psiperEvent not working

[SignorLab]

psiperEvent not working

[Max-Tomlinson]

I was having the same issue but after a few hours of troubleshooting I've identified the problem...

The psiPerIsoform command will work with an expression matrix with or without an ID column, in your case 'Names', but for some reason psiPerEvent doesn't like this, so I moved my ID column to the row names and everything worked fine.

Hope this helps!

[EduEyras]

Dear Sarah, Did you get an output for some events? It could be possible that this happens only for events that do not have expression for the associated transcripts. You could try modifying the number of NA cases that are allowed per event. I hope this helps Eduardo

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On Wed, 17 May 2023 at 01:47, Sarah Signor ***@***.***> wrote: I am able to complete psiperIsoform without issues and get a differential splicing result. However, for psiperEvent I get the following error when I try to create the psi file: INFO:lib.tools:File quants/FR_ETOH_expression_TPM.sf opened in reading mode. INFO:psiCalculator:Buffering transcript expression levels. ERROR:lib.tools:1, in line 2. Skipping line... ERROR:lib.tools:2, in line 3. Skipping line... ERROR:lib.tools:3, in line 4. Skipping line... ERROR:lib.tools:4, in line 5. Skipping line... ... ERROR:lib.tools:32958, in line 32959. Skipping line... ERROR:lib.tools:32959, in line 32960. Skipping line... ERROR:lib.tools:32960, in line 32961. Skipping line... ERROR:lib.tools:32961, in line 32962. Skipping line... ERROR:lib.tools:32962, in line 32963. Skipping line... ERROR:lib.tools:32963, in line 32964. Skipping line... ERROR:lib.tools:32964, in line 32965. Skipping line... ERROR:lib.tools:32965, in line 32966. Skipping line... INFO:lib.tools:File quants/FR_ETOH_expression_TPM.sf closed. ERROR:psiCalculator:No expression values have been buffered. ERROR:psiCalculator:Unknown error: 1 The code is as follows: `` suppa.py psiPerEvent -e expression_TPM.sf -i dmel -o psi_suppa.ioe The ioe file was made with the following code: suppa.py generateEvents -i Drosophila_melanogaster.BDGP6.32.109.gtf -o dmel -f ioi --pool-genes And an example of what it looks like is here: seqname gene_id event_id alternative_transcripts total_transcripts 3R FBgn0011290 FBgn0011290;SE:3R:11679184-11679354:11679398-11679567:- FBtr0335213 FBtr0335213,FBtr0290205 3R FBgn0038725 FBgn0038725;SE:3R:19655672-19656205:19656372-19657582:- FBtr0345271 FBtr0345270,FBtr0345271 3R FBgn0037837 FBgn0037837;SE:3R:10812213-10812314:10812664-10812798:- FBtr0339140,FBtr0336710 FBtr0300078,FBtr0339140,FBtr0082301,FBtr0336710 3R FBgn0259139 FBgn0259139;SE:3R:11816757-11817194:11817338-11818006:- FBtr0089917,FBtr0089919 FBtr0089919,FBtr0089918,FBtr0089917 3R FBgn0265276 FBgn0265276;SE:3R:11771300-11777474:11778621-11778982:- FBtr0110876 FBtr0307086,FBtr0110876 3R FBgn0265276 FBgn0265276;SE:3R:11771300-11777474:11778621-11778858:- FBtr0305186 FBtr0305186,FBtr0307083 3R FBgn0003165 FBgn0003165;SE:3R:9081022-9141320:9141331-9157118:- FBtr0305197 FBtr0333668,FBtr0305197 3R FBgn0003165 FBgn0003165;SE:3R:9081022-9098696:9098737-9157118:- FBtr0081994 FBtr0333668,FBtr0081994 3R FBgn0027492 FBgn0027492;SE:3R:27568591-27580157:27580325-27582002:- FBtr0085204 FBtr0479866,FBtr0085204,FBtr0085203 3R FBgn0027492 FBgn0027492;SE:3R:27568591-27580157:27580325-27581144:- FBtr0085209 FBtr0085208,FBtr0085209 My expression TPM file looks like what follows: Names sample1 sample2 sample3 sample4 sample5 sample6 sample7 sample8 sample9 FBtr0308931 0.134402 0.233132 0.194543 0.000000 0.148624 0.479496 0.487405 56.666367 1.282022 FBtr0308932 0.000000 0.000000 0.000000 0.937857 0.000000 0.000000 0.000000 0.668767 0.000000 FBtr0070634 232.840518 396.445007 159.553419 140.755644 263.318480 236.227050 394.708294 210.230086 187.888669 FBtr0070635 317.499025 345.006916 375.252327 329.685911 385.136797 355.924015 620.179425 334.390078 392.112750 FBtr0337066 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 FBtr0337067 42.777204 48.561146 57.471017 52.749531 56.579878 50.621997 61.651118 26.885212 50.110896 FBtr0345714 8.680178 14.161588 12.604554 3.276385 5.098316 4.650082 9.928081 4.824662 8.217879 FBtr0344479 0.857818 0.471674 0.368677 0.469706 0.503530 0.810262 0.540480 0.197929 0.379062 FBtr0344480 0.086538 0.000000 0.037693 0.079004 0.120589 0.044486 0.048852 0.035409 0.146661 FBtr0445669 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 4.205787 0.305157 FBtr0308924 0.000000 0.047815 0.020123 0.000000 0.000000 0.043046 0.000000 0.039629 0.000000 FBtr0340166 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.044757 3.826418 0.000000 FBtr0332036 0.000000 0.105939 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.067182 Most of what I can find about this error suggests that the transcript names potentially don't match between files, but I was able to successfully do a per Isoform analysis with the same files and I am able to grep some transcript names from each file. if you have any ideas it would be most appreciated. — Reply to this email directly, view it on GitHub <#162>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADCZKB2OO57EJ53E56U7S23XGOOSDANCNFSM6AAAAAAYD3HNZY> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[SignorLab]

No, it creates an empty file.

[EduEyras]

Have you checked that there is no difference in the transcript IDs? E.g. hidden characters, additional spaces, etc... or missing headers where needed? Alternatively, it would be the missing values, but you seem to still get the results for the isoform events. I would need to run it on a portion of the input files to check if there is anything wrong. E.

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On Thu, 25 May 2023 at 01:51, Sarah Signor ***@***.***> wrote: No, it creates an empty file. — Reply to this email directly, view it on GitHub <#162 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADCZKB5SFCMRYX5H556GQJDXHYU6ZANCNFSM6AAAAAAYD3HNZY> . You are receiving this because you commented.Message ID: ***@***.***>

[TimvanderWiel1]

I have the same issue, i generated a TPM file with FeatureCounts in Galaxy. And the .ioe files with Suppa GenerateEvents. The geneID in the .ioe and TPM file are the same. But i keep getting the error:
ERROR:lib.tools:13116, in line 13117. Skipping line...
ERROR:lib.tools:13117, in line 13118. Skipping line...
ERROR:lib.tools:13118, in line 13119. Skipping line...
ERROR:lib.tools:13119, in line 13120. Skipping line...
ERROR:lib.tools:13120, in line 13121. Skipping line...
INFO:lib.tools:File /mnt/studentfiles/2023/2023MBI_05/analysis/full_suppa_analysis/TPM_tabs/Col_ant_rep1_tpm_values_tabs.tpm closed.
ERROR:psiCalculator:No expression values have been buffered.
ERROR:psiCalculator:Unknown error: 1

I use this command: suppa.py psiPerEvent -i "/mnt/studentfiles/2023/2023MBI_05/analysis/full_suppa_analysis/suppa_generate_events/col_ant_rep1_merged.ioe" -e "/mnt/studentfiles/2023/2023MBI_05/analysis/full_suppa_analysis/TPM_tabs/Col_ant_rep1_tpm_values_tabs.tpm" -o "/mnt/studentfiles/2023/2023MBI_05/analysis/full_suppa_analysis/suppa_test/"

What can i adjust to the files or script, to avoid this error?

[EduEyras]

What python version are you using? E.

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On Mon, 5 Jun 2023 at 19:08, TimvanderWiel1 ***@***.***> wrote: I have the same issue, i generated a TPM file with FeatureCounts in Galaxy. And the .ioe files with Suppa GenerateEvents. The geneID in the .ioe and TPM file are the same. But i keep getting the error: ERROR:lib.tools:13116, in line 13117. Skipping line... ERROR:lib.tools:13117, in line 13118. Skipping line... ERROR:lib.tools:13118, in line 13119. Skipping line... ERROR:lib.tools:13119, in line 13120. Skipping line... ERROR:lib.tools:13120, in line 13121. Skipping line... INFO:lib.tools:File /mnt/studentfiles/2023/2023MBI_05/analysis/full_suppa_analysis/TPM_tabs/Col_ant_rep1_tpm_values_tabs.tpm closed. ERROR:psiCalculator:No expression values have been buffered. ERROR:psiCalculator:Unknown error: 1 I use this command: suppa.py psiPerEvent -i "/mnt/studentfiles/2023/2023MBI_05/analysis/full_suppa_analysis/suppa_generate_events/col_ant_rep1_merged.ioe" -e "/mnt/studentfiles/2023/2023MBI_05/analysis/full_suppa_analysis/TPM_tabs/Col_ant_rep1_tpm_values_tabs.tpm" -o "/mnt/studentfiles/2023/2023MBI_05/analysis/full_suppa_analysis/suppa_test/" What can i adjust to the files or script, to avoid this error? — Reply to this email directly, view it on GitHub <#162 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADCZKB3AMJID74KF4BBPGKTXJWOZFANCNFSM6AAAAAAYD3HNZY> . You are receiving this because you commented.Message ID: ***@***.***>