Add scripts to trim fastq at 75 and 100 bp

fastq_trimming.py

+#! /usr/bin/env python3
+
+#Anne-Sophie Denommé-Pichon
+#AGPLv3
+
+import sys
+
+def trimmsample(size):
+    """
+    size: size of the read you want
+    """
+    try:
+        while True: # boucle infinie pour lire les lignes 4 par 4
+            title_line = next(sys.stdin).rstrip()
+            sequence_line = next(sys.stdin).rstrip()
+            plus_line = next(sys.stdin).rstrip()
+            quality_line = next(sys.stdin).rstrip()
+            print(title_line)
+            print(sequence_line[:size])
+            print(plus_line)
+            print(quality_line[:size])
+
+    except StopIteration: # quand erreur StopIteration, arrêter
+        pass
+    
+if __name__ == '__main__':
+    if len(sys.argv) == 2:
+        trimmsample(int(sys.argv[1]))
+    else:
+        print("Usage: fastq_trimming.py <size> < input.fastq > output.fastq", file=sys.stderr)
+        sys.exit(1)
+    

trimming.sh

+#! /bin/sh
+
+#Anne-Sophie Denommé-Pichon
+#AGPLv3
+
+for fastq in /work/gad/shared/analyse/STR/Data/*fastq.gz
+do
+    dijen="$(basename "$fastq" | sed 's#\(dijen[0-9]\+\)\.R[1-2]\.fastq\.gz#\1#')"
+    end_name="$(basename "$fastq" | sed 's#dijen[0-9]\+\(\.R[1-2]\.fastq\.gz\)#\1#')"
+    for i in 75 100
+    do
+	gunzip -c "$fastq" | /user1/gad/an1770de/Scripts/trimming/fastq_trimming.py "$i" | gzip -1 > "/work/gad/shared/analyse/STR/Data/$dijen/${dijen}_trimming_$i${end_name}"
+    done &
+done