Adding MBC/UMI RX tag to read name

Question

[Christian]

Hi all,

I have a BAM/SAM file with molecular barcode (MBC) / unique molecular identifier (UMI) stored in the RX tag (after preprocessing with AGeNT Trimmer). Here is an example, where RX:Z: is the tag containing the UMI TCA-TTA.

A00620:188:HVMYMDSX2:4:2213:4255:9392   147 chr1    10000   0   96M =   10005   -91 ATAACCCTAACCCTAACACTAACACTAACCCTAACCCTATCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC,;-<--9:=<9-8:,;9+.:86.,9;><,,@;8<A-@;7(--A<?+-9/28>--A<?6-AA<?6A8.;><@@@;=;@?@:=;?>>9=:>==:=;>9 ZA:Z:TCACT  ZB:Z:TTAGT  BC:Z:GTCTCTTC+GAGGCTTC  MC:Z:96M    MD:Z:17C5C15A56 RG:Z:@A00620:188:HVMYMDSX2:4:1101:6470:1016 MI:Z:TCATTA NM:i:3  AS:i:81 XS:i:80 QX:Z:FFF FFF    RX:Z:TCA-TTA

I am trying to append the UMI to the read name (requirement for a tool I am trying to implement).This is what I have tried:

samtools view -H tmp.sam > tmp_header.sam
samtools view tmp.sam | awk '{OFS = "\t"} {for(i=1;i<=NF;i++)  if ($i ~ /^RX:Z:/) {$1=$1"_"$i; gsub("RX:Z:","",$1); print}}' >> tmp_header.sam

(see also this Bioinformatics Stack Exchange answer)

The last step throws an error, as samtools cannot parse the file after the modification:

[E::aux_parse] unrecognized type '\t'
[W::sam_read1_sam] Parse error at line 101

This is the line that cannot be parsed when opened with vim:

A00620:188:HVMYMDSX2:4:2213:4255:9392_TCA-TTA   147     chr1    10000   0       96M     =       10005   -91     ATAACCCTAACCCTAACACTAACACTAACCCTAACCCTATCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACC        ,;-<--9:=<9-8:,;9+.:86.,9;><,,@;8<A-@;7(--A<?+-9/28>--A<?6-AA<?6A8.;><@@@;=;@?@:=;?>>9=:>==:=;>9        ZA:Z:TCACT      ZB:Z:TTAGT      BC:Z:GTCTCTTC+GAGGCTTC  MC:Z:96M        MD:Z:17C5C15A56 RG:Z:@A00620:188:HVMYMDSX2:4:1101:6470:1016     MI:Z:TCATTA     NM:i:3  AS:i:81 XS:i:80 QX:Z:FFF        FFF     RX:Z:TCA-TTA      

This looks very close to what I am trying to do - the tag has been appended to the read name. I cannot quite figure out what causes the parsing error. Any help would be appreciated.

Best wishes

Christian

Answer 1

[Christian]

# this script takes a BAM file and moves the UMI tag from the RX tag
# and appends it to the read name
# argument 1: input file
# argument 2: output file

import pysam
import re
import sys

# open the input BAM file
input1 = sys.argv[1]
input_bam = pysam.AlignmentFile(input1, "rb")

# define and open the output BAM file
output_bam = pysam.AlignmentFile(sys.argv[2], "wb", template=input_bam)

# iterate over reads
for read in input_bam:
    umi = read.get_tag("RX")
    umi = re.sub(r'\W+', '', umi)
    read.qname = f"{read.qname}_{umi}"
    output_bam.write(read)

# close connection
input_bam.close()
output_bam.close()

This is how I ended up solving it.