diffSplice ERROR:__main__:Unknown error: (<class 'UnboundLocalError'>, UnboundLocalError("local variable 'i' referenced before assignment",), <traceback object at 0x7fede986dd48>)

Hi I am getting this cryptic error with suppa 2.3. Most of the other splice types are working fine.

suppa.py diffSplice         --method empirical         --input suppa_results/treated_vs_untreated/AS_events/events_SE_variable_10.ioe         --psi suppa_results/treated_vs_untreated/SE_CONTROL.psi suppa_results/treated_vs_untreated/SE_EXPERIMENT.psi         --tpm suppa_results/treated_vs_untreated/quantification/CONTROL.tsv suppa_results/treated_vs_untreated/quantification/EXPERIMENT.tsv         --area 1000         -gc         --lower-bound 0.00         --gene-correction         --output Delta_psi_SE --mode DEBUG
Calculating differential analysis between conditions: SE_CONTROL and SE_EXPERIMENT 
ERROR:__main__:Unknown error: (<class 'UnboundLocalError'>, UnboundLocalError("local variable 'i' referenced before assignment",), <traceback object at 0x7fede986dd48>)

Here are the relevant files. They should be public: https://debugsuppa.s3.amazonaws.com/CONTROL.tsv https://debugsuppa.s3.amazonaws.com/events_SE_variable_10.ioe https://debugsuppa.s3.amazonaws.com/EXPERIMENT.tsv https://debugsuppa.s3.amazonaws.com/SE_CONTROL.psi https://debugsuppa.s3.amazonaws.com/SE_EXPERIMENT.psi https://debugsuppa.s3.amazonaws.com/iso_tpm_enst.txt

Thanks!

[leipzig]

Thanks for your quick response - you saved me many hours of frustration there. Also thank you for developing SUPPA - it’s wicked fast!

[EduEyras]

Sorry about the cryptic message.

I tried running the command and reproduced your error.

After a quick look at the files, I saw that there are may nan’s

If you use the option -nan followed by a proportion (e.g. 0.5) it will run.

I tried with -nan 0.5 but only a handful of events were actually computed. You may have to increase the proportion.

I hope this helps

E.

On Fri, 16 Jul 2021 at 22:37, Jeremy Leipzig @.***> wrote:

That sounds possible I guess but then why would the other splice types (RI/AF/AL/A3/A5) work? I’m only having trouble with SE and MX.

head suppa_results/treated_vs_untreated/quantification/CONTROL.tsv SRR5009496 SRR5009521 SRR5009474 ENST00000456328.2 0.0 0.0 0.0 ENST00000450305.2 0.0 0.0 0.0 ENST00000488147.1 0.0 0.0 0.0 ENST00000619216.1 0.0 0.0 0.0

head suppa_results/treated_vs_untreated/quantification/EXPERIMENT.tsv SRR5009526 SRR5009487 SRR5009515 SRR5009514 SRR5009491 SRR5009381 SRR5009378 SRR5009464 SRR5009377 SRR5009459 SRR5009462 SRR5009453 ENST00000456328.2 0.18568199999999999 0.494968 0.0 0.0 1.628541 0.0 0.0 0.15219100000000002 1.448901 1.2963120000000001 1.17858 0.9594950000000001

head suppa_results/treated_vs_untreated/SE_CONTROL.psi SRR5009496 SRR5009521 SRR5009474 ENSG00000000003.15;SE:chrX:100630866-100632485:100632568-100633405:- nan nan nan ENSG00000000419.14;SE:chr20:50936262-50940865:50940933-50942031:- nan 0.03340755493129439 0.013264581195062677 ENSG00000000419.14;SE:chr20:50936262-50940865:50940955-50942031:- nan 0.02759745072023724 0.012574818141055624 ENSG00000000419.14;SE:chr20:50940933-50941105:50941209-50942031:- nan nan nan

head suppa_results/treated_vs_untreated/SE_EXPERIMENT.psi SRR5009526 SRR5009487 SRR5009515 SRR5009514 SRR5009491 SRR5009381 SRR5009378 SRR5009464 SRR5009377 SRR5009459 SRR5009462 SRR5009453 ENSG00000000003.15;SE:chrX:100630866-100632485:100632568-100633405:- 1.0 nan nan nan nan nan nan 1.0 nan 1.0 nan 0.995263396293768 ENSG00000000419.14;SE:chr20:50936262-50940865:50940933-50942031:- 0.8524355095811136 0.0508111372373003 nan nan 0.03936167118208868 nan nan 0.8445154133415559 0.002848009427951285 0.8966774526302875 0.0 0.8877515463175047

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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