diffSplice ERROR: ZeroDivisionError('float division by zero')

[maronem]

Hello,

When using the diffSplice function for local AS events, I get the following error:

Calculating differential analysis between conditions: VEH_SE and PHIP_SE 
ERROR:__main__:Unknown error: (<class 'ZeroDivisionError'>, ZeroDivisionError('float division by zero'), <traceback object at 0x130c868c0>)

I tried adjusting the -nan parameter to 0.5 or 0.6 but otherwise I am not sure what to change. The diffSplice function worked fine for transcript events but is only giving me this error for local events. Here is the head of the TPM and PSI files:

V_PSI:

VEH_A	VEH_B	VEH_C
ENSG00000000003;SE:X:100630866-100632485:100632568-100633405:-	0.9992742748388505	0.9980592981457552	0.966225610879026
ENSG00000000419;SE:20:50936262-50940865:50940933-50942031:-	0.838073146431139	0.912347174741068	0.8839306176205728
ENSG00000000419;SE:20:50936262-50940865:50940955-50942031:-	0.0852470154801853	0.1169938925104915	0.1964907279811411
ENSG00000000419;SE:20:50940933-50941105:50941209-50942031:-	0.5199872032289099	0.3862789312753591	0.1532904230378323

P_PSI

PHIP_A	PHIP_B	PHIP_C
ENSG00000000003;SE:X:100630866-100632485:100632568-100633405:-	0.997894232696006	0.9980735083354434	0.9988672307916387
ENSG00000000419;SE:20:50936262-50940865:50940933-50942031:-	0.9016469700940491	0.905131606987124	0.9026195052896686
ENSG00000000419;SE:20:50936262-50940865:50940955-50942031:-	0.2600154284534668	0.1625397868005549	0.1018985065352294
ENSG00000000419;SE:20:50940933-50941105:50941209-50942031:-	0.1526377630296339	0.2443064454092021	0.3304291273869533

V_TPM

VEH_A	VEH_B	VEH_C
ENST00000362106	0.0	0.0	0.0
ENST00000467751	0.0	0.023684	0.0
ENST00000464905	0.0	0.0	0.0
ENST00000434641	0.0	0.0	0.0

P_TPM

PHIP_A	PHIP_B	PHIP_C
ENST00000362106	0.219294	0.0	0.0
ENST00000467751	0.0	0.0	0.0
ENST00000464905	0.0	0.0	0.0
ENST00000434641	0.0	0.0	0.0

SE.ioe

seqname	gene_id	event_id	alternative_transcripts	total_transcripts
1	ENSG00000232596	ENSG00000232596;SE:1:4571629-4572470:4572592-4593052:+	ENST00000667354,ENST00000659059	ENST00000666685,ENST00000659059,ENST00000634256,ENST00000667354
1	ENSG00000232596	ENSG00000232596;SE:1:4571629-4575322:4575450-4593052:+	ENST00000659083	ENST00000666685,ENST00000659083,ENST00000634256
1	ENSG00000232596	ENSG00000232596;SE:1:4572592-4582277:4582574-4583083:+	ENST00000420522	ENST00000661628,ENST00000420522
1	ENSG00000149527	ENSG00000149527;SE:1:2497010-2497502:2497609-2498523:+	ENST00000449969,ENST00000378486,ENST00000419816,ENST00000343889	ENST00000343889,ENST00000378486,ENST00000449969,ENST00000419816,ENST00000278878

Thanks in advance!

[EduEyras]

Hi, is this with the "classical" or the "empirical" method? Also, are you running with the latest version v2.4 of the code from the github? Thanks Eduardo

…

On Wed, 29 Jan 2025 at 08:35, Michael Marone ***@***.***> wrote: Hello, When using the diffSplice function for local AS events, I get the following error: Calculating differential analysis between conditions: VEH_SE and PHIP_SE ERROR:__main__:Unknown error: (<class 'ZeroDivisionError'>, ZeroDivisionError('float division by zero'), <traceback object at 0x130c868c0>) I tried adjusting the -nan parameter to 0.5 or 0.6 but otherwise I am not sure what to change. The diffSplice function worked fine for transcript events but is only giving me this error for local events. Here is the head of the TPM and PSI files: V_PSI: VEH_A VEH_B VEH_C ENSG00000000003;SE:X:100630866-100632485:100632568-100633405:- 0.9992742748388505 0.9980592981457552 0.966225610879026 ENSG00000000419;SE:20:50936262-50940865:50940933-50942031:- 0.838073146431139 0.912347174741068 0.8839306176205728 ENSG00000000419;SE:20:50936262-50940865:50940955-50942031:- 0.0852470154801853 0.1169938925104915 0.1964907279811411 ENSG00000000419;SE:20:50940933-50941105:50941209-50942031:- 0.5199872032289099 0.3862789312753591 0.1532904230378323 P_PSI PHIP_A PHIP_B PHIP_C ENSG00000000003;SE:X:100630866-100632485:100632568-100633405:- 0.997894232696006 0.9980735083354434 0.9988672307916387 ENSG00000000419;SE:20:50936262-50940865:50940933-50942031:- 0.9016469700940491 0.905131606987124 0.9026195052896686 ENSG00000000419;SE:20:50936262-50940865:50940955-50942031:- 0.2600154284534668 0.1625397868005549 0.1018985065352294 ENSG00000000419;SE:20:50940933-50941105:50941209-50942031:- 0.1526377630296339 0.2443064454092021 0.3304291273869533 V_TPM VEH_A VEH_B VEH_C ENST00000362106 0.0 0.0 0.0 ENST00000467751 0.0 0.023684 0.0 ENST00000464905 0.0 0.0 0.0 ENST00000434641 0.0 0.0 0.0 P_TPM PHIP_A PHIP_B PHIP_C ENST00000362106 0.219294 0.0 0.0 ENST00000467751 0.0 0.0 0.0 ENST00000464905 0.0 0.0 0.0 ENST00000434641 0.0 0.0 0.0 SE.ioe seqname gene_id event_id alternative_transcripts total_transcripts 1 ENSG00000232596 ENSG00000232596;SE:1:4571629-4572470:4572592-4593052:+ ENST00000667354,ENST00000659059 ENST00000666685,ENST00000659059,ENST00000634256,ENST00000667354 1 ENSG00000232596 ENSG00000232596;SE:1:4571629-4575322:4575450-4593052:+ ENST00000659083 ENST00000666685,ENST00000659083,ENST00000634256 1 ENSG00000232596 ENSG00000232596;SE:1:4572592-4582277:4582574-4583083:+ ENST00000420522 ENST00000661628,ENST00000420522 1 ENSG00000149527 ENSG00000149527;SE:1:2497010-2497502:2497609-2498523:+ ENST00000449969,ENST00000378486,ENST00000419816,ENST00000343889 ENST00000343889,ENST00000378486,ENST00000449969,ENST00000419816,ENST00000278878 Thanks in advance! — Reply to this email directly, view it on GitHub <#204>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADCZKB4PZTWGZIBQSPM72MD2M7ZZBAVCNFSM6AAAAABWBOPOP2VHI2DSMVQWIX3LMV43ASLTON2WKOZSHAYTMNZVHE3DGOI> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[maronem]

Hi Eduardo,

This is using the empirical method. I am also running using v2.3 previously downloaded from github, I can download 2.4 and try rerunning.

Would I need to reproduce the .ioe and psi files using 2.4 or should it not make a difference?

Thanks

[maronem]

Updating to SUPPA 2.4 fixed the issue and I did not have to adjust any parameters! Thank you for your help!