This script takes in the list of SRR terms and download the .fastq.gz files from ENA database

get_fastq_files_from_ENA.sh

#!/bin/bash

### Usage ###
# This script takes in the list of SRR terms and download the .fastq.gz files from ENA database

### Comments ###
# Create a file named "SRRs_to_process.txt" in the same directory as the script file and this file should have a list of single SRR ID as entries in every line.
# Fastq files will be downloaded in the same directory where the script is located. Script also generates an output file named "Number_of_reads_in_fastq_files.txt" which has information on the status of download of the fastq files and number of reads in the fastq file downloaded.
# Note: This script was tested in both Mac OS and linux OS and it requires "curl".

ena_fastq_dir="ftp://ftp.sra.ebi.ac.uk/vol1/fastq"

if [[ ! -e ./Number_of_reads_in_fastq_files.txt ]]; then
    touch ./Number_of_reads_in_fastq_files.txt
fi

while IFS= read -r line
do

  IFS=' ' read -a SRR <<< "$line"
  length=${#SRR}

  if [ "$length" == "9" ]
  then
    if curl ${ena_fastq_dir}/${SRR:0:6}/${SRR}/ > temp
    then echo "Temp file download successful" |& tee -a Number_of_reads_in_fastq_files.txt
    else echo "Temp file download failed" |& tee -a Number_of_reads_in_fastq_files.txt
    fi
    f="temp"
    num_l=$(zgrep . $f | wc -l)

    dt=$(date '+%d/%m/%Y %H:%M:%S');echo $dt |& tee -a Number_of_reads_in_fastq_files.txt
    echo ${SRR} |& tee -a Number_of_reads_in_fastq_files.txt
    if curl ${ena_fastq_dir}/${SRR:0:6}/${SRR}/${SRR}_1.fastq.gz > ${SRR}_1.fastq.gz
    then echo "Download successful" |& tee -a Number_of_reads_in_fastq_files.txt
    else 
      if curl ${ena_fastq_dir}/${SRR:0:6}/${SRR}/${SRR}.fastq.gz > ${SRR}_1.fastq.gz
      then echo "Download successful" |& tee -a Number_of_reads_in_fastq_files.txt
      else echo "Download failed" |& tee -a Number_of_reads_in_fastq_files.txt
      fi
    fi
    f=${SRR}_1.fastq.gz
    num_r=$(zgrep . $f | wc -l)
    echo "Fastq file: $f; Number of lines: $num_r; Number of reads: $(echo "scale=2; $num_r/4" | bc)" |& tee -a Number_of_reads_in_fastq_files.txt
    
    if [ "$num_l" == "2" ]
    then
      dt=$(date '+%d/%m/%Y %H:%M:%S');echo $dt |& tee -a Number_of_reads_in_fastq_files.txt
      echo ${SRR} |& tee -a Number_of_reads_in_fastq_files.txt
      if curl ${ena_fastq_dir}/${SRR:0:6}/${SRR}/${SRR}_2.fastq.gz > ${SRR}_2.fastq.gz
      then echo "Download successful" |& tee -a Number_of_reads_in_fastq_files.txt
      else echo "Download failed" |& tee -a Number_of_reads_in_fastq_files.txt
      fi
      f=${SRR}_2.fastq.gz
      num_r=$(zgrep . $f | wc -l)
      echo "Fastq file: $f; Number of lines: $num_r; Number of reads: $(echo "scale=2; $num_r/4" | bc)" |& tee -a Number_of_reads_in_fastq_files.txt
    fi
  fi

  if [ "$length" == "10" ]
  then
    if curl ${ena_fastq_dir}/${SRR:0:6}/00${SRR:9:10}/${SRR}/ > temp
    then echo "Temp file download successful" |& tee -a Number_of_reads_in_fastq_files.txt
    else echo "Download failed" |& tee -a Number_of_reads_in_fastq_files.txt
    fi
    f="temp"
    num_l=$(zgrep . $f | wc -l)

    dt=$(date '+%d/%m/%Y %H:%M:%S');echo $dt |& tee -a Number_of_reads_in_fastq_files.txt
    echo ${SRR} |& tee -a Number_of_reads_in_fastq_files.txt
    if curl ${ena_fastq_dir}/${SRR:0:6}/00${SRR:9:10}/${SRR}/${SRR}_1.fastq.gz > ${SRR}_1.fastq.gz
    then echo "Download successful" |& tee -a Number_of_reads_in_fastq_files.txt
    else 
      if curl ${ena_fastq_dir}/${SRR:0:6}/00${SRR:9:10}/${SRR}/${SRR}.fastq.gz > ${SRR}_1.fastq.gz
      then echo "Download successful" |& tee -a Number_of_reads_in_fastq_files.txt
      else echo "Download failed" |& tee -a Number_of_reads_in_fastq_files.txt
      fi
    fi
    f=${SRR}_1.fastq.gz
    num_r=$(zgrep . $f | wc -l)
    echo "Fastq file: $f; Number of lines: $num_r; Number of reads: $(echo "scale=2; $num_r/4" | bc)" |& tee -a Number_of_reads_in_fastq_files.txt

    if [ "$num_l" == "2" ]
    then
      dt=$(date '+%d/%m/%Y %H:%M:%S');echo $dt |& tee -a Number_of_reads_in_fastq_files.txt
      echo ${SRR} |& tee -a Number_of_reads_in_fastq_files.txt
      if curl ${ena_fastq_dir}/${SRR:0:6}/00${SRR:9:10}/${SRR}/${SRR}_2.fastq.gz > ${SRR}_2.fastq.gz
      then echo "Download successful" |& tee -a Number_of_reads_in_fastq_files.txt
      else echo "Download failed" |& tee -a Number_of_reads_in_fastq_files.txt
      fi
      f=${SRR}_2.fastq.gz
      num_r=$(zgrep . $f | wc -l)
      echo "Fastq file: $f; Number of lines: $num_r; Number of reads: $(echo "scale=2; $num_r/4" | bc)" |& tee -a Number_of_reads_in_fastq_files.txt
    fi
  fi

  if [ "$length" == "11" ]
  then
    if curl ${ena_fastq_dir}/${SRR:0:6}/0${SRR:9:11}/${SRR}/ > temp
    then echo "Temp file download successful" |& tee -a Number_of_reads_in_fastq_files.txt
    else echo "Temp file download failed" |& tee -a Number_of_reads_in_fastq_files.txt
    fi
    f="temp"
    num_l=$(zgrep . $f | wc -l)

    dt=$(date '+%d/%m/%Y %H:%M:%S');echo $dt |& tee -a Number_of_reads_in_fastq_files.txt
    echo ${SRR} |& tee -a Number_of_reads_in_fastq_files.txt
    if curl ${ena_fastq_dir}/${SRR:0:6}/0${SRR:9:11}/${SRR}/${SRR}_1.fastq.gz > ${SRR}_1.fastq.gz
    then echo "Download successful" |& tee -a Number_of_reads_in_fastq_files.txt
    else  
      if curl ${ena_fastq_dir}/${SRR:0:6}/0${SRR:9:11}/${SRR}/${SRR}.fastq.gz > ${SRR}_1.fastq.gz
      then echo "Download successful" |& tee -a Number_of_reads_in_fastq_files.txt
      else echo "Download failed" |& tee -a Number_of_reads_in_fastq_files.txt
      fi
    fi
    f=${SRR}_1.fastq.gz
    num_r=$(zgrep . $f | wc -l)
    echo "Fastq file: $f; Number of lines: $num_r; Number of reads: $(echo "scale=2; $num_r/4" | bc)" |& tee -a Number_of_reads_in_fastq_files.txt

    if [ "$num_l" == "2" ]
    then
      dt=$(date '+%d/%m/%Y %H:%M:%S');echo $dt |& tee -a Number_of_reads_in_fastq_files.txt
      echo ${SRR} |& tee -a Number_of_reads_in_fastq_files.txt
      if curl ${ena_fastq_dir}/${SRR:0:6}/0${SRR:9:11}/${SRR}/${SRR}_2.fastq.gz > ${SRR}_2.fastq.gz
      then echo "Download successful" |& tee -a Number_of_reads_in_fastq_files.txt
      else echo "Download failed" |& tee -a Number_of_reads_in_fastq_files.txt
      fi
      f=${SRR}_2.fastq.gz
      num_r=$(zgrep . $f | wc -l)
      echo "Fastq file: $f; Number of lines: $num_r; Number of reads: $(echo "scale=2; $num_r/4" | bc)" |& tee -a Number_of_reads_in_fastq_files.txt
    fi
  fi

done < "SRRs_to_process.txt" # File containing list of SRRs to download

rm -rf temp