How to only change/substitute every QNAME(Read ID) from a Bam file?

Question

[Joe]

Hi, I need to substitute a bam file's QNAME to another bam file's QNAME, but without change header, sequence and everything else. Here is Example ( I don't show seq and others here): I have A.bam:

A.bamHeader

M04402:7:000000000-ANGUV:1:1106:13178:9134 147  chr1    17027   0 ...............

M04402:7:000000000-ANGUV:1:1106:13178:9134 99   chr1    17205   0....................

M04402:7:000000000-ANGUV:1:2115:20665:6740 147  chr1    17344   0.................
and so on......

I have another B.bam. the QNAME is

M00601:223:AM07W:1:1102:11074:13214 163 chr1    19754   24.............

M00601:223:AM07W:1:2101:17585:17440 99  chr1    17205   0....................

and so on......

I want to change all the A.bam QNAMEs (eg:M04402:7:000000000-ANGUV:1:1106:13178:9134) to B.bam QNAMEs(eg:M00601:223:AM07W:1:1102:11074:13214). But only change the QNAME, not other things.

What I can think about is use command line "sed".

Thanks!

[GenoMax]

While it can probably be done using the code posted by @i.sudbery I can't figure out the use case. Why do you want to do this?

[Joe]

The reason I want to do this is How to merge two identical BAM files? I want to change QNAME, then redo the thing I post in the link.

[GenoMax]

I see. You are creating a fake duplicate with same sequence data but different headers. You could just change ANGUV to BNGUV which would make it a new flowcell :-)

[Joe]

It works, thanks a lot

Answer 1

[i.sudbery]

It would be easy with pysam in Python, assuming that the order of both BAM files was to be maintained:

from pysam import AlignmentFile
from itertools import izip

bam1 = AlignmentFile("A.bam")
bam2 = AlignmentFile("B.bam")
outbam = AlignmentFile("C.bam", "wb", template = bam1)

for read1, read2 in izip(bam1.fetch(until_eof=True), bam2.fetch(until_eof=True)):
    read1.query_name = read2.query_name
    outbam.write(read1)

outbam.close()