Ryan Dale

Can you provide a concrete example (with input GFF) so I can help address this?

Sorry for the painfully long time before replying. If this is still an issue, can you provide a concrete example I can use to investigate options?

Thanks @ewallace. This issue has been lower priority across my projects, so unfortunately I haven't made any progress. It would be great if you could add something to gffutils, and...

I hadn't heard of graph databases until you brought them up. After reading up on them a little, I'm pretty sure they would provide a substantial performance boost. But I...

Thanks, nice find. So to use this in gffutils it would take some playing around to figure out if 2 databases are needed or if graphlite can work with an...

This sounds like a good idea, and pretty simple to implement. Sort of a special-case scenario for when your GFF file has a known, gene-centric format (which is the format...

Yarden & Brad: It's great to get you guys involved. I'll try and go through your comments sequentially . . . Yarden **(API):** The piping CLI API looks very cool....

As of 73d7df0a5471a641d7bb4506e3ffc9386bbe45c1 I added the script `gffutils-cli`. It should be usable as-is, but there are some pieces missing. Specifically, the subcommands fetch, children, parents, create, and search are working....

For reading, simply iterating over a `pybedtools.BedTool` object parses each line into an `Interval` object. ``` python def my_func(f): f.chrom = "chromosome_" + f.chrom return f for interval in pybedtools.BedTool('a.bed'):...

By the way, in the future you can use https://github.com/daler/pybedtools/issues directly. I've just created an issue for this, https://github.com/daler/pybedtools/issues/127