Process 10x .mtx matrix, feature, and barcode files into single CSV

process_10x_files.sh

#!/bin/bash
# set -x

# Inspired by https://kb.10xgenomics.com/hc/en-us/articles/360023793031-How-can-I-convert-the-feature-barcode-matrix-from-Cell-Ranger-3-to-a-CSV-file-

FILES="GSM*_barcodes.tsv"

for i in $FILES
do
    filename="${i%_*}" # Extract prefix before _barcodes.txv
    echo "Working on $filename..."
    echo -e "\tSorting features, barcodes, & matrix files."

    # Print line number along with contents of _barcodes.tsv and _genes.tsv
    cat "${filename}_barcodes.tsv" | awk -F "\t" 'BEGIN { OFS = "," }; {print NR,$1}' | sort -t, -k 1b,1 > tmp.barcodes.numbered &
    cat "${filename}_features.tsv" | awk -F "\t" 'BEGIN { OFS = "," }; {print NR,$1,$2}' | sort -t, -k 1b,1 > tmp.features.numbered &
    # Skip the header lines and sort _matrix.mtx
    cat "${filename}_matrix.mtx" | tail -n +4 | awk -F " " 'BEGIN { OFS = "," }; {print $1,$2,$3}' | sort -t, -k 1b,1 > tmp.feature_sorted_mtx &
    cat "${filename}_matrix.mtx" | tail -n +4 | awk -F " " 'BEGIN { OFS = "," }; {print $1,$2,$3}' | sort -t, -k 2b,2 > tmp.barcode_sorted_mtx &

    echo -e "\t... (waiting for completion)"
    wait $(jobs -p)

    echo -e "\tGenerating final matrix."
    # echo "barcode,feature_id,feature_name,umi_count" > "${filename}.final_matrix.csv"
    # Use join to replace line number with barcodes and genes
    join -t, -1 1 -2 1 tmp.features.numbered tmp.feature_sorted_mtx | cut -d, -f 2,3,4,5,6 | sort -t, -k 3b,3 | join -t, -1 1 -2 3 tmp.barcodes.numbered - | cut -d, -f 2,3,4,5,6 > "${filename}.final_matrix.csv"

    rm tmp.barcodes.numbered tmp.features.numbered tmp.feature_sorted_mtx tmp.barcode_sorted_mtx

done