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Version issue Biopython when importing Bio.SeqUtils.GC #3
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Thanks Ines, |
Hi Marco, the matplotlib error was I just installed matplotlib and it worked fine. I now managed to run through the whole notebook (I can post these issues separately if preferred/or change the title of this issue? but here summed up for now): Since I still had to input the cutadapt file path, it took me a while to realise that it was loading the probedesign.py from the .egg module and changing the probedesign.py file would not do much. I had not worked with modules/.egg files before so it was quicker for me to do the following:
Not sure if there is an easier way (or if this might have broken things?). Another issue I had was in the "Assign Genes to Barcode" section as I tested
I changed the values of the Lbar_ID rows "LbarID_0" in the .csv to a number (201>) and changed
Now it runs. Additionally, I was wondering if you ever had issues with duplicate sequences? I tried this pipeline with a random gene (Zfp85) and got 6 PLP sequences, 2 out of those are duplicates. Thank you! |
Hi Ines, |
Ok here I am.
I'd suggest to run the search again for these genes relaxing a bit the GC content or taking out the requirement for a terminal G/C. Maybe that will fix the issue. Keep in mind that sometimes it's impossible to design "good"probes against some genes. You can try your chances anyway, design them manually and they might work... Cheers, |
Hi Marco, thank you for the explanation! I`ll keep that in mind and will give this a go. Just to check, would lowering the target requirement to =3 or 4 potentially also help? Cheers, |
Hi Ines, |
I also just fixed the L-probe example file in a way that should now work consistently, and changed again the pandas requirements (turns out I had changed that in a test branch and not merged the changes to the main branch). |
I haven't changed the Biopython requirements, as you really get a warning rather than an error. So I'll try to fix it with a bit more time in a later release :) |
Hi Marco, thanks for the tip. I`ll test this again.
I`m also slowly going through the ISS analysis notebooks, so I will start a separate issue should I run into bugs there. :) |
Hi @mgcizzu , one more question, is the anchor sequence in the notebook the primer sequence? Since you use a pseudo-anchor as described in the supplementary, I assume the anchor in this notebook is the complementary sequence of your RCA primer? |
I just freshly set up the environment and the version of biopython installed was 1.83 where GC has changed to gc_fraction (since 1.80) - I received the below error and had to force install biopython 1.79 which helped resolve the issue. It did however tell me matplotlib was not available (which might also be unrelated?).
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