File "sashimi-plot.py", line 214, in intersect_introns a, b = next(it) StopIteration

[guigolab]

File "sashimi-plot.py", line 214, in intersect_introns a, b = next(it) StopIteration

[dgarrimar]

Hi @TOTTW,

could you please provide some sample data to try to reproduce the error?

[TOTTW]

Hi,
Thank you for your quick reply!
I draw the sashimi plot for a lot of bam flies. Most of them work very well. But for some Bam files, it comes the error. The case I showed before, I just found this bam file just have one reads. But when I check the other BAM file which have more than one read. It still has this error.
Below is another example:

(base) [myang9@sbcsmdplp001 ~]$sashimi-plot.py -s SENSE --shrink -F png -C 2 -g human/ENSEMBL/Homo_sapiens.GRCh38.94.gtf -b Bam1214CERSE233625.bam -c chr3:7686356-7691328 -o 1214_CER.SE_233625
Traceback (most recent call last):
File "sashimi-plot.py", line 214, in intersect_introns
a, b = next(it)
StopIteration

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File "sashimi-plot.py", line 644, in
intersected_introns = list(intersect_introns(introns))
RuntimeError: generator raised StopIteration

The GitHub not support to upload the bam file. So I put it to my google drive. Thank you very much!
https://drive.google.com/drive/folders/1xTeSMmS40vVCsIE6ck-LrT53GzboqX8Y?usp=sharing

[dgarrimar]

Hi,

I have run the command you provided in one of your bam files:

sashimi-plot.py -s SENSE --shrink -F png -C 2 -g Homo_sapiens.GRCh38.94.gtf -b Bam1214CERSE233625.bam -c chr3:7686356-7691328 -o 1214_CER.SE_233625

with Python 3.5.6. However I could not reproduce the error. The only difference could come from Homo_sapiens.GRCh38.94.gtf. I got it directly from ftp://ftp.ensembl.org/pub/release-94/gtf/homo_sapiens/Homo_sapiens.GRCh38.94.gtf.gz

Does this exact command fail for you?

[TOTTW]

Thank you for your help!

[ajw2329]

Hi all - I wanted to comment briefly here that I recently encountered this error while using python v3.7.3, only when plotting exclusively samples that do not actually contain any junction reads. Switching to python 3.6.3 solved the problem. It seems like this might specifically relate to PEP 479 involving changes to generator behavior. I'll dig in some more and update soon.