example_pipeline_custom.sh

#!/bin/bash

# Example of a TAD_Pathways Analysis applied to a Custom SNP list
# For this example, the custom SNP list is the GWAS findings for
# Prostate Cancer. The the data is used as a custom input.
set -o errexit

# Define filenames
tad_file='data/hESC_domains_hg19.bed'
candidate_snp_file='custom_example.csv'
candidate_snp_location_file='results/custom_example_location.tsv'
candidate_snp_tad_file='results/custom_example_tad_results.tsv'
nearest_gene_file='results/custom_example_tad_results_nearest_gene.tsv'
trait='custom'
evidence_file='results/custom_gene_evidence.csv'
pathway_p_values_file='gestalt/custom_pvals.tsv'

# Generate index files (maps to TAD identifiers to enable fast lookup)
# 1000G SNP / genes / repeat elements
python scripts/generate_index_files.py --TAD-Boundary 'hESC' --TAD-File $tad_file

# Visualize SNPs and Genes in TADs
# Output histograms and line graphs of SNP/Gene/Repeat locations in TADs
# and gc content distribution across human and mouse tads
python scripts/visualize_genomic_elements.py --TAD-Boundary 'hESC' 
python scripts/visualize_gc_and_divergence.py --TAD-Boundary 'hESC' --TAD-File $tad_file

# Map SNPs to genomic location
Rscript --vanilla scripts/build_snp_list.R \
        --snp_file $candidate_snp_file \
        --output_file $candidate_snp_location_file

# Build a customized genelist based on SNP locations
python scripts/build_custom_tad_genelist.py \
        --snp_data_file $candidate_snp_location_file \
        --output_file $candidate_snp_tad_file \
        --TAD-Boundary 'hESC'

# Perform WebGestalt pathway analysis and parse results
Rscript --vanilla scripts/webgestalt_run.R \
        --tad_genelist_file $candidate_snp_tad_file \
        --output_name $trait

# Construct an evidence file - Nearest gene to gwas or not
python scripts/construct_evidence.py \
            --trait $trait \
            --gwas $nearest_gene_file \
            --pathway $pathway_p_values_file

# Summarize the evidence file
python scripts/summarize_evidence.py \
            --evidence $evidence_file \
            --snps $candidate_snp_tad_file \
            --output_file 'results/custom_gene_evidence_summary.tsv'

# Visualize overlap in TAD pathways curation
R --no-save --args $evidence_file \
                < scripts/integrative_summary.R