AS event-types mentioned in documentation and those supported by code do not match

[soumitrakp]

I recently downloaded SUPPA2 using git clone. As per the documentation on GitHub following 7 event types are advertised to be supported.

SE A3 A5 MX RI AF AL

But when I run suppa to generate events from gtf file, it gives following error:

$ suppa.py generateEvents -i dmel-all-r6.32.gtf -o events -e SE A3 A5 MX RI AF AL -f ioe
usage: SUPPA generateEvents [-h] -i INPUT_FILE -o OUTPUT_FILE
                            [-e {SE,SS,MX,RI,FL} [{SE,SS,MX,RI,FL} ...]]
                            [-b {S,V}] [-t THRESHOLD] [-p] [-l EXON_LENGTH]
                            [-m MODE] -f {ioe,ioi}
SUPPA generateEvents: error: argument -e/--event-type: invalid choice: 'A3' (choose from 'SE', 'SS', 'MX', 'RI', 'FL')

[EduEyras]

Hi Soumitra

thanks for your email. Apologies for the possible confusion. The type of events are called alternative 5' (A5) and 3' (A3) splice sites. However, to calculate them, both at the same time, you must use the flag "SS"

This is because the calculation itself is very similar for A5 and A3 events in both strands, that is why we decided to merge them into one single parameter "SS".

A similar thing happens with AF and AL, which are combined into a single parameter "FL"

So if you run

suppa.py generateEvents -i dmel-all-r6.32.gtf -o events -e SE SS MX RI FL -f ioe

It should work

I hope this helps

Eduardo

On Sat, 24 Apr 2021 at 07:21, Soumitra Pal @.***> wrote:

I recently downloaded SUPPA2 using git clone. As per the documentation on GitHub following 7 event types are advertised to be supported.

SE A3 A5 MX RI AF AL

But when I run suppa to generate events from gtf file, it gives following error:

$ suppa.py generateEvents -i dmel-all-r6.32.gtf -o events -e SE A3 A5 MX RI AF AL -f ioe usage: SUPPA generateEvents [-h] -i INPUT_FILE -o OUTPUT_FILE [-e {SE,SS,MX,RI,FL} [{SE,SS,MX,RI,FL} ...]] [-b {S,V}] [-t THRESHOLD] [-p] [-l EXON_LENGTH] [-m MODE] -f {ioe,ioi} SUPPA generateEvents: error: argument -e/--event-type: invalid choice: 'A3' (choose from 'SE', 'SS', 'MX', 'RI', 'FL')

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-- Prof. E Eyras EMBL Australia Group Leader The John Curtin School of Medical Research - Australian National University https://github.com/comprna http://scholar.google.com/citations?user=LiojlGoAAAAJ

[soumitrakp]

Thank you for the reply. Yes I noticed that if I used SS then it generates both A3,A5 and so on. Just mentioning this in the documentation upfront would help. You may close this issue.