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bcgsc / mavis

Merging, Annotation, Validation, and Illustration of Structural variants
http://mavis.bcgsc.ca
GNU General Public License v3.0
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dash being inserted between letters in gene names while annotating with ncrna file #195

Closed alexjfortuna closed 5 years ago

alexjfortuna commented 5 years ago

MAVIS version: 2.2.5

Python version: 3.6.4

OS: Centos/SGE

Expected Behaviour

Samples annotating correctly and annotations in final summary file named correctly mavis_Qz8stepNwGy4kJuh6cMnnb-v2-a1-chr10_chr10-C10orf68_CCDC7.legend.json

Actual Behaviour

files are named like so:

filenames: mavis_Qz8stepNwGy4kJuh6cMnnb-v2-a1-chr10_chr10-C-1-0-o-r-f-6-8_C-C-D-C-7.legend.json

gene1_aliases | gene2_aliases 7;C;C;C;D | 0;1;6;8;C;f;o;r 7;C;C;C;D | 0;1;6;8;C;f;o;r 4;I;N;S;T | M;N;T 1;9;C;D;K;T | 7;B;P;R;R

Steps to Reproduce the Behaviour

Ran MAVIS as specified in documentation

Have you seen this behavior?

creisle commented 5 years ago

@alexjfortuna , that looks like something must be wrong with the aliases column in the annotations file. I'll check it out

creisle commented 5 years ago

@alexjfortuna sorry about that, I've replaced the annotations file at the original link with a new one I just generated. Could you try again with the new file? (download from the same link. should be 147M not instead of 146M). You won't need to update mavis itself, just the annotations file.

alexjfortuna commented 5 years ago

Hi @creisle we are testing now with new file, will report back! thank you for speedy assistance with this.

alexjfortuna commented 5 years ago

HI @creisle everything annotating correctly. Thank you.