Create fastq_upsampling.py

fastq_upsampling.py

+#! /usr/bin/env python3
+
+#Anne-Sophie Denommé-Pichon
+#AGPLv3
+
+import sys
+
+def upsample(upsampling_read_count, read_id):
+    """
+    upsampling_read_count : number of additional reads
+    read_id : id of the read you want to repeat
+    """
+    try:
+        max_lane = 0
+        max_tile = 0
+        max_x = 0
+        max_y = 0
+        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)
+            print(plus_line)
+            print(quality_line)
+            
+            lane = int(title_line.split(':')[2])
+            if lane > max_lane:
+                max_lane = lane
+            
+            tile = int(title_line.split(':')[3])
+            if tile > max_tile:
+                max_tile = tile
+            
+            x = int(title_line.split(':')[4])
+            if x > max_x:
+                max_x = x
+
+            y = int(title_line.split(':')[5])
+            if y > max_y:
+                max_y = y
+
+            if title_line == read_id:
+                title_line_str = title_line
+                sequence_line_str = sequence_line
+                plus_line_str = plus_line
+                quality_line_str = quality_line
+
+    except StopIteration: # quand erreur StopIteration, arrêter
+        pass
+    
+    for i in range(1, upsampling_read_count + 1):
+        print(':'.join(title_line_str.split(':')[0:2] + [str(max_lane + i), str(max_tile + i), str(max_x + i), str(max_y + i)]))
+        print(sequence_line_str)
+        print('+')
+        print(quality_line_str)
+
+if __name__ == '__main__':
+    if len(sys.argv) == 3:
+        upsample(int(sys.argv[1]), sys.argv[2])
+    else:
+        print("Usage: fastq_upsampling.py <upsampling_read_count> <read_id> < input.fastq > output.fastq", file=sys.stderr)
+        sys.exit(1)
+