SRR_first

convert.sh

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+#!/usr/bin/bash
+
+# load modules 
+module load sra-tools
+module load samtools
+
+help(){
+    echo "Usage: use this script to convert SRA files to fastq or bam"
+    echo 
+    echo "Options :"
+    echo " -b : convert to bam file. "
+    echo " -q : convert to fastq file. "
+    echo " -h : show this help message and exit"
+    echo 
+    echo " dont forget to change the output directory inside the script"
+    echo "if not the output will be ./"
+    exit 1
+}
+
+# change your own path here
+destination="./"
+
+conversion_type=""
+
+while getopts "bq:h" op; do
+    case $op in
+        q)
+            conversion_type="fastq"
+            ;;
+        b)
+            conversion_type="bam"
+            ;;
+        h)
+            help
+            ;;
+        \?)
+            echo "wrong operator: -$OPTARG" >&2
+            help
+            ;;
+    esac
+done
+
+if [ -z "$conversion_type" ]; then
+    echo " you need to specify a conversion option: -q or -b"
+    help
+fi
+
+find . -name "*.sra" -exec mv {} $destination \;
+
+for sra_file in $destination*.sra; do
+    echo "running $sra_file..."
+
+    base_name=$(basename "$sra_file" .sra)
+
+    case $conversion_type in
+        fastq) 
+            echo "conversion of $sra_file in fastq...."
+            fastq-dump.3 --ngc a.ngc "$sra_file"
+            ;;
+        bam)
+            echo "conversion of $sra_file in bam....."
+            sam_dump.3 --ngc a.ngc $sra_file | samtools view -bS - > "${base_name}.bam"
+            ;;
+    esac
+
+done 
+
+echo "treatment's over"
+

fastqfetch.sh

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+#!/usr/bin/bash
+help(){
+    echo "this script is going to download the SRA files from a sra list provided after sorting the id from a sra table"
+    echo "and place them inside of a new folder"
+    echo "no argument is needed"
+    echo
+    echo " this script is functioning if the table file has a header"
+    echo " if not, just change the done by the one behind a #"
+    exit 1
+}
+# Add sratoolkit to PATH
+export PATH="/scratch/user/uqsdemon/ApplicationGNN/gnnenvo/bin/sratoolkit.3.1.1-ubuntu64/bin:$PATH"
+
+# Charger les modules nécessaires (if still required)
+module load sra-tools
+module load samtools
+
+# Chemin du fichier contenant les identifiants SRR
+fastq_ids_file="/scratch/user/uqsdemon/rnewbashscriptvf/SRRIDS/fastq_ids.txt"
+# Liste des identifiants à exclure
+exclude_ids_file="/scratch/user/uqsdemon/rnewbashscriptvf/filedone.txt"
+outputpath="/QRISdata/Q7361/SRRIDS/fastqfilesncbi"
+keypath="/scratch/user/uqsdemon/rnewbashscriptvf/prj_33410_D38764.ngc"
+
+# Vérifiez que sra-tools est chargé correctement
+if ! command -v fasterq-dump &> /dev/null; then
+  echo "fasterq-dump could not be found. Please check your sratoolkit installation and PATH."
+  help
+fi
+
+if [ ! -f "$fastq_ids_file" ]; then
+    echo "Error: the file with sra ids does not exist."
+    help
+fi
+
+if [ ! -f "$keypath" ]; then
+    echo "Erreur : le fichier NGC n'existe pas au chemin spécifié."
+    help
+fi
+
+# Charger les identifiants à exclure dans un tableau
+mapfile -t exclude_ids < "$exclude_ids_file"
+
+temp_path="/QRISdata/Q7361/temp"
+
+# Assurez-vous que le répertoire temporaire existe
+mkdir -p "$temp_path"
+
+# Lire chaque ligne du fichier fastq_ids.txt
+while read -r srr_id; do
+  # Vérifier si l'identifiant est dans la liste des exclusions
+  if printf '%s\n' "${exclude_ids[@]}" | grep -qx "$srr_id"; then
+    echo "Skipping excluded ID: $srr_id"
+    continue
+  fi
+  echo "Téléchargement et conversion de $srr_id en format fastq depuis NCBI..."
+  # Télécharger et convertir le fichier SRA en fichiers fastq
+  mkdir -p "$outputpath/$srr_id"
+  fasterq-dump --ngc "$keypath" --split-files "$srr_id" -O "$outputpath/$srr_id" --temp "$temp_path"
+done < "$fastq_ids_file"
+
+echo "download over"