CODEWITHSUNDEEP
pythonbioinformaticssamtoolspysam
rbierman
rbierman

Reputation: 81

Pysam view yield reads one at a time

I'm trying to using pysam to filter a .bam file for mapping quality and excluding flags.

I know I can use .fetch() and iterate through reads that way, but I'm guessing it's faster to first use pysam.view()

However, when I try this on a large .bam, it appears to be trying to read in the entire file before returning any output. I want it to "yield" one read at a time. Is there a way to do this?

Here's my code:

for r in pysam.view('-q','255','-F','3840',input_bam):
    print(r)
    break

It's just hanging and never gets to the print statement because I believe it's trying to read in the whole .bam file before providing any output.

Upvotes: 1

Views: 177

Answers (0)

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