create_gistic_plots.sh

#!/bin/bash

# Settings
subsets=( tumor metastasis ) # pattern to recognize desired files (from sample_id) tumor metastasis

aceseq_seg_path=.
project_path=/dh-projects/pedion/A05R/analysis
gistic_path=/applications/otp/software/gistic2/2.0.23
ref_gene_path=/applications/otp/software/gistic2/2.0.23/refgenefiles/hg19.mat
conda_path=~/miniconda3/bin
ctrl=control # blood-01

# Processing
pid_path="$project_path/whole_genome_sequencing/results_per_pid"
source $conda_path/activate gistic

for sub in "${subsets[@]}"; do   # The quotes are necessary here

    files=$(ls $pid_path/*/ACEseq*$sub*$ctrl*/*desired_info.txt | paste -s -d, -)

    # gistic requires the folder to exist
    mkdir -p $sub

    perl $aceseq_seg_path/aceseq2seg.pl -f $files > $sub/$sub.seg

    # $gistic_path/gp_gistic2_from_seg -b $sub -seg $sub.seg -refgene $ref_gene_path
    $gistic_path/gistic2 -b $sub -seg $sub/$sub.seg -refgene $ref_gene_path

    perl gistic_2_dataframe_for_plotting.pl $sub/scores.gistic $sub/del_genes.conf_75.txt $sub/amp_genes.conf_75.txt > $sub/gistic_table.tsv

    R -f plot_gistic_table.r --args $sub/gistic_table.tsv

done