psiperEvent not working #162
Comments
|
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
…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: ***@***.***>
|
|
No, it creates an empty file. |
|
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.
…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:
***@***.***>
|
|
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! |
|
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: 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? |
|
What python version are you using?
E.
…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:
***@***.***>
|
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
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:
The code is as follows:
The ioe file was made with the following code:
And an example of what it looks like is here:
My expression TPM file looks like what follows:
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.
The text was updated successfully, but these errors were encountered: