Hi everyone,

I am trying to pipe pysam.view() into pysam.sort() in a program. Since both are wrappers for samtools, it is quite easy to read a bam file and generate a new (filtered or sorted) bam file from them.

My aim, however, is to filter reads by certain criteria and pipe the filtered reads output directly to the sorting function without passing through an intermediate filtered file. This is because the bam file intermediate would take a lot of space on our hard drive, while RAM is not a problem.

Is there a way to do so?

My code at the moment:

import pysam 

infile = "test.bam" 
outfile = "test.f.bam"
open(outfile, "w").close()
pysam.view("-F", "0x0100", "-F", "0x4", "-b", "-h", "-o", outfile, infile, catch_stdout=False)
pysam.sort("-n", "-m", "4G", "-@", "20", "-T", "test", "--output-fmt", "bam", "-o", "test.fs.bam", "test.f.bam")