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comprna / SUPPA

SUPPA: Fast quantification of splicing and differential splicing
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diffSplice ERROR:__main__:Unknown error: (<class 'UnboundLocalError'>, UnboundLocalError("local variable 'i' referenced before assignment",), <traceback object at 0x7fede986dd48>) #127

Closed leipzig closed 3 years ago

leipzig commented 3 years ago

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 commented 3 years ago

this generates an entirely different error with classical, similar to https://github.com/comprna/SUPPA/issues/32

suppa.py diffSplice         --method classical         --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 -nan 0.01 -th 0.5 
Calculating differential analysis between conditions: SE_CONTROL and SE_EXPERIMENT 
/home/ec2-user/miniconda3/envs/clk/lib/python3.6/site-packages/scipy/stats/stats.py:7028: RuntimeWarning: divide by zero encountered in double_scalars
  z = (bigu - meanrank) / sd
ERROR:__main__:Unknown error: (<class 'TypeError'>, TypeError("calculate_delta_psi() missing 1 required positional argument: 'nan_th'",), <traceback object at 0x7ffa160ee788>)
EduEyras commented 3 years ago

Hi Jeremy,

Sorry about the cryptic error.

I saw this recently on another issue sent to the github. If my memory still works, it was related to the sample IDs in the PSI and TPM files being different. Did you check that? If not that, I'll take a deeper look.

Thanks

E.

On Fri, 16 Jul 2021 at 22:12, Jeremy Leipzig @.***> wrote:

this generates an entirely different error with classical, similar to #32 https://github.com/comprna/SUPPA/issues/32

suppa.py diffSplice --method classical --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 -nan 0.01 -th 0.5 Calculating differential analysis between conditions: SE_CONTROL and SE_EXPERIMENT /home/ec2-user/miniconda3/envs/clk/lib/python3.6/site-packages/scipy/stats/stats.py:7028: RuntimeWarning: divide by zero encountered in double_scalars z = (bigu - meanrank) / sd ERROR:main:Unknown error: (<class 'TypeError'>, TypeError("calculate_delta_psi() missing 1 required positional argument: 'nan_th'",), <traceback object at 0x7ffa160ee788>)

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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

leipzig commented 3 years ago

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
EduEyras commented 3 years ago

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

leipzig commented 3 years ago

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