hotdogee / django-blast Goto Github PK

This is an odd error.
"MultipleObjectsReturned: get() returned more than one Sequence -- it returned 2!"

Internal Server Error: /webapp/blast/api/seq/Mdes007966-RA/
Traceback (most recent call last):
File "/usr/local/i5k/virtualenv/py2.7/lib/python2.7/site-packages/django/core/handlers/base.py", line 132, in get_response
response = wrapped_callback(request, _callback_args, *_callback_kwargs)
File "/usr/local/i5k/rest_framework/viewsets.py", line 78, in view
return self.dispatch(request, _args, *_kwargs)
File "/usr/local/i5k/virtualenv/py2.7/lib/python2.7/site-packages/django/views/decorators/csrf.py", line 58, in wrapped_view
return view_func(_args, *_kwargs)
File "/usr/local/i5k/rest_framework/views.py", line 401, in dispatch
response = self.handle_exception(exc)
File "/usr/local/i5k/rest_framework/views.py", line 398, in dispatch
response = handler(request, _args, *_kwargs)
File "/usr/local/i5k/rest_framework/mixins.py", line 106, in retrieve
self.object = self.get_object()
File "/usr/local/i5k/rest_framework/generics.py", line 335, in get_object
obj = get_object_or_404(queryset, *_filter_kwargs)
File "/usr/local/i5k/rest_framework/generics.py", line 35, in get_object_or_404
return _get_object_or_404(queryset, *filter_args, *_filter_kwargs)
File "/usr/local/i5k/virtualenv/py2.7/lib/python2.7/site-packages/django/shortcuts.py", line 155, in get_object_or_404
return queryset.get(_args, *_kwargs)
File "/usr/local/i5k/virtualenv/py2.7/lib/python2.7/site-packages/django/db/models/query.py", line 338, in get
(self.model._meta.object_name, num)
MultipleObjectsReturned: get() returned more than one Sequence -- it returned 2!

Hello. I'm interested in running a django-blast server, but I have been unable to determine the licensing terms. Can you please clarify this by adding a LICENSE.md file to your project with the licensing terms. Thanks!

Would it be possible to have the HSPs colored dynamically so it follows the same coloring scale currently in the BLAST output?

The idea came to me from an update Scot Cain did for the WormBase JBrowse, where feature height is a function of score. I'm not sure about using dynamic feature height, but I think that dynamic coloring could be useful.

http://jbrowse.wormbase.org/?data=data%2Fc_elegans_PRJNA13758&loc=X%3A13998647..14003046&tracks=RNASeq%20introns&highlight=

After choosing organisms, mouse over on 'All organisms' and click search, sanity check will be triggered incorrectly.

Using FireFox 36.0.1, OS X 10.10.2.
When selecting a file for the blastdb, the "Select" button if not visible in firefox. It is present in Chrome.

In upload screen, remove the unneeded file types. (For example, no one should be uploading WMV files).

To prevent name collisions, can you add an option to add a prepend string to the defline? Changing this tag would require rerunning all of the processing steps.

Hi,
By any chance, do you django-blast in a Docker container?

Thank you in advance,

Michal

Could there be more informative error reporting? Currently, it simply flashes an error and then disappears without describing what caused the problem. The issue ended up being filesystem permissions, but it was not clear at all through the interface.

Hi,
How is it possible to allow the user to click on the blast result and apollo will open and highlight the BLAST hit region?

Thank you in advance,

Michal

When I changed the fastafile for a BLAST db, the status indicators for Sequences does not get updated to reflect that they need to be rebuilt. This can lead to confusion as looks like it is correct when it probably won't be.

For folks that are interested in django-blast which was a project originally developed at i5k workspace at NAL, we have a successor project of django-blast also developed by i5k workspace called genomics-workspace. It containes all the functionality of django-blast and with lots of update and additional functionality. Please check our new repo: https://github.com/NAL-i5K/genomics-workspace/ for further information.

Save the output of makeblastdb in a log file somewhere.

This seems to be unresponsive and/or slow when checking/unchecking “All organisms” Any optimizations possible

If the sequence is added before databases are selected, the program is reset to blastn. I replicated this using different combinations of databases and query sequences.

Currently the exported gff3 includes only e-value. Could you also export the bitscore and percent identity for each hsp?