From cad3462229d60ba4cf74d7e28115940eb2401ac0 Mon Sep 17 00:00:00 2001
From: Meeta Mistry <meeta.mistry@gmail.com>
Date: Thu, 6 Jun 2024 14:16:56 -0400
Subject: [PATCH] Create bcbio_output_summary.sh

---
 chipseq/bcbio_output_summary.sh | 54 +++++++++++++++++++++++++++++++++
 1 file changed, 54 insertions(+)
 create mode 100644 chipseq/bcbio_output_summary.sh

diff --git a/chipseq/bcbio_output_summary.sh b/chipseq/bcbio_output_summary.sh
new file mode 100644
index 0000000..61bc933
--- /dev/null
+++ b/chipseq/bcbio_output_summary.sh
@@ -0,0 +1,54 @@
+#/bin/bash
+# Written by Will Gammerdinger at HSPH on September 15th, 2022.
+
+# Assign input and output files to variables
+metadata_file=/n/data1/cores/bcbio/PIs/andrew_lassar/hbc_lassar_mouse_TF_profiling_FoxC_atac_cutnrun_rnaseq_hbc04930/cutnrun/meta/FOXC.csv
+multiqc_file=/n/data1/cores/bcbio/PIs/andrew_lassar/hbc_lassar_mouse_TF_profiling_FoxC_atac_cutnrun_rnaseq_hbc04930/cutnrun/final/2024-02-01_FOXC/multiqc/multiqc_data/multiqc_general_stats.txt
+sample_directory=/n/data1/cores/bcbio/PIs/andrew_lassar/hbc_lassar_mouse_TF_profiling_FoxC_atac_cutnrun_rnaseq_hbc04930/cutnrun/final/
+sample_prefix=X
+input_antibody_label=input
+output_file=/n/data1/cores/bcbio/PIs/andrew_lassar/hbc_lassar_mouse_TF_profiling_FoxC_atac_cutnrun_rnaseq_hbc04930/cutnrun/final/summarized_report.txt
+
+# Print Header line
+echo -e "sample\tantibody\ttreatment\treads\tmapped_reads\tmapping_percent\tpeaks\tRiP_percent\tPBC1\tPBC2\tBottlenecking\tNRF\tComplexity\tGC_percent" > $output_file;
+
+# Determine the column number for the columns on interest
+antibody_column=`awk -F ',' 'NR==1{for (i=1; i<=NF; i++) { if ($i == "antibody") { print i } }}' $metadata_file`
+phenotype_column=`awk -F ',' 'NR==1{for (i=1; i<=NF; i++) { if ($i == "phenotype") { print i } }}' $metadata_file`
+treatment_column=`awk -F ',' 'NR==1{for (i=1; i<=NF; i++) { if ($i == "treatment") { print i } }}' $metadata_file`
+reads_column=`awk 'NR==1{for (i=1; i<=NF; i++) { if ($i == "bcbio_mqc-generalstats-bcbio-Total_reads") { print i } }}' $multiqc_file`
+mapped_reads_column=`awk 'NR==1{for (i=1; i<=NF; i++) { if ($i == "bcbio_mqc-generalstats-bcbio-Mapped_reads") { print i } }}' $multiqc_file`
+mapping_percent_column=`awk 'NR==1{for (i=1; i<=NF; i++) { if ($i == "Samtools_mqc-generalstats-samtools-reads_mapped_percent") { print i } }}' $multiqc_file`
+RiP_percent_column=`awk 'NR==1{for (i=1; i<=NF; i++) { if ($i == "bcbio_mqc-generalstats-bcbio-RiP_pct") { print i } }}' $multiqc_file`
+PBC1_column=`awk 'NR==1{for (i=1; i<=NF; i++) { if ($i == "bcbio_mqc-generalstats-bcbio-PBC1") { print i } }}' $multiqc_file`
+PBC2_column=`awk 'NR==1{for (i=1; i<=NF; i++) { if ($i == "bcbio_mqc-generalstats-bcbio-PBC2") { print i } }}' $multiqc_file`
+Bottlenecking_column=`awk 'NR==1{for (i=1; i<=NF; i++) { if ($i == "bcbio_mqc-generalstats-bcbio-bottlenecking") { print i } }}' $multiqc_file`
+NRF_column=`awk 'NR==1{for (i=1; i<=NF; i++) { if ($i == "bcbio_mqc-generalstats-bcbio-NRF") { print i } }}' $multiqc_file`
+Complexity_column=`awk 'NR==1{for (i=1; i<=NF; i++) { if ($i == "bcbio_mqc-generalstats-bcbio-complexity") { print i } }}' $multiqc_file`
+GC_percent_column=`awk 'NR==1{for (i=1; i<=NF; i++) { if ($i == "FastQC_mqc-generalstats-fastqc-percent_gc") { print i } }}' $multiqc_file`
+
+# For each sample gather the various statistics and print to a the summarized report
+for i in ${sample_directory}${sample_prefix}*; do 
+    sample=`basename $i`
+    antibody=`grep $sample $metadata_file | awk -F ',' -v antibody_column=$antibody_column '{print $antibody_column}'`
+    sample_type=`grep $sample $metadata_file | awk -F ',' -v phenotype_column=$phenotype_column '{print $phenotype_column}'`
+    treatment=`grep $sample $metadata_file | awk -F ',' -v treatment_column=$treatment_column '{print $treatment_column}'`
+    reads=`grep $sample $multiqc_file | awk -F'\t' -v reads_column=$reads_column '{print $reads_column}' | sed 's/.0$//g'`
+    mapped_reads=`grep $sample $multiqc_file | awk -F'\t' -v mapped_reads_column=$mapped_reads_column '{print $mapped_reads_column}' | sed 's/.0$//g'`
+    mapping_percent=`grep $sample $multiqc_file  | awk -F'\t' -v mapping_percent_column=$mapping_percent_column '{print $mapping_percent_column}' | head -c 5`
+    if [[ $antibody == $input_antibody_label ]]; then
+        peaks="NA"
+    else
+        peaks=`wc -l ${sample_directory}${sample}/macs2/${sample}_peaks.* | awk 'NR==1{print $1}'`
+    fi
+    RiP_percent=`grep $sample $multiqc_file | awk -F'\t' -v RiP_percent_column=$RiP_percent_column '{print $RiP_percent_column}'`
+    PBC1=`grep $sample $multiqc_file | awk -F'\t' -v PBC1_column=$PBC1_column '{print $PBC1_column}' | head -c 5`
+    PBC2=`grep $sample $multiqc_file | awk -F'\t' -v PBC2_column=$PBC2_column '{print $PBC2_column}' | head -c 5`
+    Bottlenecking=`grep $sample $multiqc_file | awk -F'\t' -v Bottlenecking_column=$Bottlenecking_column '{print $Bottlenecking_column}'`
+    NRF=`grep $sample $multiqc_file | awk -F'\t' -v NRF_column=$NRF_column '{print $NRF_column}' | head -c 5`
+    Complexity=`grep $sample $multiqc_file | awk -F'\t' -v Complexity_column=$Complexity_column '{print $Complexity_column}'`
+    GC_percent=`grep $sample $multiqc_file | awk -F'\t' -v GC_percent_column=$GC_percent_column '{print $GC_percent_column}'`
+    echo -e  "$sample\t$antibody\t$treatment\t$reads\t$mapped_reads\t$mapping_percent\t$peaks\t$RiP_percent\t$PBC1\t$PBC2\t$Bottlenecking\t$NRF\t$Complexity\t$GC_percent" >> $output_file;
+done
+
+echo -e "The summarized report has been created and can be found here:\n\t$output_file"