--- a
+++ b/singlecellmultiomics/modularDemultiplexer/demultiplexedFastqConversion.py
@@ -0,0 +1,59 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+import os
+import sys
+import collections
+import argparse
+import singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods
+from singlecellmultiomics.fastqProcessing.fastqIterator import FastqIterator
+
+if __name__ == '__main__':
+    argparser = argparse.ArgumentParser(
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+        description="""Extract features from a demultiplexed fastq file.
+     Example usage: -seqfeatures BC,RX,SEQ -qualityfeatures QT,RQ,QUAL | gzip > bc_umi.fastq.gz
+
+     """)  # -o ./bc_umi.fastq.gz
+    argparser.add_argument(
+        '-seqfeatures',
+        type=str,
+        help="Features to put into the ",
+        required=True)
+    argparser.add_argument(
+        '-qualityfeatures',
+        type=str,
+        help="Features to put into ",
+        required=True)
+    argparser.add_argument(
+        'fastqfiles',
+        nargs='*',
+        type=str,
+        help="Input demultiplexed fastq files")
+
+    argparser.add_argument('-format', type=str, help="Output format: fq, tsv")
+    #argparser.add_argument('-o',  type=str, help="output file path", required=True)
+    args = argparser.parse_args()
+
+    seqfeatures = args.seqfeatures.split(',')
+    qualityfeatures = args.qualityfeatures.split(',')
+    if len(seqfeatures) != len(qualityfeatures):
+        raise ValueError('Supply a quality feature for every sequence feature')
+
+    TagDefinitions = singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods.TagDefinitions
+    for reads in FastqIterator(*args.fastqfiles):
+        for readIndex, record in enumerate(reads):
+            tr = singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods.TaggedRecord(
+                TagDefinitions)
+            tr.fromTaggedFastq(record)
+            sequence = ''.join(
+                (record.sequence if tag == 'SEQ' else tr.tags.get(tag) for tag in seqfeatures))
+            qualities = ''.join(
+                (record.qual if tag == 'QUAL' else tr.tags.get(tag) for tag in qualityfeatures))
+            if len(sequence) != len(qualities):
+                raise ValueError(
+                    'Length of base qualities does not match the length of the selected sequence features')
+
+            if args.format == 'fq':
+                print(f'{record.header}\n{sequence}\n+\n{qualities}')
+            elif args.format == 'tsv':
+                print()