Recent commit breaks the example blobplot with log(0)

[josiahseaman]

Straight from installation I ran into a showstopper bug. It looks like self.max_cov and possibly others failed to initialize:

$ ./blobtools plot  -i example/blobDB.json  -o example/
[+] Reading BlobDB example/blobDB.json
[+]     Loading BlobDB into memory ...
[+]     Deserialising BlobDB (using 'ujson' module) (this may take a while) ...
[+]     Finished in 0.00183987617493s
[+] Extracting data for plots ...
/python2.7/site-packages/matplotlib/axes/_base.py:3193: UserWarning: Attempting to set identical bottom==top results
in singular transformations; automatically expanding.
bottom=100.0, top=100.0
  'bottom=%s, top=%s') % (bottom, top))
Traceback (most recent call last):
  File "./blobtools/lib/blobplot.py", line 183, in <module>
    main()
  File "./blobtools/lib/blobplot.py", line 175, in main
    plotObj.plotScatter(cov_lib, info_flag, out_f)
  File "./blobtools/lib/BtPlot.py", line 598, in plotScatter
    fig, axScatter, axHistx, axHisty, axLegend, top_bins, right_bins = self.setupPlot(self.plot)
  File "./blobtools/lib/BtPlot.py", line 495, in setupPlot
    right_bins = logspace(0, (int(math.log(self.max_cov)) + 1), 200, base=10.0)
ValueError: math domain error

I deduced that 58633de837ea71f1c90ac937e670e24db69fac2d introduced this bug because it changes some relevant code and reverting it fixes the problem.

$ git checkout 2a236ea194e1129e97e9f85cb64f81030c70a856
$ ./blobtools plot  -i example/blobDB.json  -o example/
[+] Reading BlobDB example/blobDB.json
[+]     Loading BlobDB into memory ...
[+]     Deserialising BlobDB (using 'ujson' module) (this may take a while) ...
[+]     Finished in 0.00210118293762s
[+] Extracting data for plots ...
[I]     no-hit : sequences = 1, span = 0.01 MB, N50 = 6,273 nt
[I]     Nematoda : sequences = 3, span = 0.01 MB, N50 = 4,060 nt
[I]     Actinobacteria : sequences = 4, span = 0.0 MB, N50 = 951 nt
[I]     unresolved : sequences = 1, span = 0.0 MB, N50 = 2,346 nt
[I]     Tardigrada : sequences = 1, span = 0.0 MB, N50 = 216 nt
[+] Plotting example/blobDB.json.bestsum.phylum.p7.span.100.blobplot.bam0.png
[+] Plotting example/blobDB.json.bestsum.phylum.p7.span.100.blobplot.read_cov.bam0.png
[+] Writing example/blobDB.json.bestsum.phylum.p7.span.100.blobplot.stats.txt

Good luck and thanks for the great tool.

[DRL]

Hi, thank you for this.

I did this recently while a was working on some legacy BlobDB files and noticed the current version didn't like it when there was no read coverage.

I assumed this would not cause problems and I find I hard to believe that it does, since the changes in 58633de affect a function which is only called by view and not by the plotting function. The issue might rather be the 'legacy' example/blobDB.json file i create for test purposes and then got uploaded. I have removed that file now.

Did you create an test blobDB or did you just run the plotting command on the example file in the folder?

cheers,

dom

[DRL]

I made a new release removing redundant example files as the folder was a bit chaotic...

Please let me know if the issue persists on your side.

cheers,

dom

[josiahseaman]

I can verify that fixed the issue. Thanks!