GESS exon skipping error

Question

[fk1qaz]

Hello,

I am attempting to use GESS to determine the exon skipping event of a bam file, however after execute the command, GESS reported error, here is the error message:

Traceback (most recent call last):
  File "/share/home/kai.feng/software/gess/GESS.py", line 122, in <module>
    main()
  File "/share/home/kai.feng/software/gess/GESS.py", line 64, in main
    global_data = GESS_patternScanning(options,global_data) ####
  File "/share/home/kai.feng/software/gess/impl/SkipPatternProc.py", line 168, in GESS_patternScanning
    global_data = skipPatternProc.process()
  File "/share/home/kai.feng/software/gess/impl/SkipPatternProc.py", line 35, in process
    patterns = self.getSkipPattern(spliceGraph)
  File "/share/home/kai.feng/software/gess/impl/SkipPatternProc.py", line 74, in getSkipPattern
    chrid = component[0].split(':')[0]
TypeError: 'set' object does not support indexing

I've tried different Python versions and indexed the reference genome, still cannot solve this,

any help will be appreciated.

Thanks,

Kai

[WouterDeCoster]

I added markup to your post for increased readability. You can do this by selecting the text and clicking the 101010 button. When you compose or edit a post that button is in your toolbar, see image below:

This looks like a scripting error. If component is a Python set it does not support indexing and also isn't ordered. Have you tried contacting the maintainers?

[fk1qaz]

I contacted the maintainers but there is no response yet, but I figured out the problem, it is actually what you said, component is a set, by adding a line in the script convert the set into list, GESS worked properly, thank you for your reply!

Kai

[WouterDeCoster]

Hi Kai,

It's indeed possible that this works, but I feel like a warning is in place here:
since a set does not have an explicit order, it's not guaranteed that the order doesn't change. By casting the set to a list and then using indices to get features out you may or may not run in to trouble sooner or later.

[fk1qaz]

Hi Wouter,

I checked the code and print the component set, each component was categorized by chromosome:pos, and only have one chromosome number. And the code this line only return the chromosome number, so I don't think this step will gave me any error.

Kai

[23bhodge23]

Hi Kai,

I ran into the same problem. Would you mind sharing your script that you used? Thanks!!