20251125

99.scripts/trinity_utils/util/misc/validate_fastqs.py

@@ -0,0 +1,103 @@
+#!/usr/bin/env python3
+# encoding: utf-8
+
+import os, sys, re
+import logging
+import argparse
+import gzip
+from collections import defaultdict
+
+def main():
+
+    parser = argparse.ArgumentParser(description="validate fastqs", formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+
+    
+    parser.add_argument("--left_fq", required=True, type=str, help="left fastq file")
+
+    parser.add_argument("--right_fq", required=False, type=str, help="right fastq file")
+    
+    args = parser.parse_args()
+
+    left_fq = args.left_fq
+    right_fq = args.right_fq
+
+
+
+
+    left_fq_iterator = fastq_iterator(left_fq)
+    right_fq_iterator = None
+    if right_fq:
+        right_fq_iterator = fastq_iterator(right_fq)
+
+
+
+    counter = 0
+    
+    for left_read_tuple in left_fq_iterator:
+        left_readname, left_readseq, left_L3, left_quals = left_read_tuple
+        left_readseq_len = len(left_readseq)
+        left_quals_len = len(left_quals)
+
+        counter += 1
+        if counter % 10000 == 0:
+            sys.stderr.write(f"\r[{counter}]  ")
+
+        
+        assert left_readseq_len == left_quals_len, f"Error, left seqlen and quals len dont match:\n{left_readname}\n{left_readseq}\n{left_L3}\n{left_quals}\n"
+        
+        
+        if right_fq_iterator is not None:
+
+            right_read_tuple = next(right_fq_iterator)
+            right_readname, right_readseq, right_L3, right_quals = right_read_tuple
+            right_readseq_len = len(right_readseq)
+            right_quals_len = len(right_quals)
+            
+
+            assert right_readseq_len == right_quals_len, f"Error, right seqlen and quals len dont match:\n{right_readname}\n{right_readseq}\n{right_L3}\n{right_quals}\n"
+
+            assert core_readname(left_readname) == core_readname(right_readname), f"Error, fastq pair read names aren't consistent: {left_readname} vs. {right_readname}"
+            
+
+    print("fastq(s) validate")
+    
+    sys.exit(0)
+
+
+
+def core_readname(readname):
+
+    core_readname = readname.split(" ")[0]
+
+    core_readname = re.sub("/[12]$", "", core_readname)
+
+    return core_readname
+
+
+
+def fastq_iterator(fastq_filename):
+
+    if re.search(".gz$", fastq_filename):
+        fh = gzip.open(fastq_filename, 'rt', encoding='utf-8')
+    else:
+        fh = open(fastq_filename, 'rt', encoding='utf-8')
+
+    have_records = True
+    while have_records:
+        readname = next(fh).rstrip()
+        readseq = next(fh).rstrip()
+        L3 = next(fh).rstrip()
+        quals = next(fh).rstrip()
+
+        yield (readname, readseq, L3, quals)
+
+        if not readname:
+            break
+
+    return
+        
+
+
+
+if __name__=='__main__':
+    main()