olgabot
commented
7 years ago Thank you! I'm working on a fix where you would explicitly state where the bed files are for all the splice types so this should be addressed
On Thu, Apr 20, 2017, 15:51 navarrereed notifications@github.com wrote:
Description
As a test, ran outrigger index with the --splice-types "se" argument because other tests on truncated test data (link below) were showing no "mxe" events. Crashed due to an "mxe" key error in the events dictionary (KeyError: 'mxe'). Only tested on 1000-line SJ.out.tab files to avoid gff database id clash issue #69 https://github.com/YeoLab/outrigger/issues/69 while testing other features; in future testing will try longer and more sample files that include genic regions expected to have splicing (identified by JunctionSeq). Steps to Reproduce
Gist: https://gist.github.com/navarrereed/b0373b4196f8172dc9612d4da2761c5a Test SJ.out.tab files (1000 lines, anonymized): https://www.dropbox.com/sh/xqa3aslx9jktggk/AABysawqnoSAMAM8eAe4qTKya?dl=0
- cd /.../outrigger_test_sjout
- outrigger index --sj-out-tab *SJ.out.tab --gtf /.../genomes/gencode.vM13.annotation.gtf --splice-types "se"
Expected behavior: Successful indexing of skipped exon events.
Actual behavior: Crashed due to key error for non-target mxe event. Versions
outrigger --version outrigger 1.0.0
python --version Python 3.5.3
conda --version conda 4.3.16
OS: Ubuntu 14.04
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Olga Botvinnik PhD Program in Bioinformatics and Systems Biology http://bioinformatics.ucsd.edu/ Gene Yeo Laboratory http://yeolab.ucsd.edu/yeolab/Home.html | Sanford Consortium for Regenerative Medicine http://www.sanfordconsortium.org/ University of California, San Diego http://ucsd.edu/ www http://olgabotvinnik.com/ | blog http://blog.olgabotvinnik.com/ | github http://github.com/olgabot | twitter http://twitter.com/olgabot | linkedin http://www.linkedin.com/in/olgabotvinnik
Description
As a test, ran outrigger index with the --splice-types "se" argument because other tests on truncated test data (link below) were showing no "mxe" events. Crashed due to an "mxe" key error in the events dictionary (KeyError: 'mxe'). Only tested on 1000-line SJ.out.tab files to avoid gff database id clash issue #69 while testing other features; in future testing will try longer and more sample files that include genic regions expected to have splicing (identified by JunctionSeq).
Steps to Reproduce
Gist: https://gist.github.com/navarrereed/b0373b4196f8172dc9612d4da2761c5a Test SJ.out.tab files (1000 lines, anonymized): https://www.dropbox.com/sh/xqa3aslx9jktggk/AABysawqnoSAMAM8eAe4qTKya?dl=0
Expected behavior: Successful indexing of skipped exon events.
Actual behavior: Crashed due to key error for non-target mxe event.
Versions
outrigger --version outrigger 1.0.0
python --version Python 3.5.3
conda --version conda 4.3.16
OS: Ubuntu 14.04