Create bigwigs in python?
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7.8 years ago
endrebak ▴ 970

I want to create bigwigs in Python. Is there a library that can do this?

Two ways of doing it that I'd rather avoid:

Currently I use rpy2 with rtracklayer and genomicranges through bioconda. This works, but is a bit heavy on the dependencies. Example code: https://github.com/endrebak/epic/blob/256ce4974a4ca6a10a0a5cca041c12a4e7ee9eb9/epic/bigwig/create_bigwigs.py

Another option is to use the UCSC binary tools: create a bedGraph and then convert it to bigwig by bedgraphtobigwig, but this is rather slow due to IO as you need to write files twice.

ChIP-Seq • 5.1k views
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Entering edit mode
7.8 years ago

You want pyBigWig. I wrote that for bigWig IO in deepTools, since we needed faster read access than bx-python provided and wanted to get rid of UCSC tools for bigWig creation.

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Wonderful, thanks for your effort! Python3 even <3

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It seems like bw.addEntries would take four enormous lists if I know all the entries upfront. I guess I should chunk the data and add a 1000 entries at a time...

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You can add one at a time, that works just as well.

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5.3 years ago
endrebak ▴ 970

Using pyBigWig, I've created a higher-level API for this in PyRanges:

import pyranges as pr
chromsizes = pr.db.ucsc.chromosome_sizes("hg19") # getting data using mysql
gr = pr.data.chipseq() # get some test data
gr.out.bigwig("newpath/chipseq.bw", chromsizes)

More info at https://biocore-ntnu.github.io/pyranges/writing-pyranges-to-disk.html

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