Add new file

scripts/rename_reads_for_bam.py

+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+# Author: Xiaofei Zeng
+# Email: xiaofei_zeng@whu.edu.cn
+# Created Time: 2023-12-18 15:27
+
+
+import argparse
+import os
+
+def rename_reads(bam):
+
+    n = 0
+    with os.popen('samtools view -h {}'.format(bam)) as f:
+        for line in f:
+            if not line.strip():
+                continue
+            if line.startswith('@'):
+                print(line, end='')
+            elif line.split()[1] != '0':
+                print('read{}\t{}'.format(n//2, line.split('\t', 1)[-1]), end='')
+                n += 1
+
+
+def main():
+    parser = argparse.ArgumentParser()
+    parser.add_argument('bam', help='paired-end bam output by wf-pore-c')
+    args = parser.parse_args()
+
+    rename_reads(args.bam)
+
+
+if __name__ == '__main__':
+    main()
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