sra_scripts/replace_srx_to_sample.sh at main · lerdruplab/sra_scripts · GitHub

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#!/bin/bash

# file containing SRR to sample name mappings
table_file="srx_sample_name_v0.2.2.csv"

# loop through each line in the table file
while IFS=',' read -r srx_name sample_name; do

    # find and rename R1 fastq.gz files
    find . -type f -name "${srx_name}_*_1.fastq.gz" | while read -r file; do

        file_dir=$(dirname "$file")
        srx_srr=$(basename "$file")
        mv $file ${file_dir}/${sample_name}.${srx_srr}
        echo "Renamed $file to ${sample_name}.${srx_srr}"

    done

    # find and rename R2 fastq.gz files if they exist
    find . -type f -name "${srx_name}_*_2.fastq.gz" | while read -r file; do

        file_dir=$(dirname "$file")
        srx_srr=$(basename "$file")
        mv $file ${file_dir}/${sample_name}.${srx_srr}
        echo "Renamed $file to ${sample_name}.${srx_srr}"

    done

    # find and rename non-paired files if they exist
    find . -type f -name "${srx_name}*.fastq.gz" | while read -r file; do

        file_dir=$(dirname "$file")
        srx_srr=$(basename "$file")
        mv $file ${file_dir}/${sample_name}.${srx_srr}
        echo "Renamed $file to ${sample_name}.${srx_srr}"

    done

done <"$table_file"