I'm feeling dumb, but I can't figure out the syntax below, and I've been googling the w/o success for a while.
Very easy, I have a bam I want to convert to bedpe with pybedtools within a script.
The following works great:
pybed_BAM = pybedtools.BedTool("path/to/sorted/bam")
bedpe = pybed_BAM.bam_to_bed().to_dataframe()
however, of course, it results in a normal bed file. If I try to add the bedpe argument as either pybed_BAM.bam_to_bed("-bedpe") or pybed_BAM.bam_to_bed("bedpe") it fails with:
TypeError: handle_kwargs() keywords must be strings
Unfortunately the bam_to_bed() page doesn't provide syntax explanation but is simply a copy-paste of the command-line tool help. The above attempts are trying to borrow the syntax from other pybedtools functions but are obviously incorrect. What am I missing?
PS the file is fine as the conversion from commandline with bedtools bamtobed works fine.
PPS I'd like to avoid subprocess pipes and use pybedtools
with an hint from Patrick Artner's suggestion I found the solution
pybed_BAM.bam_to_bed(bedpe=True) does the job!