💪 enable demultiplexing run as tagging mode

celseq2/demultiplex.py

@@ -82,6 +82,7 @@ def demultiplexing(read1_fpath, read2_fpath, dict_bc_id2seq,
                    bc_qual_min=10,
                    is_gzip=True,
                    save_unknown_bc_fastq=False,
+                   tagging_only=False,
                    do_bc_rev_complement=False,
                    do_tx_rev_complement=False,
                    verbose=False):
@@ -110,8 +111,18 @@ def demultiplexing(read1_fpath, read2_fpath, dict_bc_id2seq,
     bc_fhout['UNKNOWNBC_R2'] = join_path(outdir, 'UNKNOWN',
                                          'UNKNOWNBC_R2.fq')
 
+    if tagging_only:
+        out_fpath_tagged_fq = join_path(outdir, 'tagged.fastq')
+        out_fh_tagged_fq = open(out_fpath_tagged_fq, 'w')
+
     for bc_seq, v in bc_fhout.items():
-        bc_fhout[bc_seq] = open(v, 'w')
+        if bc_seq.startswith('UNKNOWN'):
+            bc_fhout[bc_seq] = open(v, 'w')
+            continue
+        if tagging_only:
+            bc_fhout[bc_seq] = out_fh_tagged_fq
+        else:
+            bc_fhout[bc_seq] = open(v, 'w')
 
     i = 0
     while(True):
@@ -310,6 +321,11 @@ def main():
     parser.add_argument('--save-unknown-bc-fastq',
                         dest='save_unknown_bc_fastq', action='store_true')
     parser.set_defaults(save_unknown_bc_fastq=False)
+    parser.add_argument('--tagging-only',
+                        dest='tagging_only', action='store_true',
+                        help=('Demultiplexed reads are merged to a file named'
+                              ' \"tagged.fastq\" under --out-dir.'))
+    parser.set_defaults(tagging_only=False)
     parser.add_argument('--verbose', dest='verbose', action='store_true')
     parser.set_defaults(verbose=False)
 
@@ -333,6 +349,7 @@ def main():
                          bc_qual_min=args.min_bc_quality,
                          is_gzip=args.is_gzip,
                          save_unknown_bc_fastq=args.save_unknown_bc_fastq,
+                         tagging_only=args.tagging_only,
                          do_bc_rev_complement=False,
                          do_tx_rev_complement=False,
                          verbose=args.verbose)

celseq2/helper.py

@@ -95,7 +95,7 @@ def rmfile(fpath):
 def base_name(fpath, ext=None):
     bs = os.path.basename(fpath)
     if not (ext is None or ext == ""):
-        bs.replace(ext, '')
+        bs = bs.replace(ext, '')
     bs = os.path.splitext(bs)[0]
     return(bs)
 

celseq2/version.py

-__version__ = '0.5.3'
+__version__ = '0.5.3.1'