Add compatibility with reads with a non-illumina header to demux.py

singlecellmultiomics/modularDemultiplexer/baseDemultiplexMethods.py

@@ -40,7 +40,7 @@ def metaFromRead(read, tag):
 
 
 # Clean a string to be able to be used in a fastq file header
-fastqCleanerRegex = re.compile('[^a-zA-Z0-9-_]', re.UNICODE)
+fastqCleanerRegex = re.compile('[^a-zA-Z0-9-_.]', re.UNICODE)
 
 def fqSafe(string) -> str:
     """
@@ -147,7 +147,13 @@ def has_tag(self, tag):
         return tag in self.tags
 
     def asIlluminaHeader(self):
-        return '{Is}:{RN}:{Fc}:{La}:{Ti}:{CX}:{CY}'.format(**self.tags)
+        try:
+            return '{Is}:{RN}:{Fc}:{La}:{Ti}:{CX}:{CY}'.format(**self.tags)
+        except KeyError as e:
+            if 'oh' in self.tags:
+                return self.tags['oh']
+            raise e
+
 
 
 
@@ -188,6 +194,11 @@ def parse_3dec_header(self,fastqRecord, indexFileParser,  indexFileAlias):
             'CN': controlNumber
         })
 
+    def parse_other_header(self,fastqRecord, indexFileParser,  indexFileAlias):
+        self.tags.update({
+            'oh':fastqRecord.header[1:].replace(';','').split()[0] # original header
+        })
+
 
     def _parse_illumina_header(self,header, indexFileParser = None,  indexFileAlias = None):
 
@@ -270,7 +281,10 @@ def fromRawFastq(
             if fastqRecord.header.startswith('@Is'):
                 self.parse_scmo_header(fastqRecord, indexFileParser,  indexFileAlias)
             else:
-                self.parse_3dec_header(fastqRecord, indexFileParser,  indexFileAlias)
+                if fastqRecord.header.startswith('@Cluster'):
+                    self.parse_3dec_header(fastqRecord, indexFileParser,  indexFileAlias)
+                else:
+                    self.parse_other_header(fastqRecord, indexFileParser,  indexFileAlias)
 
 
             # NS500413:32:H14TKBGXX:2:11101:16448:1664 1:N:0::
@@ -379,10 +393,11 @@ def fromTaggedFastq(self, fastqRecord):
 
     def fromTaggedBamRecord(self, pysamRecord):
         try:
+
             for keyValue in pysamRecord.query_name.strip().split(';'):
                 key, value = keyValue.split(':')
                 self.addTagByTag(key, value, isPhred=False)
-        except ValueError:
+        except ValueError as e:
             # Try to parse "Single Cell Discoveries" header
             # These have the following header:
             #NBXXXXXX:530:HXXXXXX:2:2:17:6;SS:GTCATTAG;CB:GTCATTAG;QT:eeeeeeee;RX:CTGAAC;RQ:aaaaae;SM:SAMPLE_NAME

singlecellmultiomics/tags/tags.py

@@ -42,6 +42,7 @@ def __repr__(self):
     SamTag('QX', 'barcodeQual', isPhred=True),
     SamTag('bc', 'rawBarcode'),
     SamTag('hd', 'hammingDistanceRawBcAssignedBc'),
+    SamTag('oh', 'originalHeader'),
 
     SamTag('bi', 'barcodeIndex'),
 

singlecellmultiomics/universalBamTagger/bamtagmultiome.py

@@ -452,7 +452,7 @@ def tag_multiome_multi_processing(
     # Remove the temp dir:
     sleep(5)
     try:
-        shutil.rmtree(temp_folder, ignore_errors=False, onerror=None)
+        shutil.rmtree(temp_folder, ignore_errors=False)
     except Exception as e:
         sys.stderr.write(f'Failed to remove {temp_folder}\n')
         sys.stderr.write(f'{e}\n')

tests/test_demultiplexing.py

@@ -248,6 +248,42 @@ def test_3DEC_UmiBarcodeDemuxMethod_matching_barcode(self):
         self.assertEqual( demultiplexed_record[0].tags['BC'], 'ACACACTA')
         self.assertEqual( demultiplexed_record[0].tags['bi'], 1)
 
+    def test_sra_header(self):
+
+        barcode_folder = str(importlib.resources.files('singlecellmultiomics').joinpath('modularDemultiplexer/barcodes/'))
+
+        barcode_parser = BarcodeParser(barcode_folder,lazyLoad='*')
+
+        r1 = FastqRecord(
+          '@SRR21016692.1 1/1',
+          'ATCACACACTATAGTCATTCAGGAGCAGGTTCTTCAGGTTCCCTGTAGTTGTGTGGTTTTGAGTGAGTTTTTTAAT',
+          '+',
+          'AAAAA#EEEEEEEEEEEAEEEEEEEAEEEEEEEEEEEEEEEEEE/EEEEEEEEEEEE/EEEEEEEEEEEEEEEEEE'
+        )
+        r2 = FastqRecord(
+          '@SRR21016692.1 1/2',
+          'ACCCCAGATCAACGTTGGACNTCNNCNTTNTNCTCNGCACCNNNNCNNNCTTATNCNNNANNNNNNNNNNTNNGN',
+          '+',
+          '6AAAAEEAEE/AEEEEEEEE#EE##<#6E#A#EEE#EAEEA####A###EE6EE#E###E##########E##A#'
+        )
+        demux = UmiBarcodeDemuxMethod(umiRead=0,
+            umiStart=0,
+            umiLength=3,
+            barcodeRead=0,
+            barcodeStart=3,
+            barcodeLength=8,
+            barcodeFileParser=barcode_parser,
+            barcodeFileAlias='maya_384NLA',
+            indexFileParser=None,
+            indexFileAlias='illumina_merged_ThruPlex48S_RP',
+            random_primer_read=None,
+            random_primer_length=6)
+
+        demultiplexed_record = demux.demultiplex([r1,r2])
+        # The barcode sequence is ACACACTA (first barcode)
+        self.assertEqual( demultiplexed_record[0].tags['BC'], 'ACACACTA')
+        self.assertEqual( demultiplexed_record[0].tags['bi'], 1)
+
 
 if __name__ == '__main__':
     unittest.main()