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ATG/Methionin in RefSeq not displayed #858
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I think it goes back to this issue #435 That was basically the first patch I ever contributed to JBrowse >_< Here is a fix that I think helps, instead of modifying the "sequence", which truncates the seq and makes it so the M falls out of view (when it is on the block boundary as in your screenshots) it just corrects "which frame" to render into
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Thank you - I will try it Best Regards, |
Hi Colin, |
You're welcome to test it! Ideally the fix it can go into a release too. To test it, you may need to get a "development setup" to see the effects of making a code change. see http://gmod.org/wiki/JBrowse_FAQ#What_is_the_difference_between_JBrowse-1.12.1.zip_and_JBrowse-1.12.1-dev.zip.3F just in case it wasn't clear in my comment, the lines that have a '+' means lines of code added and '-' means lines of code removed also, the comment about modifying the sequence was a technical detail about why it happened, not anything specific to your data (this can be seen on volvox sample data too). |
That is interesting (as it is same problem as #435) but it's not something I saw after applying my patch. Can you confirm that you applied the patch correctly? For example, if you have the github clone, you could try looking at the "fix_sequence_zoom_out" branch ( Same branch as shown here #859 |
Hi, sorry for the late reply.
What I see is that in the second picture there is a difference. I removed the line I've tried this combination out, but it changed nothing. |
thanks for the detailed report. I guess the only other thing I could recommend is clearing cache to ensure that your changes are applied if it is still a problem it might be good to get test data on this case I thought maybe a good approach would be to add unit testing for this so I started adding jasmine tests on #859 but using my test cases, they pass, so need to find a failing test case in order to fix any further. |
I emptied the cache and it has still not changed. Can I provide you more information to solve this? |
Sure! if you have a public instance of jbrowse with link to region where it occurs that would be fine (if not public instance, maybe look on the volvox sample data to find region where it occurs) |
I have a public instance running, but it is not the "corrected" development version. And the affected feature is: PP7435_Chr1-1036 |
If I download the sequence data from your remote web server, then I can view it locally with the patched genome browser (#859 changes) The command to get sequence dir just for completeness sake "wget -r -k -np -p http://pichiagenome-ext.boku.ac.at/jbrowse/pichia/data/cbs7435/seq/" And, with the patched genome browser, I see it as fixed now! |
Thank you for trying. I will have a look again, what I have might done wrong. To this point I thought I did everything as you've mentioned. |
I'm pretty certain that the #859 solves it. If anyone wants to check it out and verify that might be I didn't mean to leave burden on your @Rhinogradentia |
Hi there,
I've stumbled upon a display "problem". Normally ATGs/Methionins in the RefSeq are displayed/marked from a certain zoom level on. But I have one case where a certain ATG isn't displayed/colored unless you zoom in to the next-to-last zoom-level. All others are colored all the time.
You can try it here:
http://pichiagenome-ext.boku.ac.at/jbrowse/pichia/?data=data%2Fcbs7435&loc=cbs7435_chr1%3A1872565..1872707&tracks=DNA%2Ccbs7435_gene_2%2Ccbs7435_mRNA&highlight=
Maybe this is something easy to fix...
Thanks
By
Nadine
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