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change_quality.py

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+import argparse
+import random
+import os
+
+
+
+### FORWARD
+def generate_quality_first_bases_fw():
+    return ''.join(random.choice('?@ABCD') for _ in range(2))
+
+def generate_quality_next_bases_fw():
+    return ''.join(random.choice('ABCDEG') for _ in range(3))
+
+def generate_quality_middle_bases_fw():
+    return ''.join(random.choice('CDEFGH') for _ in range(5))
+
+def generate_quality_last_bases_fw():
+    return ''.join(random.choice('HI') for _ in range(200))
+
+def generate_quality_decreasing_200_220_fw():
+    return ''.join(random.choice('CDEFGH') for _ in range(30))
+
+def generate_quality_decreasing_220_260_fw():
+    return ''.join(random.choice('ABCDEG') for _ in range(25))
+
+def generate_quality_decreasing_260_290_fw():
+    return ''.join(random.choice('?@ABCD') for _ in range(25))
+
+def generate_quality_decreasing_290_300_fw():
+    return ''.join(random.choice('?@') for _ in range(10))
+
+def change_quality_fw(input_file, output_file):
+    with open(input_file, 'r') as f_in, open(output_file, 'w') as f_out:
+        for line_num, line in enumerate(f_in):
+            if line_num % 4 == 0:
+                f_out.write(line)
+            elif line_num % 4 == 1:
+                f_out.write(line)
+            elif line_num % 4 == 2:
+                f_out.write(line)
+            else:
+                new_quality = (
+                    generate_quality_first_bases_fw() +
+                    generate_quality_next_bases_fw() +
+                    generate_quality_middle_bases_fw() +
+                    generate_quality_last_bases_fw() +
+                    generate_quality_decreasing_200_220_fw() +
+                    generate_quality_decreasing_220_260_fw() +
+                    generate_quality_decreasing_260_290_fw() +
+                    generate_quality_decreasing_290_300_fw()
+                )
+                f_out.write(new_quality + '\n')
+
+
+### REVERSE
+def generate_quality_first_bases_rv(read_length):
+    return ''.join(random.choice('?@ABCD') for _ in range(read_length * 0.01))
+
+def generate_quality_next_bases_rv(read_length):
+    return ''.join(random.choice('ABCDEG') for _ in range(read_length * 0.02))
+
+def generate_quality_middle_bases_rv(read_length):
+    return ''.join(random.choice('CDEFGH') for _ in range(read_length * 0.02))
+
+def generate_quality_main_bases_rv(read_length):
+    return ''.join(random.choice('HI') for _ in range((read_length * 0.10 * 6) + (read_length * 0.05)))
+
+def generate_quality_decreasing_175_200_rv(read_length):
+    return ''.join(random.choice('CDEFGH') for _ in range(read_length * 0.10))
+
+def generate_quality_decreasing_200_220_rv(read_length):
+    return ''.join(random.choice('ABCDEG') for _ in range(read_length * 0.10))
+
+def generate_quality_decreasing_220_260_rv(read_length):
+    return ''.join(random.choice('?@ABCD') for _ in range(read_length * 0.05))
+
+def generate_quality_decreasing_260_290_rv(read_length):
+    return ''.join(random.choice('?@ABC') for _ in range(read_length * 0.04))
+
+def generate_quality_decreasing_290_300_rv(read_length):
+    return ''.join(random.choice('?@AB') for _ in range(read_length * 0.01))
+
+def change_quality_rv(input_file, output_file):
+    with open(input_file, 'r') as f_in, open(output_file, 'w') as f_out:
+        for line_num, line in enumerate(f_in):
+            if line_num % 4 == 0:
+                f_out.write(line)
+            elif line_num % 4 == 1:
+                f_out.write(line)
+            elif line_num % 4 == 2:
+                f_out.write(line)
+            else:
+                new_quality = (
+                    generate_quality_first_bases_rv() +
+                    generate_quality_next_bases_rv() +
+                    generate_quality_middle_bases_rv() +
+                    generate_quality_main_bases_rv() +
+                    generate_quality_decreasing_175_200_rv() +
+                    generate_quality_decreasing_200_220_rv() +
+                    generate_quality_decreasing_220_260_rv() +
+                    generate_quality_decreasing_260_290_rv() +
+                    generate_quality_decreasing_290_300_rv()
+                )
+                f_out.write(new_quality + '\n')
+
+
+
+### COMMANDS
+# Create the parser
+parser = argparse.ArgumentParser(description='Script to change the quality of a FASTQ file.')
+
+# Mandatory commands
+parser.add_argument('-i', '--input', type=str, required=True, help='Input ".fastq" file')
+parser.add_argument('-o', '--output', type=str, required=True, help='Output file')
+parser.add_argument('-ow', '--overwrite', action='store_true', help='Force overwrite output')
+
+# Mutually exclusive group of arguments
+group = parser.add_mutually_exclusive_group(required=True)
+group.add_argument('-fw', '--forward', action='store_true', help='Forward mode (default)')
+group.add_argument('-rv', '--reverse', action='store_true', help='Reverse mode')
+
+# Parse the arguments
+args = parser.parse_args()
+
+
+def main():
+    # Check if input file is 'fastq'
+    if not args.input.endswith('.fastq'):
+        print("The input needs to be '.fastq'")
+        return
+
+    # Check if the input file not exists
+    if not os.path.exists(args.input):
+        print("The input file does not exists")
+        return
+
+    # Check if output file is 'fastq'
+    if not args.output.endswith('.fastq'):
+        print("The output needs to be '.fastq'")
+        return
+
+    # Check if the input and the output are the same
+    if os.path.abspath(args.input) == os.path.abspath(args.output):
+        base, ext = os.path.splitext(args.output)
+        args.output = base + "_changed" + ext
+        print("The input file are the same as output file.")
+        print("Saving the output as: ", args.output)
+
+    # Check if the output file exists
+    if not args.overwrite and os.path.exists(args.output):
+        print(args.output, "file already exists, use -ow to force the overwrite")
+        return
+
+    # Execute change quality
+    if args.forward:
+        change_quality_fw(args.input, args.output)
+        print("Qualitys changed successfully (forward) and saved at:", args.output)
+    elif args.reverse:
+        change_quality_rv(args.input, args.output)
+        print("Qualitys changed successfully (reverse) and saved at:", args.output)
+
+if __name__ == "__main__":
+    main()