercoloc.rds\n", "4 /home/hs3393/cb_Mar/simulation_result/hyprcoloc/hyp_real_simulation_10trait/result/sample_0_real_simulation_4_ncausal_10_trait_ntr_10_hypercoloc.rds\n", "5 /home/hs3393/cb_Mar/simulation_result/hyprcoloc/hyp_real_simulation_10trait/result/sample_1_real_simulation_1_ncausal_10_trait_ntr_10_hypercoloc.rds\n", "6 /home/hs3393/cb_Mar/simulation_result/hyprcoloc/hyp_real_simulation_10trait/result/sample_1_real_simulation_2_ncausal_10_trait_ntr_10_hypercoloc.rds" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "result = readRDS(\"/home/hs3393/cb_Mar/simulation_result/hyprcoloc/hyp_real_simulation_10trait/summary/result_summary.rds\")\n", "head(result)" ] }, { "cell_type": "markdown", "id": "e2de6b0e-0b66-4325-a064-31e8e687e059", "metadata": { "kernel": "SoS" }, "source": [ "## Summary code" ] }, { "cell_type": "code", "execution_count": null, "id": "f8d52708-d069-41f2-a3a9-6f475a9726cc", "metadata": { "kernel": "SoS" }, "outputs": [], "source": [ "[coloc_summary]\n", "parameter: folder = path\n", "parameter: cwd = path(\"output\")\n", "parameter: job_size = 1\n", "parameter: walltime = \"50h\"\n", "parameter: mem = \"30G\"\n", "parameter: numThreads = 1\n", "parameter: container = \"\"\n", "input: folder , group_by = 1\n", "output: f'{cwd:a}/{_input[0]:b}_summary.rds'\n", "task: trunk_workers = 1, trunk_size = job_size, walltime = walltime, mem = mem, cores = numThreads, tags = f'{step_name}_{_output[0]:bn}'\n", "R: expand = '${ }', stdout = f\"{_output:n}.stdout\", stderr = f\"{_output:n}.stderr\", container = container\n", " library(\"tidyverse\")\n", " source(\"/home/hs3393/cloud_colocalization/simulation_code/colocboost_summary.r\")\n", " filenames <- list.files(${folder:r}, pattern=\"*.rds$\", full.names=TRUE, recursive = T)\n", " read_and_extract_rds <- function(file_path) {\n", " rds_file <- readRDS(file_path) # Read the RDS file\n", " if(length(rds_file$coloc_set) == 0){\n", " rds_file$coloc_set = NULL\n", " }\n", " data = colocboost_summary(rds_file$true_variant, \n", " rds_file$true_trait, rds_file$coloc_set, rds_file$coloc_trait)\n", " table <- tibble(total_causal_var_number = data$total_causal_var_number,\n", " perfect_causal_var_number = data$perfect_causal_var_number,\n", " partial_causal_var_number = data$partial_causal_var_number,\n", " true_trait_number = data$true_trait_number,\n", " predict_trait_number = data$predict_trait_number,\n", " total_trait_number = data$total_trait_number,\n", " true_set_number = data$true_set_number,\n", " total_set_number = data$total_set_number,\n", " single_set_number = length(rds_file$csets),\n", " max_causal = max(rds_file$true_trait %>% unlist() %>% table()),\n", " file = rds_file$file,\n", " out_file = file_path)\n", " return(table)\n", " }\n", "\n", " combined_table <- map_dfr(filenames, read_and_extract_rds)\n", " saveRDS(combined_table, ${_output:r})" ] }, { "cell_type": "markdown", "id": "edee427f-bd66-4c86-bfd5-ad24645cf07b", "metadata": { "kernel": "SoS" }, "source": [ "## Summary Bash commands" ] }, { "cell_type": "markdown", "id": "b27f35b5-7328-4900-bb84-e31bc03df6c8", "metadata": { "kernel": "SoS" }, "source": [ "### ColocBoost summary" ] }, { "cell_type": "code", "execution_count": null, "id": "79aec1c7-7792-4758-a82f-b9c061cbbfbe", "metadata": { "kernel": "SoS" }, "outputs": [], "source": [ "## 2 trait summary\n", "\n", "data_dir=\"/home/hs3393/cb_Mar/simulation_result/real_simulation_2trait/\"\n", "mkdir -p ${data_dir}/summary\n", "cd ${data_dir}/summary\n", "\n", "cat << 'EOF' > summary_script\n", "#!/bin/bash -l\n", "# NOTE the -l flag!\n", "#\n", "#SBATCH -t 10:00:00\n", "#SBATCH --mem=30000\n", "#SBATCH -J summary\n", "#SBATCH -o DATA_DIR/log/summary.\"%j\".out\n", "#SBATCH -e DATA_DIR/log/summary.\"%j\".err\n", "\n", "source ~/mamba_activate.sh\n", "\n", "sos run /home/hs3393/cb_Mar/simulation_code/4.Result_Summary.ipynb coloc_summary \\\n", " --folder DATA_DIR/result \\\n", " --cwd DATA_DIR/summary\n", "EOF\n", "\n", "\n", "base_script=\"summary_script\"\n", "output_script=\"summary.sh\"\n", "cat ${base_script}| sed \"s|DATA_DIR|${data_dir}|g\" > ${output_script}\n", "sbatch ${output_script}\n", "\n", "## 5 trait summary\n", "\n", "data_dir=\"/home/hs3393/cb_Mar/simulation_result/real_simulation_5trait/\"\n", "mkdir -p ${data_dir}/summary\n", "cd ${data_dir}/summary\n", "\n", "cat << 'EOF' > summary_script\n", "#!/bin/bash -l\n", "# NOTE the -l flag!\n", "#\n", "#SBATCH -t 10:00:00\n", "#SBATCH --mem=30000\n", "#SBATCH -J summary\n", "#SBATCH -o DATA_DIR/log/summary.\"%j\".out\n", "#SBATCH -e DATA_DIR/log/summary.\"%j\".err\n", "\n", "source ~/mamba_activate.sh\n", "\n", "sos run /home/hs3393/cb_Mar/simulation_code/4.Result_Summary.ipynb coloc_summary \\\n", " --folder DATA_DIR/result \\\n", " --cwd DATA_DIR/summary\n", "EOF\n", "\n", "\n", "base_script=\"summary_script\"\n", "output_script=\"summary.sh\"\n", "cat ${base_script}| sed \"s|DATA_DIR|${data_dir}|g\" > ${output_script}\n", "sbatch ${output_script}\n", "\n", "## 10 trait summary\n", "\n", "data_dir=\"/home/hs3393/cb_Mar/simulation_result/real_simulation_10trait/\"\n", "mkdir -p ${data_dir}/summary\n", "cd ${data_dir}/summary\n", "\n", "cat << 'EOF' > summary_script\n", "#!/bin/bash -l\n", "# NOTE the -l flag!\n", "#\n", "#SBATCH -t 10:00:00\n", "#SBATCH --mem=30000\n", "#SBATCH -J summary\n", "#SBATCH -o DATA_DIR/log/summary.\"%j\".out\n", "#SBATCH -e DATA_DIR/log/summary.\"%j\".err\n", "\n", "source ~/mamba_activate.sh\n", "\n", "sos run /home/hs3393/cb_Mar/simulation_code/4.Result_Summary.ipynb coloc_summary \\\n", " --folder DATA_DIR/result \\\n", " --cwd DATA_DIR/summary\n", "EOF\n", "\n", "\n", "base_script=\"summary_script\"\n", "output_script=\"summary.sh\"\n", "cat ${base_script}| sed \"s|DATA_DIR|${data_dir}|g\" > ${output_script}\n", "sbatch ${output_script}\n", "\n", "## 20 trait summary\n", "\n", "data_dir=\"/home/hs3393/cb_Mar/simulation_result/real_simulation_20trait/\"\n", "mkdir -p ${data_dir}/summary\n", "cd ${data_dir}/summary\n", "\n", "cat << 'EOF' > summary_script\n", "#!/bin/bash -l\n", "# NOTE the -l flag!\n", "#\n", "#SBATCH -t 10:00:00\n", "#SBATCH --mem=30000\n", "#SBATCH -J summary\n", "#SBATCH -o DATA_DIR/log/summary.\"%j\".out\n", "#SBATCH -e DATA_DIR/log/summary.\"%j\".err\n", "\n", "source ~/mamba_activate.sh\n", "\n", "sos run /home/hs3393/cb_Mar/simulation_code/4.Result_Summary.ipynb coloc_summary \\\n", " --folder DATA_DIR/result \\\n", " --cwd DATA_DIR/summary\n", "EOF\n", "\n", "\n", "base_script=\"summary_script\"\n", "output_script=\"summary.sh\"\n", "cat ${base_script}| sed \"s|DATA_DIR|${data_dir}|g\" > ${output_script}\n", "sbatch ${output_script}" ] }, { "cell_type": "markdown", "id": "09899580-cec9-481e-a0b3-1fb68c120473", "metadata": { "kernel": "SoS" }, "source": [ "### Hyprcoloc summary" ] }, { "cell_type": "code", "execution_count": null, "id": "845bf29f-2126-4234-bc7b-2c10d1d32f69", "metadata": { "kernel": "SoS" }, "outputs": [], "source": [ "data_dir=\"/home/hs3393/cb_Mar/simulation_result/hyprcoloc/hyp_real_simulation_2trait/\"\n", "mkdir -p ${data_dir}/summary\n", "cd ${data_dir}/summary\n", "\n", "cat << 'EOF' > summary_script\n", "#!/bin/bash -l\n", "# NOTE the -l flag!\n", "#\n", "#SBATCH -t 10:00:00\n", "#SBATCH --mem=30000\n", "#SBATCH -J summary\n", "#SBATCH -o DATA_DIR/log/summary.\"%j\".out\n", "#SBATCH -e DATA_DIR/log/summary.\"%j\".err\n", "\n", "source ~/mamba_activate.sh\n", "\n", "sos run /home/hs3393/cb_Mar/simulation_code/4.Result_Summary.ipynb coloc_summary \\\n", " --folder DATA_DIR/result \\\n", " --cwd DATA_DIR/summary\n", "EOF\n", "\n", "\n", "base_script=\"summary_script\"\n", "output_script=\"summary.sh\"\n", "cat ${base_script}| sed \"s|DATA_DIR|${data_dir}|g\" > ${output_script}\n", "sbatch ${output_script}\n", "\n", "\n", "data_dir=\"/home/hs3393/cb_Mar/simulation_result/hyprcoloc/hyp_real_simulation_5trait/\"\n", "mkdir -p ${data_dir}/summary\n", "cd ${data_dir}/summary\n", "\n", "cat << 'EOF' > summary_script\n", "#!/bin/bash -l\n", "# NOTE the -l flag!\n", "#\n", "#SBATCH -t 10:00:00\n", "#SBATCH --mem=30000\n", "#SBATCH -J summary\n", "#SBATCH -o DATA_DIR/log/summary.\"%j\".out\n", "#SBATCH -e DATA_DIR/log/summary.\"%j\".err\n", "\n", "source ~/mamba_activate.sh\n", "\n", "sos run /home/hs3393/cb_Mar/simulation_code/4.Result_Summary.ipynb coloc_summary \\\n", " --folder DATA_DIR/result \\\n", " --cwd DATA_DIR/summary\n", "EOF\n", "\n", "\n", "base_script=\"summary_script\"\n", "output_script=\"summary.sh\"\n", "cat ${base_script}| sed \"s|DATA_DIR|${data_dir}|g\" > ${output_script}\n", "sbatch ${output_script}\n", "\n", "data_dir=\"/home/hs3393/cb_Mar/simulation_result/hyprcoloc/hyp_real_simulation_10trait/\"\n", "mkdir -p ${data_dir}/summary\n", "cd ${data_dir}/summary\n", "\n", "cat << 'EOF' > summary_script\n", "#!/bin/bash -l\n", "# NOTE the -l flag!\n", "#\n", "#SBATCH -t 10:00:00\n", "#SBATCH --mem=30000\n", "#SBATCH -J summary\n", "#SBATCH -o DATA_DIR/log/summary.\"%j\".out\n", "#SBATCH -e DATA_DIR/log/summary.\"%j\".err\n", "\n", "source ~/mamba_activate.sh\n", "\n", "sos run /home/hs3393/cb_Mar/simulation_code/4.Result_Summary.ipynb coloc_summary \\\n", " --folder DATA_DIR/result \\\n", " --cwd DATA_DIR/summary\n", "EOF\n", "\n", "\n", "base_script=\"summary_script\"\n", "output_script=\"summary.sh\"\n", "cat ${base_script}| sed \"s|DATA_DIR|${data_dir}|g\" > ${output_script}\n", "sbatch ${output_script}\n", "\n", "data_dir=\"/home/hs3393/cb_Mar/simulation_result/hyprcoloc/hyp_real_simulation_20trait/\"\n", "mkdir -p ${data_dir}/summary\n", "cd ${data_dir}/summary\n", "\n", "cat << 'EOF' > summary_script\n", "#!/bin/bash -l\n", "# NOTE the -l flag!\n", "#\n", "#SBATCH -t 10:00:00\n", "#SBATCH --mem=30000\n", "#SBATCH -J summary\n", "#SBATCH -o DATA_DIR/log/summary.\"%j\".out\n", "#SBATCH -e DATA_DIR/log/summary.\"%j\".err\n", "\n", "source ~/mamba_activate.sh\n", "\n", "sos run /home/hs3393/cb_Mar/simulation_code/4.Result_Summary.ipynb coloc_summary \\\n", " --folder DATA_DIR/result \\\n", " --cwd DATA_DIR/summary\n", "EOF\n", "\n", "\n", "base_script=\"summary_script\"\n", "output_script=\"summary.sh\"\n", "cat ${base_script}| sed \"s|DATA_DIR|${data_dir}|g\" > ${output_script}\n", "sbatch ${output_script}" ] }, { "cell_type": "markdown", "id": "32a64b70-af4b-4bfe-8842-92bab51d2030", "metadata": { "kernel": "SoS" }, "source": [ "### MOLOC summary" ] }, { "cell_type": "code", "execution_count": null, "id": "226c329c-1651-46a9-8204-427fc5082c74", "metadata": { "kernel": "SoS" }, "outputs": [], "source": [ "# moloc \n", "\n", "data_dir=\"/home/hs3393/cb_Mar/simulation_result/moloc/moloc_real_simulation_2trait/\"\n", "mkdir -p ${data_dir}/summary\n", "cd ${data_dir}/summary\n", "\n", "cat << 'EOF' > summary_script\n", "#!/bin/bash -l\n", "# NOTE the -l flag!\n", "#\n", "#SBATCH -t 8:00:00\n", "#SBATCH --mem=30000\n", "#SBATCH -J sum\n", "#SBATCH -o DATA_DIR/log/summary.\"%j\".out\n", "#SBATCH -e DATA_DIR/log/summary.\"%j\".err\n", "\n", "source ~/mamba_activate.sh\n", "\n", "sos run /home/hs3393/cb_Mar/simulation_code/4.Result_Summary.ipynb coloc_summary \\\n", " --folder DATA_DIR/result \\\n", " --cwd DATA_DIR/summary\n", "EOF\n", "\n", "\n", "base_script=\"summary_script\"\n", "output_script=\"summary.sh\"\n", "cat ${base_script}| sed \"s|DATA_DIR|${data_dir}|g\" > ${output_script}\n", "sbatch ${output_script}\n" ] }, { "cell_type": "markdown", "id": "780b76cb-8c50-44c9-b13a-5da06b4e2c71", "metadata": { "kernel": "SoS" }, "source": [ "### SuSiE coloc summary" ] }, { "cell_type": "code", "execution_count": null, "id": "faf6e4e9-0759-4630-bbf5-a9fce89ed607", "metadata": { "kernel": "SoS" }, "outputs": [], "source": [ "data_dir=\"/home/hs3393/cb_Mar/simulation_result/susie_coloc/susie_coloc_real_simulation_2trait\"\n", "mkdir -p ${data_dir}/summary\n", "cd ${data_dir}/summary\n", "\n", "cat << 'EOF' > summary_script\n", "#!/bin/bash -l\n", "# NOTE the -l flag!\n", "#\n", "#SBATCH -t 8:00:00\n", "#SBATCH --mem=30000\n", "#SBATCH -J sum\n", "#SBATCH -o DATA_DIR/log/summary.\"%j\".out\n", "#SBATCH -e DATA_DIR/log/summary.\"%j\".err\n", "\n", "source ~/mamba_activate.sh\n", "\n", "sos run /home/hs3393/cb_Mar/simulation_code/4.Result_Summary.ipynb coloc_summary \\\n", " --folder DATA_DIR/result \\\n", " --cwd DATA_DIR/summary\n", "EOF\n", "\n", "\n", "base_script=\"summary_script\"\n", "output_script=\"summary.sh\"\n", "cat ${base_script}| sed \"s|DATA_DIR|${data_dir}|g\" > ${output_script}\n", "sbatch ${output_script}\n" ] } ], "metadata": { "kernelspec": { "display_name": "SoS", "language": "sos", "name": "sos" }, "language_info": { "codemirror_mode": "sos", "file_extension": ".sos", "mimetype": "text/x-sos", "name": "sos", "nbconvert_exporter": "sos_notebook.converter.SoS_Exporter", "pygments_lexer": "sos" }, "sos": { "kernels": [ [ "R", "ir", "R", "", "" ], [ "SoS", "sos", "", "", "sos" ] ], "version": "0.24.3" } }, "nbformat": 4, "nbformat_minor": 5 }