How to extract all - strand mapped reads location of reference genome using BAM file?

Question

[BioGeek]

How to extract all - strand mapped reads location of reference genome using BAM file and save in a tab file?

[Devon Ryan]

What exactly would you like in the "tab" file? The answer to this, btw, is to write a little script with pysam (or perhaps jvarkit).

[BioGeek]

Can you please give me some hints, to achieve it. I want to print the followings Scaffold \tStart \tEnd \tStrand

[Devon Ryan]

Something along the following lines is a start for you:

#!/usr/bin/env python
import sys
import pysam

bam = pysam.AlignmentFile(sys.argv[1])
output = open("output.tab", "w")
for read in bam.fetch():
    # Do whatever filtering you want
    # ...
    if not read.is_reverse:
        continue
    output.write("{}\t{}\t{}\t-\n".format(bam.get_reference_name(read.get_tid()), read.pos, read.reference_end()))
output.close()
bam.close()