error accesing remote bigWig

[diekhans]

I am attempting to access a ENCODE bigWig by URL

wiggletools overlaps promoter-region.bb https://encode-public.s3.amazonaws.com/2017/10/03/ad2c0f17-0824-4647-a749-74276daca7da/ENCFF278CUB.bigWig

I get the error:

[urlOpen] curl_easy_perform received an error: Failed writing received data to disk/application File https://encode-public.s3.amazonaws.com/2017/10/03/ad2c0f17-0824-4647-a749-74276daca7da/ENCFF278CUB.bigWig is not in BigWig format

If the bigWig is download locally, this works fine.

The bigBed containes one record:
chr19 6925784 6926845

thanks!

[dzerbino]

Hello @diekhans,

I suspect this has to do with the LibBigWig library that we use in WiggleTools.

I'll create a reproducible test then send it their way.

Cheers,

Daniel

[dzerbino]

Now discussed here: dpryan79/libBigWig#49

[dzerbino]

Hello @diekhans ,

Thanks to Devon's advice I now got it working on remote files. Naturally, this is much slower than on a local file, no miracle there.

HTH,

Daniel

[diekhans]

So if I do an overlaps, does it still pull the whole wig? The runtime make is appear like it does: wiggletools overlaps ../promoter-region.bb https://encode-public.s3.amazonaws.com/2016/11/15/ab269604-0eeb-4fad-8754-c3cf4674fe91/ENCFF516HJR.bigWig I can continue to do what I did to workaround the remote access error bigWigToBedGraph -chrom=chr19 -start=6925784 -end=6926845 $url $bg bedGraphToBigWig $bg /hive/data/genomes/hg38/chrom.sizes $bw although random access in wiggletools would be useful. Daniel Zerbino <notifications@github.com> writes:

…

Hello @diekhans , Thanks to Devon's advice I now got it working on remote files. Naturally, this is much slower than on a local file, no miracle there. HTH, Daniel -- You are receiving this because you were mentioned. Reply to this email directly or view it on GitHub: #49 (comment) Hello @diekhans , Thanks to Devon's advice I now got it working on remote files. Naturally, this is much slower than on a local file, no miracle there. HTH, Daniel — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or unsubscribe.*

[dzerbino]

Yes, it does pull the whole wig.

What exactly is you use case? Why do you want to use WiggleTools rather than bigWigToBedGraph?

• If you want to do some fancy analysis downstream for a single region you could use the wiggletools seek function.
• If you want to compute a statistic at multiple regions, you could use apply
• If you convince me of a good alternate use case, then I could quite quickly implement a seek_regions function, that goes through a bed file like like the existing apply function, seeks those regions, then iterates through them.

[diekhans]

I want to compute AUC on a 1kb region of a crazy transcript over lots of dataasets. I didn't see the "seek" operator because it isn't in the help message ;-) this seems to be exactly what I want ! Daniel Zerbino <notifications@github.com> writes:

…

Yes, it does pull the whole wig. What exactly is you use case? Why do you want to use WiggleTools rather than bigWigToBedGraph? - If you want to do some fancy analysis downstream for a single region you could use the `wiggletools seek` function. - If you want to compute a statistic at multiple regions, you could use `apply` - If you convince me of a good alternate use case, then I could quite quickly implement a `seek_regions` function, a bit like the existing `apply` functions. -- You are receiving this because you were mentioned. Reply to this email directly or view it on GitHub: #49 (comment) Yes, it does pull the whole wig. What exactly is you use case? Why do you want to use WiggleTools rather than bigWigToBedGraph? • If you want to do some fancy analysis downstream for a single region you could use the wiggletools seek function. • If you want to compute a statistic at multiple regions, you could use apply • If you convince me of a good alternate use case, then I could quite quickly implement a seek_regions function, a bit like the existing apply functions. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or unsubscribe.*

[dzerbino]

Ahhh you should have said so:
wiggletools apply AUC regions.bed signal.wig

This does random access and allows you to check multiple regions.

apply_paste may also be of interest.