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Edinburgh-Genome-Foundry / DnaChisel

:pencil2: A versatile DNA sequence optimizer
https://edinburgh-genome-foundry.github.io/DnaChisel/
MIT License
213 stars 38 forks source link

Geneblocks not displaying gene image on optimization report #64

Closed kelsi-kw closed 2 years ago

kelsi-kw commented 2 years ago

Hello! I have ran dnachisel.reports.write_optimization_report(problem=problem, target=".") and the report consists of every component except for the gene graphs/ geneblocks.

The only way I have been able to see the geneblocks image is by running separate code, shown below, and it is saved as an extra PNG file. seq_1 = dnachisel.sequence_to_biopython_record(problem.sequence_before) seq_2 = problem.to_record() diff_blocks = DiffBlocks.from_sequences(seq_1, seq_2) ax1, ax2 = diff_blocks.merged().plot(figure_width=8) But I would really like to see them in the optimization report. Any help would be appreciated. Thanks!

veghp commented 2 years ago

Hi, thanks for reporting this. Do you have any message in the pdf report in place of the image?

If not, then the problem is likely the version of Python, described here: https://github.com/Edinburgh-Genome-Foundry/DnaChisel/issues/58#issuecomment-828569548

The solution is to use Python v3.6 as described here: How to install and use EGF packages , until we update the packages for a later version.

kelsi-kw commented 2 years ago

Thank you so much for the quick response. I will try that!