outrigger index --splice-types error - KeyError: 'mxe'

[ghost]

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

1. cd /.../outrigger_test_sjout
2. 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

[olgabot]

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 ***@***.***> 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 <#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 1. cd /.../outrigger_test_sjout 2. 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 — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#81>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAxNcEc4um8UV7dH8Vnc85xwCS66pvy1ks5rx-GDgaJpZM4NDq3M> .

-- --- 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>