Using Pysam to extract paired reads

Question

[Linda]

I am using Pysam to process a bam file containing paired reads. However, I get the error

AttributeError: 'csamtools.AlignedRead' object has no attribute 'rnext'

when I try to extract the chromosome that the mate of a read is aligned to. What am I doing wrong?

for row in samfile:
    print(samfile.getrname(row.rname)+' '+samfile.getrname(row.rnext))

It gives the read's reference properly, however it gives an error for the mate's reference.

[rohan]

There are known issues with insufficient documentation for pysam. If you are comfortable with perl, you can try Bio::DB::Sam instead. It will do the same job with enough documentation for troubleshooting.

Answer 1

[Andreas]

Hi,

Looks like your pysam installation is too old and doesn't support rnext (see also QA3.2 here). Which version are you using? According to the logs rnext was introduced end of 2011, i.e. any version >= 0.6 should work.

Andreas

[Linda]

Yea, it is an old version that came along with the Enthought Python Distribution. Got it sorted out.